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Saturday, August 5, 2023

Chimera Detection - 2

Where da chimera at?
I. How To

This post explains an easy way to peruse the appendices posted in the first episode of this series, beginning with the first appendix.

In the Firefox Web Browser (or compatible browser);

1) Follow the link to (Chimera Detection - Appendix 1);

2) Press "Ctrl F" and type "NC_000003.12" in the search-box that appears;

3) Notice that the first instance is located at "Full Genome Table: 2" where the details include "Nucleotide count: 198,100,135; 'N' Nucleotide Count: 195,424";

4) Press the down arrow associated with the search-box to go to the next instance of "NC_000003.12" which is located at "Promoter-Terminator Genes Table: 2 (Gene Count: 32)" where the details include "Nucleotide count: 82,163" (i.e. the total number of nucleotides in all of the 32 genes/TATA Box); (note that a promoter is "TATAAA" and a terminator is "TATCTC");

5) press the down arrow again to go to the next instance of "NC_000003.12" which is located at "Cleaned Genes Table: 2 (Gene Count: 32)" where the details include "Nucleotide count: 82,162; 'N' Nucleotide Count: 1";

6) Notice that when my software isolated then parsed each of the 32 genes/TATA Boxes it found a gene/TATA Box containing a nucleotide that was not a part of any valid standard codon;

Thus, one of the TATA Box and/or gene areas is chimeric, and that should be an issue:

"The FDA, in its response to a lawsuit filed by the Center for Food Safety in 1998, admitted in court that it had made “no dispositive scientific findings,” whatsoever, about the safety of genetically engineered foods.  In other words, the FDA has given the biotech industry carte blanche to produce and market any number of genetically engineered foods without mandatory agency oversight or safety testing and without a scientific showing that these foods are safe to consume."

(GE Food & Your Health). Perhaps both meat and vegetable genomes should be considered?

II. Explanation

The results are uniform when the genome and genes/TATA Box/transcription areas have standard codons, such as the "NC_000015.10" genome, however, the results vary when a chimeric status ensues.

Sometimes the "Promoter-Terminator Genes Table" and/or the "Cleaned Genes Table" are omitted because there was no promoter-terminator pair (TATA Box) in the genome.

III. Closing Comments

The discovery of the ~(32/35/25/6) fingerprint pattern in DNA which I announced in Dredd Blog post Quantum Biology - 22 is simple enough to use in a sophisticated word processor.

But since that is very tedious I may publish the software in a future post here on Dredd Blog.

The next post in this series is here, the previous post in this series is here.




Friday, August 4, 2023

Chimera Detection

Genieology, Geneology
I. Background

In a recent post I wrote:

"In a future post I will show how it can be used to detect chimera genomes so one doesn't use a chimera genome when only a sound genome is called for, or one does use a chimera genome when analyzing only chimera cases."

(Quantum Biology - 22). Regular readers know that Dredd Blog has considered, for quite a while, instances of generic chimera caused by antibiotics and other toxic chemicals (e.g. Some Of My Best Friends Are Germs - 2; MetaSUB - 3).

The mass media folk like to talk about only the chimera that are 'natural', (whatever that means), but that is if anything, a 'drop in the bucket' of the increasing quantities of the phenomenon.

Lots of software, perhaps even AI, are already developed or in the process of being developed (GitHub-1, Improving Long Read Assembly of Microbial Genomes and Plasmids, chimeric reads...cause severe disruption in many single-cell studies, Chimera genetics(Wikipedia), Chimera molecular biology(Wikipedia), Chimera virus (Wikipedia), ChimPipe: Accurate detection ... chimeras from RNA-seq data, How DNA is forensically extracted, Shotgun Sequencing, Github).

If you don't want to spend countless hours perusing one "chimera fixing" software package after another, I don't either (but 'it is a thing': The "It's In Your Genes" Myth - 2).

Even though I am more capable of fathoming them after decades of software engineer work, it is still more trouble than it is worth ("got AI" ... LOL).

II. Chimera Detecting Technique (Counting Atoms)

So, as regular readers know, I am working on a technique that may detect chimera before they put icing on the cake to cover it up.

The appendices today show results that are being used with the atom counting technique (Appendix 1, Appendix 2, Appendix 3, Appendix 4, Appendix 5, Appendix 6, Appendix 7, Appendix 8, Appendix 9).

They show results of analyses of various complete genomes, gene TATA Box areas within those genomes, and "cleaned genes" (TATA Box areas that have been "corrected").

The genomes are vary in kind from modern and ancient human chromosomes to bacteria.

III. How It Works

The nine appendices contain three types of analysis.

One type of analysis counts the atoms in every 'A','C','G', and 'T' nucleotide ("Full Genome") in the relevant genome of the GenBank database; another type of analysis extracts only the gene nucleotides between a promoter and a terminator ("Promoter-Terminator Genes"); and the final type of analysis used in these appendices is of the same genes, but they have had chimera or other invalid codons removed ("Cleaned Genes").

In other words, all three use the same genome to begin with, but the difference in outcome is that genes, not single nucleotides, are selected for atom counting, one is the full gene, the other is after bad condons have been removed.

The result is that in the case of the gene analysis, not as many are valid, so there are fewer "Table" print outs of gene atom counts.

If you haven't already, see the MIT video below for an example transcription because it lays out the dynamics that take place in DNA/RNA.

The variations in the tables is caused by the construct of the genomes which can be caused by improper collection of samples, improper analysis by the researchers, or database errors, or by the degradation of the samples prior to their being collected.

So far then, the ~32/35/25/6 fingerprint pattern is not a slam dunk way of detecting chimera, but it offers clues (see episode two).

I want to try this on some COV-Sars-2 viruses in a future post of this series. 

The next post in this series is here.



APPDX Chimera 009

This is an appendix to: Chimera Detection






Full Genome
Table: 1
Link and genome info: WOEV01000423.1
Toxoplasma gondii strain TR01 Toxoplasma_gondii_Ankara_1973_182
whole genome shotgun sequence


Nucleotide count: 12,796
'N' Nucleotide Count: 351

Atom Atom Count Percent
Carbon 61,020 32.15
Hydrogen 67,188 35.40
Nitrogen 48,436 25.52
Oxygen 13,164 6.94
Totals 189,808 100.00



Full Genome
Table: 2
Link and genome info: WOEV01000413.1
Toxoplasma gondii strain TR01 Toxoplasma_gondii_Ankara_1973_204
whole genome shotgun sequence


Nucleotide count: 4,598
'N' Nucleotide Count: 3,644

Atom Atom Count Percent
Carbon 22,012 32.05
Hydrogen 24,134 35.14
Nitrogen 17,602 25.63
Oxygen 4,937 7.19
Totals 68,685 100.00



Full Genome
Table: 3
Link and genome info: WOEV01000427.1
Toxoplasma gondii strain TR01 Toxoplasma_gondii_Ankara_1973_207
whole genome shotgun sequence


Nucleotide count: 14,977
'N' Nucleotide Count: 624

Atom Atom Count Percent
Carbon 71,157 32.18
Hydrogen 78,839 35.65
Nitrogen 55,567 25.13
Oxygen 15,580 7.05
Totals 221,143 100.00



Full Genome
Table: 4
Link and genome info: WOEV01000419.1
Toxoplasma gondii strain TR01 Toxoplasma_gondii_Ankara_1973_187
whole genome shotgun sequence


Nucleotide count: 6,319
'N' Nucleotide Count: 3,845

Atom Atom Count Percent
Carbon 29,231 31.97
Hydrogen 32,677 35.74
Nitrogen 23,621 25.83
Oxygen 5,902 6.46
Totals 91,431 100.00



Full Genome
Table: 5
Link and genome info: WOEV01000411.1
Toxoplasma gondii strain TR01 Toxoplasma_gondii_Ankara_1973_31
whole genome shotgun sequence


Nucleotide count: 5,749
'N' Nucleotide Count: 289

Atom Atom Count Percent
Carbon 27,156 32.05
Hydrogen 30,047 35.47
Nitrogen 21,661 25.57
Oxygen 5,856 6.91
Totals 84,720 100.00



Full Genome
Table: 6
Link and genome info: WOEV01000429.1
Toxoplasma gondii strain TR01 Toxoplasma_gondii_Ankara_1973_44
whole genome shotgun sequence


Nucleotide count: 14,148
'N' Nucleotide Count: 2,452

Atom Atom Count Percent
Carbon 67,610 32.14
Hydrogen 74,308 35.32
Nitrogen 53,776 25.56
Oxygen 14,695 6.98
Totals 210,389 100.00



Full Genome
Table: 7
Link and genome info: WOEV01000424.1
Toxoplasma gondii strain TR01 Toxoplasma_gondii_Ankara_1973_184
whole genome shotgun sequence


Nucleotide count: 13,114
'N' Nucleotide Count: 832

Atom Atom Count Percent
Carbon 62,560 32.18
Hydrogen 68,916 35.45
Nitrogen 49,512 25.47
Oxygen 13,397 6.89
Totals 194,385 100.00



Full Genome
Table: 8
Link and genome info: WOEV01000421.1
Toxoplasma gondii strain TR01 Toxoplasma_gondii_Ankara_1973_188
whole genome shotgun sequence


