Bases

This audit counts nucleotide bases in the downloaded Genome. Provides provides internal audit counts. It can also be checked against other sources.

Test Purpose

This test is checking sanity of the data supplied from the internet.

This is perhaps the most simple possible audit, so it also tests code for scanning the genome.

Column Keys

Chromosome is the standard chromosome number. The downloaded files include 1 through 22, X, Y, and M as reported here.

Length is the number of bases in the file itself.

T A C G are the counts of the respective bases in each chromosome.

Sum is the total of T A C and G.

Audit is OK if the file length meta data matches the sum.

Base Count Audit
Chromosome Length T A C G Sum Audit
Chr: 1 248,387,328 71,705,495 73,600,418 51,017,014 52,064,401 248,387,328 OK
Chr: 2 242,696,752 72,614,972 72,424,400 48,742,800 48,914,580 242,696,752 OK
Chr: 3 201,105,948 60,661,558 61,130,447 39,737,106 