Nucleotide count: 10,265
'N' Nucleotide Count: 2,294

Atom Atom Count Percent
Carbon 48,668 32.16
Hydrogen 53,636 35.44
Nitrogen 39,078 25.82
Oxygen 9,968 6.59
Totals 151,350 100.00



Full Genome
Table: 9
Link and genome info: WOEV01000417.1
Toxoplasma gondii strain TR01 Toxoplasma_gondii_Ankara_1973_196
whole genome shotgun sequence


Nucleotide count: 8,919
'N' Nucleotide Count: 400

Atom Atom Count Percent
Carbon 41,851 32.08
Hydrogen 46,400 35.57
Nitrogen 33,692 25.83
Oxygen 8,509 6.52
Totals 130,452 100.00



Full Genome
Table: 10
Link and genome info: WOEV01000420.1
Toxoplasma gondii strain TR01 Toxoplasma_gondii_Ankara_1973_17
whole genome shotgun sequence


Nucleotide count: 8,938
'N' Nucleotide Count: 1,321

Atom Atom Count Percent
Carbon 42,250 32.09
Hydrogen 46,694 35.46
Nitrogen 33,798 25.67
Oxygen 8,921 6.78
Totals 131,663 100.00



Full Genome
Table: 11
Link and genome info: WOEV01000428.1
Toxoplasma gondii strain TR01 Toxoplasma_gondii_Ankara_1973_104
whole genome shotgun sequence


Nucleotide count: 15,421
'N' Nucleotide Count: 564

Atom Atom Count Percent
Carbon 72,398 32.10
Hydrogen 80,389 35.64
Nitrogen 57,839 25.64
Oxygen 14,945 6.63
Totals 225,571 100.00



Full Genome
Table: 12
Link and genome info: WOEV01000422.1
Toxoplasma gondii strain TR01 Toxoplasma_gondii_Ankara_1973_211
whole genome shotgun sequence


Nucleotide count: 12,246
'N' Nucleotide Count: 434

Atom Atom Count Percent
Carbon 58,345 32.09
Hydrogen 64,156 35.28
Nitrogen 46,682 25.67
Oxygen 12,659 6.96
Totals 181,842 100.00



Full Genome
Table: 13
Link and genome info: WOEV01000430.1
Toxoplasma gondii strain TR01 Toxoplasma_gondii_Ankara_1973_192
whole genome shotgun sequence


Nucleotide count: 17,272
'N' Nucleotide Count: 850

Atom Atom Count Percent
Carbon 81,068 32.12
Hydrogen 90,196 35.74
Nitrogen 64,268 25.46
Oxygen 16,856 6.68
Totals 252,388 100.00



Full Genome
Table: 14
Link and genome info: WOEV01000415.1
Toxoplasma gondii strain TR01 Toxoplasma_gondii_Ankara_1973_195
whole genome shotgun sequence


Nucleotide count: 5,486
'N' Nucleotide Count: 3,636

Atom Atom Count Percent
Carbon 25,552 32.03
Hydrogen 28,391 35.59
Nitrogen 20,791 26.06
Oxygen 5,036 6.31
Totals 79,770 100.00



Full Genome
Table: 15
Link and genome info: WOEV01000425.1
Toxoplasma gondii strain TR01 Toxoplasma_gondii_Ankara_1973_189
whole genome shotgun sequence


Nucleotide count: 8,394
'N' Nucleotide Count: 5,912

Atom Atom Count Percent
Carbon 38,877 31.99
Hydrogen 43,414 35.72
Nitrogen 31,452 25.88
Oxygen 7,797 6.42
Totals 121,540 100.00



Full Genome
Table: 16
Link and genome info: WOEV01000426.1
Toxoplasma gondii strain TR01 Toxoplasma_gondii_Ankara_1973_134
whole genome shotgun sequence


Nucleotide count: 14,894
'N' Nucleotide Count: 356

Atom Atom Count Percent
Carbon 69,960 32.10
Hydrogen 77,645 35.62
Nitrogen 55,925 25.66
Oxygen 14,433 6.62
Totals 217,963 100.00



Full Genome
Table: 17
Link and genome info: WOEV01000414.1
Toxoplasma gondii strain TR01 Toxoplasma_gondii_Ankara_1973_32
whole genome shotgun sequence


Nucleotide count: 8,639
'N' Nucleotide Count: 283

Atom Atom Count Percent
Carbon 40,607 32.11
Hydrogen 45,016 35.59
Nitrogen 32,556 25.74
Oxygen 8,297 6.56
Totals 126,476 100.00



Full Genome
Table: 18
Link and genome info: WOEV01000416.1
Toxoplasma gondii strain TR01 Toxoplasma_gondii_Ankara_1973_82
whole genome shotgun sequence


Nucleotide count: 9,017
'N' Nucleotide Count: 249

Atom Atom Count Percent
Carbon 41,958 31.99
Hydrogen 46,796 35.68
Nitrogen 33,698 25.69
Oxygen 8,717 6.65
Totals 131,169 100.00



Full Genome
Table: 19
Link and genome info: WOEV01000418.1
Toxoplasma gondii strain TR01 Toxoplasma_gondii_Ankara_1973_24
whole genome shotgun sequence


Nucleotide count: 9,111
'N' Nucleotide Count: 463

Atom Atom Count Percent
Carbon 43,189 32.15
Hydrogen 47,833 35.61
Nitrogen 33,989 25.30
Oxygen 9,332 6.95
Totals 134,343 100.00



Full Genome
Table: 20
Link and genome info: WOEV01000412.1
Toxoplasma gondii strain TR01 Toxoplasma_gondii_Ankara_1973_212
whole genome shotgun sequence


Nucleotide count: 7,177
'N' Nucleotide Count: 305

Atom Atom Count Percent
Carbon 33,339 32.00
Hydrogen 37,168 35.67
Nitrogen 26,944 25.86
Oxygen 6,745 6.47
Totals 104,196 100.00



Grand Totals For The Tables Above:
(Total atom count: 124,457,346,482)

Atom Type Atom Type Count Average
Carbon 40,340,454,919 32.41%
Hydrogen 44,546,428,783 35.79%
Nitrogen 31,153,300,949 25.03%
Oxygen 8,417,161,831 6.76%





Promoter-Terminator Genes
Table: 3 (Gene Count: 1)
Link and genome info: WOEV01000427.1
Toxoplasma gondii strain TR01 Toxoplasma_gondii_Ankara_1973_207
whole genome shotgun sequence


Nucleotide count: 7,723
'N' Nucleotide Count: 335

Atom Atom Count Percent
Carbon 36,554 32.16
Hydrogen 40,586 35.71
Nitrogen 28,580 25.15
Oxygen 7,930 6.98
Totals 113,650 100.00



Promoter-Terminator Genes
Table: 9 (Gene Count: 2)
Link and genome info: WOEV01000417.1
Toxoplasma gondii strain TR01 Toxoplasma_gondii_Ankara_1973_196
whole genome shotgun sequence


Nucleotide count: 3,530
'N' Nucleotide Count: 110

Atom Atom Count Percent
Carbon 16,534 32.09
Hydrogen 18,346 35.61
Nitrogen 13,330 25.87
Oxygen 3,313 6.43
Totals 51,523 100.00



Promoter-Terminator Genes
Table: 13 (Gene Count: 1)
Link and genome info: WOEV01000430.1
Toxoplasma gondii strain TR01 Toxoplasma_gondii_Ankara_1973_192
whole genome shotgun sequence


Nucleotide count: 447
'N' Nucleotide Count: 6

Atom Atom Count Percent
Carbon 2,131 32.33
Hydrogen 2,367 35.91
Nitrogen 1,631 24.75
Oxygen 462 7.01
Totals 6,591 100.00



Promoter-Terminator Genes
Table: 16 (Gene Count: 1)
Link and genome info: WOEV01000426.1
Toxoplasma gondii strain TR01 Toxoplasma_gondii_Ankara_1973_134
whole genome shotgun sequence


Nucleotide count: 9,026
'N' Nucleotide Count: 169

Atom Atom Count Percent
Carbon 42,465 32.11
Hydrogen 47,078 35.60
Nitrogen 33,956 25.68
Oxygen 8,752 6.62
Totals 132,251 100.00



Promoter-Terminator Genes
Table: 19 (Gene Count: 1)
Link and genome info: WOEV01000418.1
Toxoplasma gondii strain TR01 Toxoplasma_gondii_Ankara_1973_24
whole genome shotgun sequence


Nucleotide count: 3,650
'N' Nucleotide Count: 100

Atom Atom Count Percent
Carbon 17,260 32.10
Hydrogen 19,044 35.42
Nitrogen 13,888 25.83
Oxygen 3,570 6.64
Totals 53,762 100.00



Grand Totals For The Tables Above:
(Total Atom count: 1,812,037,898)
Atom Type Atom Type Count Average
Carbon 585,762,157 32.33%
Hydrogen 646,557,606 35.68%
Nitrogen 457,501,086 25.25%
Oxygen 122,217,049 6.74%





Cleaned Genes
Table: 3 (Gene Count: 1)
Link and genome info: WOEV01000427.1
Toxoplasma gondii strain TR01 Toxoplasma_gondii_Ankara_1973_207
whole genome shotgun sequence


Nucleotide count: 7,723
'N' Nucleotide Count: 335

Atom Atom Count Percent
Carbon 36,554 32.16
Hydrogen 40,586 35.71
Nitrogen 28,580 25.15
Oxygen 7,930 6.98
Totals 113,650 100.00



Cleaned Genes
Table: 9 (Gene Count: 2)
Link and genome info: WOEV01000417.1
Toxoplasma gondii strain TR01 Toxoplasma_gondii_Ankara_1973_196
whole genome shotgun sequence


Nucleotide count: 3,530
'N' Nucleotide Count: 110

Atom Atom Count Percent
Carbon 16,534 32.09
Hydrogen 18,346 35.61
Nitrogen 13,330 25.87
Oxygen 3,313 6.43
Totals 51,523 100.00



Cleaned Genes
Table: 13 (Gene Count: 1)
Link and genome info: WOEV01000430.1
Toxoplasma gondii strain TR01 Toxoplasma_gondii_Ankara_1973_192
whole genome shotgun sequence


Nucleotide count: 447
'N' Nucleotide Count: 6

Atom Atom Count Percent
Carbon 2,131 32.33
Hydrogen 2,367 35.91
Nitrogen 1,631 24.75
Oxygen 462 7.01
Totals 6,591 100.00



Cleaned Genes
Table: 16 (Gene Count: 1)
Link and genome info: WOEV01000426.1
Toxoplasma gondii strain TR01 Toxoplasma_gondii_Ankara_1973_134
whole genome shotgun sequence


Nucleotide count: 9,026
'N' Nucleotide Count: 169

Atom Atom Count Percent
Carbon 42,465 32.11
Hydrogen 47,078 35.60
Nitrogen 33,956 25.68
Oxygen 8,752 6.62
Totals 132,251 100.00



Cleaned Genes
Table: 19 (Gene Count: 1)
Link and genome info: WOEV01000418.1
Toxoplasma gondii strain TR01 Toxoplasma_gondii_Ankara_1973_24
whole genome shotgun sequence


Nucleotide count: 3,650
'N' Nucleotide Count: 100

Atom Atom Count Percent
Carbon 17,260 32.10
Hydrogen 19,044 35.42
Nitrogen 13,888 25.83
Oxygen 3,570 6.64
Totals 53,762 100.00



Grand Totals For The Tables Above:
(Total Atom count: 1,812,011,100)
Atom Type Atom Type Count Average
Carbon 585,753,663 32.33%
Hydrogen 646,547,150 35.68%
Nitrogen 457,495,846 25.25%
Oxygen 122,214,441 6.74%

APPDX Chimera 008

This is an appendix to: Chimera Detection






Full Genome
Table: 1
Link and genome info: WOEV01000387.1
Toxoplasma gondii strain TR01 Toxoplasma_gondii_Ankara_1973_105
whole genome shotgun sequence


Nucleotide count: 3,020
'N' Nucleotide Count: 59

Atom Atom Count Percent
Carbon 14,054 32.02
Hydrogen 15,676 35.72
Nitrogen 11,280 25.70
Oxygen 2,880 6.56
Totals 43,890 100.00



Full Genome
Table: 2
Link and genome info: WOEV01000402.1
Toxoplasma gondii strain TR01 Toxoplasma_gondii_Ankara_1973_210
whole genome shotgun sequence


Nucleotide count: 4,081
'N' Nucleotide Count: 287

Atom Atom Count Percent
Carbon 19,057 32.04
Hydrogen 21,186 35.62
Nitrogen 15,366 25.84
Oxygen 3,861 6.49
Totals 59,470 100.00



Full Genome
Table: 3
Link and genome info: WOEV01000379.1
Toxoplasma gondii strain TR01 Toxoplasma_gondii_Ankara_1973_311
whole genome shotgun sequence


Nucleotide count: 2,480
'N' Nucleotide Count: 79

Atom Atom Count Percent
Carbon 11,751 32.10
Hydrogen 12,976 35.45
Nitrogen 9,374 25.61
Oxygen 2,502 6.84
Totals 36,603 100.00



Full Genome
Table: 4
Link and genome info: WOEV01000383.1
Toxoplasma gondii strain TR01 Toxoplasma_gondii_Ankara_1973_629
whole genome shotgun sequence


Nucleotide count: 2,772
'N' Nucleotide Count: 35

Atom Atom Count Percent
Carbon 13,021 32.16
Hydrogen 14,485 35.77
Nitrogen 10,307 25.45
Oxygen 2,679 6.62
Totals 40,492 100.00



Full Genome
Table: 5
Link and genome info: WOEV01000386.1
Toxoplasma gondii strain TR01 Toxoplasma_gondii_Ankara_1973_74
whole genome shotgun sequence


Nucleotide count: 2,990
'N' Nucleotide Count: 42

Atom Atom Count Percent
Carbon 14,187 32.18
Hydrogen 15,681 35.56
Nitrogen 11,231 25.47
Oxygen 2,993 6.79
Totals 44,092 100.00



Full Genome
Table: 6
Link and genome info: WOEV01000376.1
Toxoplasma gondii strain TR01 Toxoplasma_gondii_Ankara_1973_604
whole genome shotgun sequence


Nucleotide count: 2,269
'N' Nucleotide Count: 125

Atom Atom Count Percent
Carbon 10,818 32.03
Hydrogen 11,883 35.18
Nitrogen 8,677 25.69
Oxygen 2,395 7.09
Totals 33,773 100.00



Full Genome
Table: 7
Link and genome info: WOEV01000407.1
Toxoplasma gondii strain TR01 Toxoplasma_gondii_Ankara_1973_682
whole genome shotgun sequence


Nucleotide count: 5,273
'N' Nucleotide Count: 138

Atom Atom Count Percent
Carbon 25,727 32.77
Hydrogen 28,229 35.96
Nitrogen 19,497 24.84
Oxygen 5,044 6.43
Totals 78,497 100.00



Full Genome
Table: 8
Link and genome info: WOEV01000394.1
Toxoplasma gondii strain TR01 Toxoplasma_gondii_Ankara_1973_183
whole genome shotgun sequence


Nucleotide count: 3,252
'N' Nucleotide Count: 175

Atom Atom Count Percent
Carbon 15,495 32.04
Hydrogen 17,030 35.21
Nitrogen 12,420 25.68
Oxygen 3,417 7.07
Totals 48,362 100.00



Full Genome
Table: 9
Link and genome info: WOEV01000395.1
Toxoplasma gondii strain TR01 Toxoplasma_gondii_Ankara_1973_431
whole genome shotgun sequence


Nucleotide count: 3,413
'N' Nucleotide Count: 112

Atom Atom Count Percent
Carbon 16,165 32.19
Hydrogen 17,905 35.66
Nitrogen 12,745 25.38
Oxygen 3,398 6.77
Totals 50,213 100.00



Full Genome
Table: 10
Link and genome info: WOEV01000382.1
Toxoplasma gondii strain TR01 Toxoplasma_gondii_Ankara_1973_543
whole genome shotgun sequence


Nucleotide count: 2,727
'N' Nucleotide Count: 43

Atom Atom Count Percent
Carbon 12,829 32.15
Hydrogen 14,249 35.70
Nitrogen 10,181 25.51
Oxygen 2,649 6.64
Totals 39,908 100.00



Full Genome
Table: 11
Link and genome info: WOEV01000396.1
Toxoplasma gondii strain TR01 Toxoplasma_gondii_Ankara_1973_67
whole genome shotgun sequence


Nucleotide count: 3,384
'N' Nucleotide Count: 186

Atom Atom Count Percent
Carbon 15,992 32.04
Hydrogen 17,592 35.25
Nitrogen 13,048 26.14
Oxygen 3,280 6.57
Totals 49,912 100.00



Full Genome
Table: 12
Link and genome info: WOEV01000405.1
Toxoplasma gondii strain TR01 Toxoplasma_gondii_Ankara_1973_138
whole genome shotgun sequence


Nucleotide count: 5,110
'N' Nucleotide Count: 136

Atom Atom Count Percent
Carbon 24,281 32.20
Hydrogen 26,788 35.52
Nitrogen 19,298 25.59
Oxygen 5,044 6.69
Totals 75,411 100.00



Full Genome
Table: 13
Link and genome info: WOEV01000375.1
Toxoplasma gondii strain TR01 Toxoplasma_gondii_Ankara_1973_205
whole genome shotgun sequence


Nucleotide count: 2,270
'N' Nucleotide Count: 107

Atom Atom Count Percent
Carbon 10,718 32.19
Hydrogen 11,872 35.65
Nitrogen 8,520 25.59
Oxygen 2,188 6.57
Totals 33,298 100.00



Full Genome
Table: 14
Link and genome info: WOEV01000374.1
Toxoplasma gondii strain TR01 Toxoplasma_gondii_Ankara_1973_659
whole genome shotgun sequence


Nucleotide count: 2,262
'N' Nucleotide Count: 114

Atom Atom Count Percent
Carbon 10,650 32.09
Hydrogen 11,804 35.56
Nitrogen 8,508 25.63
Oxygen 2,231 6.72
Totals 33,193 100.00



Full Genome
Table: 15
Link and genome info: WOEV01000389.1
Toxoplasma gondii strain TR01 Toxoplasma_gondii_Ankara_1973_193
whole genome shotgun sequence


Nucleotide count: 3,173
'N' Nucleotide Count: 79

Atom Atom Count Percent
Carbon 14,917 32.10
Hydrogen 16,554 35.62
Nitrogen 11,902 25.61
Oxygen 3,098 6.67
Totals 46,471 100.00



Full Genome
Table: 16
Link and genome info: WOEV01000403.1
Toxoplasma gondii strain TR01 Toxoplasma_gondii_Ankara_1973_137
whole genome shotgun sequence


Nucleotide count: 4,234
'N' Nucleotide Count: 153

Atom Atom Count Percent
Carbon 19,782 32.08
Hydrogen 22,061 35.78
Nitrogen 15,721 25.50
Oxygen 4,097 6.64
Totals 61,661 100.00



Full Genome
Table: 17
Link and genome info: WOEV01000377.1
Toxoplasma gondii strain TR01 Toxoplasma_gondii_Ankara_1973_99
whole genome shotgun sequence


Nucleotide count: 2,358
'N' Nucleotide Count: 61

Atom Atom Count Percent
Carbon 11,081 32.10
Hydrogen 12,288 35.60
Nitrogen 8,878 25.72
Oxygen 2,271 6.58
Totals 34,518 100.00



Full Genome
Table: 18
Link and genome info: WOEV01000392.1
Toxoplasma gondii strain TR01 Toxoplasma_gondii_Ankara_1973_465
whole genome shotgun sequence


Nucleotide count: 3,307
'N' Nucleotide Count: 88

Atom Atom Count Percent
Carbon 15,552 32.11
Hydrogen 17,211 35.53
Nitrogen 12,541 25.89
Oxygen 3,134 6.47
Totals 48,438 100.00



Full Genome
Table: 19
Link and genome info: WOEV01000393.1
Toxoplasma gondii strain TR01 Toxoplasma_gondii_Ankara_1973_190
whole genome shotgun sequence


Nucleotide count: 3,297
'N' Nucleotide Count: 111

Atom Atom Count Percent
Carbon 15,466 32.06
Hydrogen 17,149 35.55
Nitrogen 12,455 25.82
Oxygen 3,173 6.58
Totals 48,243 100.00



Full Genome
Table: 20
Link and genome info: WOEV01000400.1
Toxoplasma gondii strain TR01 Toxoplasma_gondii_Ankara_1973_49
whole genome shotgun sequence


Nucleotide count: 3,787
'N' Nucleotide Count: 225

Atom Atom Count Percent
Carbon 18,065 32.04
Hydrogen 19,824 35.16
Nitrogen 14,528 25.76
Oxygen 3,971 7.04
Totals 56,388 100.00



Full Genome
Table: 21
Link and genome info: WOEV01000388.1
Toxoplasma gondii strain TR01 Toxoplasma_gondii_Ankara_1973_336
whole genome shotgun sequence


Nucleotide count: 3,146
'N' Nucleotide Count: 60

Atom Atom Count Percent
Carbon 14,841 32.05
Hydrogen 16,484 35.60
Nitrogen 11,690 25.25
Oxygen 3,288 7.10
Totals 46,303 100.00



Full Genome
Table: 22
Link and genome info: WOEV01000380.1
Toxoplasma gondii strain TR01 Toxoplasma_gondii_Ankara_1973_302
whole genome shotgun sequence


Nucleotide count: 2,515
'N' Nucleotide Count: 96

Atom Atom Count Percent
Carbon 11,764 32.09
Hydrogen 13,116 35.78
Nitrogen 9,330 25.45
Oxygen 2,444 6.67
Totals 36,654 100.00



Full Genome
Table: 23
Link and genome info: WOEV01000404.1
Toxoplasma gondii strain TR01 Toxoplasma_gondii_Ankara_1973_199
whole genome shotgun sequence


Nucleotide count: 4,921
'N' Nucleotide Count: 230

Atom Atom Count Percent
Carbon 22,999 32.05
Hydrogen 25,514 35.56
Nitrogen 18,666 26.01
Oxygen 4,573 6.37
Totals 71,752 100.00



Full Genome
Table: 24
Link and genome info: WOEV01000410.1
Toxoplasma gondii strain TR01 Toxoplasma_gondii_Ankara_1973_139
whole genome shotgun sequence


Nucleotide count: 5,460
'N' Nucleotide Count: 297

Atom Atom Count Percent
Carbon 25,993 32.23
Hydrogen 28,779 35.69
Nitrogen 20,249 25.11
Oxygen 5,621 6.97
Totals 80,642 100.00



Full Genome
Table: 25
Link and genome info: WOEV01000390.1
Toxoplasma gondii strain TR01 Toxoplasma_gondii_Ankara_1973_29
whole genome shotgun sequence


Nucleotide count: 3,256
'N' Nucleotide Count: 53

Atom Atom Count Percent
Carbon 15,528 32.09
Hydrogen 17,099 35.34
Nitrogen 12,319 25.46
Oxygen 3,438 7.11
Totals 48,384 100.00



Full Genome
Table: 26
Link and genome info: WOEV01000399.1
Toxoplasma gondii strain TR01 Toxoplasma_gondii_Ankara_1973_573
whole genome shotgun sequence


Nucleotide count: 3,832
'N' Nucleotide Count: 162

Atom Atom Count Percent
Carbon 17,981 32.04
Hydrogen 19,973 35.59
Nitrogen 14,363 25.59
Oxygen 3,802 6.77
Totals 56,119 100.00



Full Genome
Table: 27
Link and genome info: WOEV01000385.1
Toxoplasma gondii strain TR01 Toxoplasma_gondii_Ankara_1973_318
whole genome shotgun sequence


Nucleotide count: 2,899
'N' Nucleotide Count: 19

Atom Atom Count Percent
Carbon 13,644 32.13
Hydrogen 15,151 35.68
Nitrogen 10,825 25.49
Oxygen 2,845 6.70
Totals 42,465 100.00



Full Genome
Table: 28
Link and genome info: WOEV01000406.1
Toxoplasma gondii strain TR01 Toxoplasma_gondii_Ankara_1973_140
whole genome shotgun sequence


Nucleotide count: 5,136
'N' Nucleotide Count: 253

Atom Atom Count Percent
Carbon 24,398 32.06
Hydrogen 26,808 35.22
Nitrogen 19,732 25.92
Oxygen 5,174 6.80
Totals 76,112 100.00



Full Genome
Table: 29
Link and genome info: WOEV01000401.1
Toxoplasma gondii strain TR01 Toxoplasma_gondii_Ankara_1973_186
whole genome shotgun sequence


Nucleotide count: 4,093
'N' Nucleotide Count: 105

Atom Atom Count Percent
Carbon 19,389 32.23
Hydrogen 21,438 35.63
Nitrogen 15,394 25.59
Oxygen 3,940 6.55
Totals 60,161 100.00



Full Genome
Table: 30
Link and genome info: WOEV01000373.1
Toxoplasma gondii strain TR01 Toxoplasma_gondii_Ankara_1973_496
whole genome shotgun sequence


Nucleotide count: 2,347
'N' Nucleotide Count: 27

Atom Atom Count Percent
Carbon 11,076 32.07
Hydrogen 12,251 35.47
Nitrogen 8,869 25.68
Oxygen 2,345 6.79
Totals 34,541 100.00



Full Genome
Table: 31
Link and genome info: WOEV01000384.1
Toxoplasma gondii strain TR01 Toxoplasma_gondii_Ankara_1973_28
whole genome shotgun sequence


Nucleotide count: 2,787
'N' Nucleotide Count: 56

Atom Atom Count Percent
Carbon 13,274 32.11
Hydrogen 14,609 35.34
Nitrogen 10,591 25.62
Oxygen 2,862 6.92
Totals 41,336 100.00



Full Genome
Table: 32
Link and genome info: WOEV01000372.1
Toxoplasma gondii strain TR01 Toxoplasma_gondii_Ankara_1973_206
whole genome shotgun sequence


Nucleotide count: 2,123
'N' Nucleotide Count: 238

Atom Atom Count Percent
Carbon 9,921 32.02
Hydrogen 11,038 35.63
Nitrogen 7,958 25.69
Oxygen 2,065 6.67
Totals 30,982 100.00



Full Genome
Table: 33
Link and genome info: WOEV01000381.1
Toxoplasma gondii strain TR01 Toxoplasma_gondii_Ankara_1973_27
whole genome shotgun sequence


Nucleotide count: 2,558
'N' Nucleotide Count: 71

Atom Atom Count Percent
Carbon 12,141 32.17
Hydrogen 13,379 35.45
Nitrogen 9,725 25.77
Oxygen 2,499 6.62
Totals 37,744 100.00



Full Genome
Table: 34
Link and genome info: WOEV01000408.1
Toxoplasma gondii strain TR01 Toxoplasma_gondii_Ankara_1973_136
whole genome shotgun sequence


Nucleotide count: 5,411
'N' Nucleotide Count: 77

Atom Atom Count Percent
Carbon 25,397 32.10
Hydrogen 28,183 35.62
Nitrogen 20,355 25.72
Oxygen 5,191 6.56
Totals 79,126 100.00



Full Genome
Table: 35
Link and genome info: WOEV01000409.1
Toxoplasma gondii strain TR01 Toxoplasma_gondii_Ankara_1973_132
whole genome shotgun sequence


Nucleotide count: 1,663
'N' Nucleotide Count: 4,078

Atom Atom Count Percent
Carbon 7,799 32.05
Hydrogen 8,651 35.55
Nitrogen 6,275 25.79
Oxygen 1,607 6.60
Totals 24,332 100.00



Full Genome
Table: 36
Link and genome info: WOEV01000378.1
Toxoplasma gondii strain TR01 Toxoplasma_gondii_Ankara_1973_100
whole genome shotgun sequence


Nucleotide count: 132
'N' Nucleotide Count: 2,406

Atom Atom Count Percent
Carbon 632 32.08
Hydrogen 691 35.08
Nitrogen 511 25.94
Oxygen 136 6.90
Totals 1,970 100.00



Full Genome
Table: 37
Link and genome info: WOEV01000398.1
Toxoplasma gondii strain TR01 Toxoplasma_gondii_Ankara_1973_499
whole genome shotgun sequence


Nucleotide count: 3,800
'N' Nucleotide Count: 85

Atom Atom Count Percent
Carbon 17,846 32.14
Hydrogen 19,818 35.69
Nitrogen 14,238 25.64
Oxygen 3,622 6.52
Totals 55,524 100.00



Full Genome
Table: 38
Link and genome info: WOEV01000391.1
Toxoplasma gondii strain TR01 Toxoplasma_gondii_Ankara_1973_564
whole genome shotgun sequence


Nucleotide count: 3,301
'N' Nucleotide Count: 88

Atom Atom Count Percent
Carbon 15,536 32.07
Hydrogen 17,245 35.60
Nitrogen 12,347 25.49
Oxygen 3,318 6.85
Totals 48,446 100.00



Full Genome
Table: 39
Link and genome info: WOEV01000397.1
Toxoplasma gondii strain TR01 Toxoplasma_gondii_Ankara_1973_169
whole genome shotgun sequence


Nucleotide count: 3,323
'N' Nucleotide Count: 427

Atom Atom Count Percent
Carbon 15,777 32.24
Hydrogen 17,579 35.92
Nitrogen 12,047 24.61
Oxygen 3,540 7.23
Totals 48,943 100.00



Grand Totals For The Tables Above:
(Total atom count: 124,454,297,198)

Atom Type Atom Type Count Average
Carbon 40,339,476,111 32.41%
Hydrogen 44,545,344,940 35.79%
Nitrogen 31,152,520,062 25.03%
Oxygen 8,416,956,085 6.76%





Promoter-Terminator Genes
Table: 21 (Gene Count: 1)
Link and genome info: WOEV01000388.1
Toxoplasma gondii strain TR01 Toxoplasma_gondii_Ankara_1973_336
whole genome shotgun sequence


Nucleotide count: 1,550
'N' Nucleotide Count: 8

Atom Atom Count Percent
Carbon 7,306 32.05
Hydrogen 8,141 35.72
Nitrogen 5,689 24.96
Oxygen 1,658 7.27
Totals 22,794 100.00



Promoter-Terminator Genes
Table: 29 (Gene Count: 1)
Link and genome info: WOEV01000401.1
Toxoplasma gondii strain TR01 Toxoplasma_gondii_Ankara_1973_186
whole genome shotgun sequence


Nucleotide count: 299

Atom Atom Count Percent
Carbon 1,426 32.26
Hydrogen 1,562 35.34
Nitrogen 1,156 26.15
Oxygen 276 6.24
Totals 4,420 100.00



Grand Totals For The Tables Above:
(Total Atom count: 1,811,680,121)
Atom Type Atom Type Count Average
Carbon 585,647,213 32.33%
Hydrogen 646,430,185 35.68%
Nitrogen 457,409,701 25.25%
Oxygen 122,193,022 6.74%





Cleaned Genes
Table: 21 (Gene Count: 1)
Link and genome info: WOEV01000388.1
Toxoplasma gondii strain TR01 Toxoplasma_gondii_Ankara_1973_336
whole genome shotgun sequence


Nucleotide count: 1,550
'N' Nucleotide Count: 8

Atom Atom Count Percent
Carbon 7,306 32.05
Hydrogen 8,141 35.72
Nitrogen 5,689 24.96
Oxygen 1,658 7.27
Totals 22,794 100.00



Cleaned Genes
Table: 29 (Gene Count: 1)
Link and genome info: WOEV01000401.1
Toxoplasma gondii strain TR01 Toxoplasma_gondii_Ankara_1973_186
whole genome shotgun sequence


Nucleotide count: 299

Atom Atom Count Percent
Carbon 1,426 32.26
Hydrogen 1,562 35.34
Nitrogen 1,156 26.15
Oxygen 276 6.24
Totals 4,420 100.00



Grand Totals For The Tables Above:
(Total Atom count: 1,811,653,323)
Atom Type Atom Type Count Average
Carbon 585,638,719 32.33%
Hydrogen 646,419,729 35.68%
Nitrogen 457,404,461 25.25%
Oxygen 122,190,414 6.74%

APPDX Chimera 007

This is an appendix to: Chimera Detection






Full Genome
Table: 1
Link and genome info: AARPRY010000001.1
Escherichia_albertii


Nucleotide count: 728,114

Atom Atom Count Percent
Carbon 3,451,968 32.21
Hydrogen 3,821,031 35.65
Nitrogen 2,721,983 25.40
Oxygen 723,481 6.75
Totals 10,718,463 100.00



Full Genome
Table: 2
Link and genome info: NZ_CAJGZT010000001.1
Psychrobacter_immobilis


Nucleotide count: 365,899

Atom Atom Count Percent
Carbon 1,745,720 32.34
Hydrogen 1,932,442 35.80
Nitrogen 1,353,104 25.07
Oxygen 366,170 6.78
Totals 5,397,436 100.00



Full Genome
Table: 3
Link and genome info: JARKIC010000015.1
Mycena olivaceomarginata strain CBHHK47/15 B0H14scaffold_15
whole genome shotgun sequence


Nucleotide count: 895,908

Atom Atom Count Percent
Carbon 4,254,944 32.19
Hydrogen 4,700,560 35.57
Nitrogen 3,367,288 25.48
Oxygen 893,881 6.76
Totals 13,216,673 100.00



Full Genome
Table: 4
Link and genome info: NC_017068.1
Selenomonas_ruminantium_subsp


Nucleotide count: 3,003,680

Atom Atom Count Percent
Carbon 14,262,013 32.19
Hydrogen 15,756,457 35.56
Nitrogen 11,291,455 25.48
Oxygen 2,998,323 6.77
Totals 44,308,248 100.00



Full Genome
Table: 5
Link and genome info: NZ_AUNL01000001.1
Mannheimia_haemolytica_D38


Nucleotide count: 181,940

Atom Atom Count Percent
Carbon 870,979 32.41
Hydrogen 963,395 35.85
Nitrogen 671,173 24.98
Oxygen 181,587 6.76
Totals 2,687,134 100.00



Full Genome
Table: 6
Link and genome info: AP019814.1
Enterococcus_avium


Nucleotide count: 3,623,727

Atom Atom Count Percent
Carbon 17,396,198 32.44
Hydrogen 19,212,709 35.83
Nitrogen 13,391,539 24.97
Oxygen 3,626,429 6.76
Totals 53,626,875 100.00



Full Genome
Table: 7
Link and genome info: JAJNOP010000001.1
Acidaminococcus_sp


Nucleotide count: 266,997

Atom Atom Count Percent
Carbon 1,266,530 32.11
Hydrogen 1,395,039 35.36
Nitrogen 1,017,913 25.80
Oxygen 265,398 6.73
Totals 3,944,880 100.00



Full Genome
Table: 8
Link and genome info: CP015622.1
Corynebacterium_crudilactis


Nucleotide count: 3,047,371
'N' Nucleotide Count: 2

Atom Atom Count Percent
Carbon 14,449,706 32.17
Hydrogen 15,974,652 35.56
Nitrogen 11,449,166 25.49
Oxygen 3,047,720 6.78
Totals 44,921,244 100.00



Full Genome
Table: 9
Link and genome info: NZ_QBUG01000001.1
Promicromonospora_sp


Nucleotide count: 1,282,267

Atom Atom Count Percent
Carbon 5,951,383 31.72
Hydrogen 6,597,245 35.16
Nitrogen 4,933,701 26.30
Oxygen 1,279,275 6.82
Totals 18,761,604 100.00



Full Genome
Table: 10
Link and genome info: JADMLJ010000010.1
Pasteurella_multocida


Nucleotide count: 72,128

Atom Atom Count Percent
Carbon 345,202 32.42
Hydrogen 382,206 35.89
Nitrogen 265,066 24.89
Oxygen 72,353 6.79
Totals 1,064,827 100.00



Full Genome
Table: 11
Link and genome info: NZ_JABGIE010000657.1
Streptococcus_agalactiae


Nucleotide count: 37,777

Atom Atom Count Percent
Carbon 182,242 32.51
Hydrogen 201,146 35.88
Nitrogen 138,816 24.76
Oxygen 38,386 6.85
Totals 560,590 100.00



Full Genome
Table: 12
Link and genome info: CP002116.1
Sediminispirochaeta_smaragdinae_DSM_11293


Nucleotide count: 4,653,970

Atom Atom Count Percent
Carbon 22,129,555 32.23
Hydrogen 24,453,496 35.61
Nitrogen 17,438,322 25.40
Oxygen 4,646,115 6.77
Totals 68,667,488 100.00



Full Genome
Table: 13
Link and genome info: DACKLI010000001.1
Staphylococcus_argenteus


Nucleotide count: 1,213,057

Atom Atom Count Percent
Carbon 5,881,162 32.62
Hydrogen 6,473,533 35.90
Nitrogen 4,472,295 24.80
Oxygen 1,203,322 6.67
Totals 18,030,312 100.00



Full Genome
Table: 14
Link and genome info: AGEX01000001.1
Shewanella_baltica_OS625


Nucleotide count: 737,933

Atom Atom Count Percent
Carbon 3,506,955 32.27
Hydrogen 3,877,848 35.69
Nitrogen 2,759,696 25.40
Oxygen 721,500 6.64
Totals 10,865,999 100.00



Full Genome
Table: 15
Link and genome info: CP047173.1
Rathayibacter_sp


Nucleotide count: 4,294,749

Atom Atom Count Percent
Carbon 19,918,006 31.69
Hydrogen 22,067,288 35.10
Nitrogen 16,581,638 26.38
Oxygen 4,294,724 6.83
Totals 62,861,656 100.00



Full Genome
Table: 16
Link and genome info: CP056682.1
Klebsiella_grimontii


Nucleotide count: 5,959,281

Atom Atom Count Percent
Carbon 28,138,563 32.07
Hydrogen 31,120,548 35.47
Nitrogen 22,508,292 25.66
Oxygen 5,962,753 6.80
Totals 87,730,156 100.00



Full Genome
Table: 17
Link and genome info: NZ_LQGG01000001.1
Histophilus_somni


Nucleotide count: 48,383

Atom Atom Count Percent
Carbon 232,133 32.47
Hydrogen 255,962 35.80
Nitrogen 180,210 25.21
Oxygen 46,663 6.53
Totals 714,968 100.00



Full Genome
Table: 18
Link and genome info: NZ_CACRUX010000002.1
Veillonella_ratti


Nucleotide count: 74,402

Atom Atom Count Percent
Carbon 353,221 32.31
Hydrogen 392,163 35.88
Nitrogen 273,973 25.06
Oxygen 73,713 6.74
Totals 1,093,070 100.00



Full Genome
Table: 19
Link and genome info: CP028105.1
Fusobacterium_ulcerans


Nucleotide count: 3,537,675

Atom Atom Count Percent
Carbon 17,143,026 32.65
Hydrogen 18,926,912 36.04
Nitrogen 12,882,066 24.53
Oxygen 3,557,732 6.78
Totals 52,509,736 100.00



Full Genome
Table: 20
Link and genome info: NZ_CAJGUS010000001.1
Carnobacterium_maltaromaticum


Nucleotide count: 132,917

Atom Atom Count Percent
Carbon 639,412 32.58
Hydrogen 710,866 36.22
Nitrogen 475,396 24.22
Oxygen 137,207 6.99
Totals 1,962,881 100.00



Full Genome
Table: 21
Link and genome info: CP024443.2
Moraxella_osloensis


Nucleotide count: 2,389,582

Atom Atom Count Percent
Carbon 11,422,950 32.34
Hydrogen 12,615,677 35.72
Nitrogen 8,894,689 25.18
Oxygen 2,384,835 6.75
Totals 35,318,151 100.00



Full Genome
Table: 22
Link and genome info: AE001438.3
Clostridium_acetobutylicum_ATCC_824


Nucleotide count: 192,000

Atom Atom Count Percent
Carbon 929,768 32.64
Hydrogen 1,027,104 36.06
Nitrogen 698,224 24.51
Oxygen 193,558 6.79
Totals 2,848,654 100.00



Full Genome
Table: 23
Link and genome info: NZ_CWFR01000011.1
Pseudomonas_aeruginosa


Nucleotide count: 45,220

Atom Atom Count Percent
Carbon 211,519 31.81
Hydrogen 233,893 35.18
Nitrogen 173,559 26.10
Oxygen 45,959 6.91
Totals 664,930 100.00



Full Genome
Table: 24
Link and genome info: LR214997.1
Mycoplasma_conjunctivae


Nucleotide count: 899,438

Atom Atom Count Percent
Carbon 4,368,674 32.69
Hydrogen 4,820,066 36.07
Nitrogen 3,271,530 24.48
Oxygen 902,393 6.75
Totals 13,362,663 100.00



Full Genome
Table: 25
Link and genome info: LEKT01000001.1
Megasphaera_cerevisiae_DSM_20462


Nucleotide count: 154,499

Atom Atom Count Percent
Carbon 740,317 32.33
Hydrogen 814,571 35.57
Nitrogen 581,911 25.41
Oxygen 153,298 6.69
Totals 2,290,097 100.00



Full Genome
Table: 26
Link and genome info: CP017415.1
Acidihalobacter_yilgarnensis


Nucleotide count: 3,566,941

Atom Atom Count Percent
Carbon 16,768,161 31.98
Hydrogen 18,550,972 35.37
Nitrogen 13,552,816 25.84
Oxygen 3,569,488 6.81
Totals 52,441,437 100.00



Full Genome
Table: 27
Link and genome info: WQQZ01000008.1
Bacteroides_caccae


Nucleotide count: 38,367

Atom Atom Count Percent
Carbon 184,567 32.37
Hydrogen 202,896 35.59
Nitrogen 144,116 25.28
Oxygen 38,558 6.76
Totals 570,137 100.00



Grand Totals For The Tables Above:
(Total atom count: 124,452,412,829)

Atom Type Atom Type Count Average
Carbon 40,338,870,567 32.41%
Hydrogen 44,544,674,691 35.79%
Nitrogen 31,152,038,101 25.03%
Oxygen 8,416,829,470 6.76%





Promoter-Terminator Genes
Table: 1 (Gene Count: 68)
Link and genome info: AARPRY010000001.1
Escherichia_albertii


Nucleotide count: 389,146

Atom Atom Count Percent
Carbon 1,845,818 32.22
Hydrogen 2,042,763 35.66
Nitrogen 1,454,807 25.40
Oxygen 385,311 6.73
Totals 5,728,699 100.00



Promoter-Terminator Genes
Table: 2 (Gene Count: 55)
Link and genome info: NZ_CAJGZT010000001.1
Psychrobacter_immobilis


Nucleotide count: 279,900

Atom Atom Count Percent
Carbon 1,335,567 32.35
Hydrogen 1,478,541 35.81
Nitrogen 1,034,511 25.06
Oxygen 280,001 6.78
Totals 4,128,620 100.00



Promoter-Terminator Genes
Table: 3 (Gene Count: 52)
Link and genome info: JARKIC010000015.1
Mycena olivaceomarginata strain CBHHK47/15 B0H14scaffold_15
whole genome shotgun sequence


Nucleotide count: 243,025

Atom Atom Count Percent
Carbon 1,155,184 32.21
Hydrogen 1,275,213 35.56
Nitrogen 914,979 25.51
Oxygen 240,957 6.72
Totals 3,586,333 100.00



Promoter-Terminator Genes
Table: 4 (Gene Count: 278)
Link and genome info: NC_017068.1
Selenomonas_ruminantium_subsp


Nucleotide count: 1,734,871

Atom Atom Count Percent
Carbon 8,245,666 32.20
Hydrogen 9,103,562 35.55
Nitrogen 6,529,356 25.50
Oxygen 1,727,021 6.74
Totals 25,605,605 100.00



Promoter-Terminator Genes
Table: 5 (Gene Count: 30)
Link and genome info: NZ_AUNL01000001.1
Mannheimia_haemolytica_D38


Nucleotide count: 128,525

Atom Atom Count Percent
Carbon 615,000 32.41
Hydrogen 680,460 35.86
Nitrogen 473,870 24.97
Oxygen 128,128 6.75
Totals 1,897,458 100.00



Promoter-Terminator Genes
Table: 6 (Gene Count: 214)
Link and genome info: AP019814.1
Enterococcus_avium


Nucleotide count: 1,348,836

Atom Atom Count Percent
Carbon 6,506,309 32.45
Hydrogen 7,136,430 35.59
Nitrogen 5,091,688 25.40
Oxygen 1,315,053 6.56
Totals 20,049,480 100.00



Promoter-Terminator Genes
Table: 7 (Gene Count: 11)
Link and genome info: JAJNOP010000001.1
Acidaminococcus_sp


Nucleotide count: 184,984

Atom Atom Count Percent
Carbon 877,712 32.10
Hydrogen 965,861 35.32
Nitrogen 707,681 25.88
Oxygen 183,198 6.70
Totals 2,734,452 100.00



Promoter-Terminator Genes
Table: 8 (Gene Count: 97)
Link and genome info: CP015622.1
Corynebacterium_crudilactis


Nucleotide count: 688,122

Atom Atom Count Percent
Carbon 3,266,729 32.16
Hydrogen 3,607,134 35.51
Nitrogen 2,593,276 25.53
Oxygen 691,600 6.81
Totals 10,158,739 100.00



Promoter-Terminator Genes
Table: 9 (Gene Count: 3)
Link and genome info: NZ_QBUG01000001.1
Promicromonospora_sp


Nucleotide count: 45,515

Atom Atom Count Percent
Carbon 211,263 31.74
Hydrogen 234,252 35.19
Nitrogen 174,920 26.28
Oxygen 45,251 6.80
Totals 665,686 100.00



Promoter-Terminator Genes
Table: 10 (Gene Count: 9)
Link and genome info: JADMLJ010000010.1
Pasteurella_multocida


Nucleotide count: 49,953

Atom Atom Count Percent
Carbon 239,161 32.43
Hydrogen 264,667 35.88
Nitrogen 183,851 24.93
Oxygen 49,878 6.76
Totals 737,557 100.00



Promoter-Terminator Genes
Table: 11 (Gene Count: 8)
Link and genome info: NZ_JABGIE010000657.1
Streptococcus_agalactiae


Nucleotide count: 22,401

Atom Atom Count Percent
Carbon 108,162 32.50
Hydrogen 119,219 35.83
Nitrogen 82,677 24.84
Oxygen 22,719 6.83
Totals 332,777 100.00



Promoter-Terminator Genes
Table: 12 (Gene Count: 10)
Link and genome info: CP002116.1
Sediminispirochaeta_smaragdinae_DSM_11293


Nucleotide count: 39,527

Atom Atom Count Percent
Carbon 188,881 32.27
Hydrogen 208,367 35.60
Nitrogen 147,931 25.27
Oxygen 40,170 6.86
Totals 585,349 100.00



Promoter-Terminator Genes
Table: 13 (Gene Count: 86)
Link and genome info: DACKLI010000001.1
Staphylococcus_argenteus


Nucleotide count: 663,172

Atom Atom Count Percent
Carbon 3,224,150 32.62
Hydrogen 3,529,063 35.71
Nitrogen 2,492,831 25.22
Oxygen 637,174 6.45
Totals 9,883,218 100.00



Promoter-Terminator Genes
Table: 14 (Gene Count: 77)
Link and genome info: AGEX01000001.1
Shewanella_baltica_OS625


Nucleotide count: 472,996

Atom Atom Count Percent
Carbon 2,247,894 32.28
Hydrogen 2,485,926 35.69
Nitrogen 1,767,970 25.39
Oxygen 462,572 6.64
Totals 6,964,362 100.00



Promoter-Terminator Genes
Table: 15 (Gene Count: 1)
Link and genome info: CP047173.1
Rathayibacter_sp


Nucleotide count: 59,658

Atom Atom Count Percent
Carbon 278,118 31.73
Hydrogen 306,847 35.00
Nitrogen 232,275 26.50
Oxygen 59,343 6.77
Totals 876,583 100.00



Promoter-Terminator Genes
Table: 16 (Gene Count: 86)
Link and genome info: CP056682.1
Klebsiella_grimontii


Nucleotide count: 444,565

Atom Atom Count Percent
Carbon 2,101,681 32.07
Hydrogen 2,321,978 35.43
Nitrogen 1,683,078 25.68
Oxygen 446,536 6.81
Totals 6,553,273 100.00



Promoter-Terminator Genes
Table: 17 (Gene Count: 5)
Link and genome info: NZ_LQGG01000001.1
Histophilus_somni


Nucleotide count: 17,034

Atom Atom Count Percent
Carbon 81,912 32.45
Hydrogen 90,080 35.69
Nitrogen 63,924 25.33
Oxygen 16,490 6.53
Totals 252,406 100.00



Promoter-Terminator Genes
Table: 18 (Gene Count: 8)
Link and genome info: NZ_CACRUX010000002.1
Veillonella_ratti


Nucleotide count: 61,356

Atom Atom Count Percent
Carbon 291,207 32.31
Hydrogen 323,156 35.85
Nitrogen 226,506 25.13
Oxygen 60,477 6.71
Totals 901,346 100.00



Promoter-Terminator Genes
Table: 19 (Gene Count: 70)
Link and genome info: CP028105.1
Fusobacterium_ulcerans


Nucleotide count: 106,855

Atom Atom Count Percent
Carbon 516,770 32.65
Hydrogen 573,283 36.22
Nitrogen 382,241 24.15
Oxygen 110,276 6.97
Totals 1,582,570 100.00



Promoter-Terminator Genes
Table: 20 (Gene Count: 23)
Link and genome info: NZ_CAJGUS010000001.1
Carnobacterium_maltaromaticum


Nucleotide count: 111,926

Atom Atom Count Percent
Carbon 538,573 32.58
Hydrogen 598,415 36.20
Nitrogen 401,161 24.27
Oxygen 114,985 6.96
Totals 1,653,134 100.00



Promoter-Terminator Genes
Table: 21 (Gene Count: 252)
Link and genome info: CP024443.2
Moraxella_osloensis


Nucleotide count: 1,652,063

Atom Atom Count Percent
Carbon 7,897,665 32.35
Hydrogen 8,723,105 35.73
Nitrogen 6,146,645 25.17
Oxygen 1,649,180 6.75
Totals 24,416,595 100.00



Promoter-Terminator Genes
Table: 22 (Gene Count: 16)
Link and genome info: AE001438.3
Clostridium_acetobutylicum_ATCC_824


Nucleotide count: 76,016

Atom Atom Count Percent
Carbon 369,550 32.64
Hydrogen 406,409 35.90
Nitrogen 280,033 24.74
Oxygen 76,092 6.72
Totals 1,132,084 100.00



Promoter-Terminator Genes
Table: 24 (Gene Count: 158)
Link and genome info: LR214997.1
Mycoplasma_conjunctivae


Nucleotide count: 771,539

Atom Atom Count Percent
Carbon 3,748,107 32.70
Hydrogen 4,133,587 36.06
Nitrogen 2,810,843 24.52
Oxygen 770,939 6.73
Totals 11,463,476 100.00



Promoter-Terminator Genes
Table: 25 (Gene Count: 21)
Link and genome info: LEKT01000001.1
Megasphaera_cerevisiae_DSM_20462


Nucleotide count: 101,602

Atom Atom Count Percent
Carbon 487,020 32.33
Hydrogen 535,619 35.56
Nitrogen 383,203 25.44
Oxygen 100,551 6.67
Totals 1,506,393 100.00



Promoter-Terminator Genes
Table: 26 (Gene Count: 115)
Link and genome info: CP017415.1
Acidihalobacter_yilgarnensis


Nucleotide count: 908,467

Atom Atom Count Percent
Carbon 4,273,742 32.00
Hydrogen 4,729,334 35.41
Nitrogen 3,444,152 25.79
Oxygen 908,862 6.80
Totals 13,356,090 100.00



Promoter-Terminator Genes
Table: 27 (Gene Count: 5)
Link and genome info: WQQZ01000008.1
Bacteroides_caccae


Nucleotide count: 22,412

Atom Atom Count Percent
Carbon 107,940 32.39
Hydrogen 118,524 35.56
Nitrogen 84,428 25.33
Oxygen 22,376 6.71
Totals 333,268 100.00



Grand Totals For The Tables Above:
(Total Atom count: 1,811,652,907)
Atom Type Atom Type Count Average
Carbon 585,638,481 32.33%
Hydrogen 646,420,482 35.68%
Nitrogen 457,402,856 25.25%
Oxygen 122,191,088 6.74%





Cleaned Genes
Table: 1 (Gene Count: 68)
Link and genome info: AARPRY010000001.1
Escherichia_albertii


Nucleotide count: 389,141
'N' Nucleotide Count: 5

Atom Atom Count Percent
Carbon 1,845,797 32.22
Hydrogen 2,042,737 35.66
Nitrogen 1,454,793 25.40
Oxygen 385,305 6.73
Totals 5,728,632 100.00



Cleaned Genes
Table: 2 (Gene Count: 55)
Link and genome info: NZ_CAJGZT010000001.1
Psychrobacter_immobilis


Nucleotide count: 279,898
'N' Nucleotide Count: 2

Atom Atom Count Percent
Carbon 1,335,559 32.35
Hydrogen 1,478,531 35.81
Nitrogen 1,034,505 25.06
Oxygen 279,999 6.78
Totals 4,128,594 100.00



Cleaned Genes
Table: 3 (Gene Count: 52)
Link and genome info: JARKIC010000015.1
Mycena olivaceomarginata strain CBHHK47/15 B0H14scaffold_15
whole genome shotgun sequence


Nucleotide count: 243,025

Atom Atom Count Percent
Carbon 1,155,184 32.21
Hydrogen 1,275,213 35.56
Nitrogen 914,979 25.51
Oxygen 240,957 6.72
Totals 3,586,333 100.00



Cleaned Genes
Table: 4 (Gene Count: 278)
Link and genome info: NC_017068.1
Selenomonas_ruminantium_subsp


Nucleotide count: 1,734,854
'N' Nucleotide Count: 17

Atom Atom Count Percent
Carbon 8,245,593 32.20
Hydrogen 9,103,472 35.55
Nitrogen 6,529,310 25.50
Oxygen 1,726,999 6.74
Totals 25,605,374 100.00



Cleaned Genes
Table: 5 (Gene Count: 30)
Link and genome info: NZ_AUNL01000001.1
Mannheimia_haemolytica_D38


Nucleotide count: 128,521
'N' Nucleotide Count: 4

Atom Atom Count Percent
Carbon 614,983 32.41
Hydrogen 680,439 35.86
Nitrogen 473,859 24.97
Oxygen 128,123 6.75
Totals 1,897,404 100.00



Cleaned Genes
Table: 6 (Gene Count: 214)
Link and genome info: AP019814.1
Enterococcus_avium


Nucleotide count: 1,348,817
'N' Nucleotide Count: 19

Atom Atom Count Percent
Carbon 6,506,226 32.45
Hydrogen 7,136,328 35.59
Nitrogen 5,091,638 25.40
Oxygen 1,315,027 6.56
Totals 20,049,219 100.00



Cleaned Genes
Table: 7 (Gene Count: 11)
Link and genome info: JAJNOP010000001.1
Acidaminococcus_sp


Nucleotide count: 184,982
'N' Nucleotide Count: 2

Atom Atom Count Percent
Carbon 877,704 32.10
Hydrogen 965,851 35.32
Nitrogen 707,675 25.88
Oxygen 183,196 6.70
Totals 2,734,426 100.00



Cleaned Genes
Table: 8 (Gene Count: 97)
Link and genome info: CP015622.1
Corynebacterium_crudilactis


Nucleotide count: 688,114
'N' Nucleotide Count: 8

Atom Atom Count Percent
Carbon 3,266,695 32.16
Hydrogen 3,607,092 35.51
Nitrogen 2,593,254 25.53
Oxygen 691,590 6.81
Totals 10,158,631 100.00



Cleaned Genes
Table: 9 (Gene Count: 3)
Link and genome info: NZ_QBUG01000001.1
Promicromonospora_sp


Nucleotide count: 45,515

Atom Atom Count Percent
Carbon 211,263 31.74
Hydrogen 234,252 35.19
Nitrogen 174,920 26.28
Oxygen 45,251 6.80
Totals 665,686 100.00



Cleaned Genes
Table: 10 (Gene Count: 9)
Link and genome info: JADMLJ010000010.1
Pasteurella_multocida


Nucleotide count: 49,951
'N' Nucleotide Count: 2

Atom Atom Count Percent
Carbon 239,152 32.43
Hydrogen 264,656 35.88
Nitrogen 183,846 24.93
Oxygen 49,875 6.76
Totals 737,529 100.00



Cleaned Genes
Table: 11 (Gene Count: 8)
Link and genome info: NZ_JABGIE010000657.1
Streptococcus_agalactiae


Nucleotide count: 22,401

Atom Atom Count Percent
Carbon 108,162 32.50
Hydrogen 119,219 35.83
Nitrogen 82,677 24.84
Oxygen 22,719 6.83
Totals 332,777 100.00



Cleaned Genes
Table: 12 (Gene Count: 10)
Link and genome info: CP002116.1
Sediminispirochaeta_smaragdinae_DSM_11293


Nucleotide count: 39,524
'N' Nucleotide Count: 3

Atom Atom Count Percent
Carbon 188,868 32.27
Hydrogen 208,351 35.60
Nitrogen 147,923 25.27
Oxygen 40,166 6.86
Totals 585,308 100.00



Cleaned Genes
Table: 13 (Gene Count: 86)
Link and genome info: DACKLI010000001.1
Staphylococcus_argenteus


Nucleotide count: 663,170
'N' Nucleotide Count: 2

Atom Atom Count Percent
Carbon 3,224,142 32.62
Hydrogen 3,529,053 35.71
Nitrogen 2,492,825 25.22
Oxygen 637,172 6.45
Totals 9,883,192 100.00



Cleaned Genes
Table: 14 (Gene Count: 77)
Link and genome info: AGEX01000001.1
Shewanella_baltica_OS625


Nucleotide count: 472,989
'N' Nucleotide Count: 7

Atom Atom Count Percent
Carbon 2,247,864 32.28
Hydrogen 2,485,889 35.69
Nitrogen 1,767,951 25.39
Oxygen 462,563 6.64
Totals 6,964,267 100.00



Cleaned Genes
Table: 15 (Gene Count: 1)
Link and genome info: CP047173.1
Rathayibacter_sp


Nucleotide count: 59,658

Atom Atom Count Percent
Carbon 278,118 31.73
Hydrogen 306,847 35.00
Nitrogen 232,275 26.50
Oxygen 59,343 6.77
Totals 876,583 100.00



Cleaned Genes
Table: 16 (Gene Count: 86)
Link and genome info: CP056682.1
Klebsiella_grimontii


Nucleotide count: 444,558
'N' Nucleotide Count: 7

Atom Atom Count Percent
Carbon 2,101,650 32.07
Hydrogen 2,321,940 35.43
Nitrogen 1,683,060 25.68
Oxygen 446,526 6.81
Totals 6,553,176 100.00



Cleaned Genes
Table: 17 (Gene Count: 5)
Link and genome info: NZ_LQGG01000001.1
Histophilus_somni


Nucleotide count: 17,034

Atom Atom Count Percent
Carbon 81,912 32.45
Hydrogen 90,080 35.69
Nitrogen 63,924 25.33
Oxygen 16,490 6.53
Totals 252,406 100.00



Cleaned Genes
Table: 18 (Gene Count: 8)
Link and genome info: NZ_CACRUX010000002.1
Veillonella_ratti


Nucleotide count: 61,356

Atom Atom Count Percent
Carbon 291,207 32.31
Hydrogen 323,156 35.85
Nitrogen 226,506 25.13
Oxygen 60,477 6.71
Totals 901,346 100.00



Cleaned Genes
Table: 19 (Gene Count: 70)
Link and genome info: CP028105.1
Fusobacterium_ulcerans


Nucleotide count: 106,850
'N' Nucleotide Count: 5

Atom Atom Count Percent
Carbon 516,748 32.65
Hydrogen 573,256 36.22
Nitrogen 382,228 24.15
Oxygen 110,269 6.97
Totals 1,582,501 100.00



Cleaned Genes
Table: 20 (Gene Count: 23)
Link and genome info: NZ_CAJGUS010000001.1
Carnobacterium_maltaromaticum


Nucleotide count: 111,926

Atom Atom Count Percent
Carbon 538,573 32.58
Hydrogen 598,415 36.20
Nitrogen 401,161 24.27
Oxygen 114,985 6.96
Totals 1,653,134 100.00



Cleaned Genes
Table: 21 (Gene Count: 252)
Link and genome info: CP024443.2
Moraxella_osloensis


Nucleotide count: 1,652,037
'N' Nucleotide Count: 26

Atom Atom Count Percent
Carbon 7,897,552 32.35
Hydrogen 8,722,966 35.73
Nitrogen 6,146,576 25.17
Oxygen 1,649,145 6.75
Totals 24,416,239 100.00



Cleaned Genes
Table: 22 (Gene Count: 16)
Link and genome info: AE001438.3
Clostridium_acetobutylicum_ATCC_824


Nucleotide count: 76,015
'N' Nucleotide Count: 1

Atom Atom Count Percent
Carbon 369,546 32.64
Hydrogen 406,404 35.90
Nitrogen 280,030 24.74
Oxygen 76,091 6.72
Totals 1,132,071 100.00



Cleaned Genes
Table: 24 (Gene Count: 158)
Link and genome info: LR214997.1
Mycoplasma_conjunctivae


Nucleotide count: 771,532
'N' Nucleotide Count: 7

Atom Atom Count Percent
Carbon 3,748,077 32.70
Hydrogen 4,133,550 36.06
Nitrogen 2,810,824 24.52
Oxygen 770,930 6.73
Totals 11,463,381 100.00



Cleaned Genes
Table: 25 (Gene Count: 21)
Link and genome info: LEKT01000001.1
Megasphaera_cerevisiae_DSM_20462


Nucleotide count: 101,601
'N' Nucleotide Count: 1

Atom Atom Count Percent
Carbon 487,016 32.33
Hydrogen 535,614 35.56
Nitrogen 383,200 25.44
Oxygen 100,550 6.67
Totals 1,506,380 100.00



Cleaned Genes
Table: 26 (Gene Count: 115)
Link and genome info: CP017415.1
Acidihalobacter_yilgarnensis


Nucleotide count: 908,457
'N' Nucleotide Count: 10

Atom Atom Count Percent
Carbon 4,273,699 32.00
Hydrogen 4,729,281 35.41
Nitrogen 3,444,125 25.79
Oxygen 908,849 6.80
Totals 13,355,954 100.00



Cleaned Genes
Table: 27 (Gene Count: 5)
Link and genome info: WQQZ01000008.1
Bacteroides_caccae


Nucleotide count: 22,412

Atom Atom Count Percent
Carbon 107,940 32.39
Hydrogen 118,524 35.56
Nitrogen 84,428 25.33
Oxygen 22,376 6.71
Totals 333,268 100.00



Grand Totals For The Tables Above:
(Total Atom count: 1,811,626,109)
Atom Type Atom Type Count Average
Carbon 585,629,987 32.33%
Hydrogen 646,410,026 35.68%
Nitrogen 457,397,616 25.25%
Oxygen 122,188,480 6.74%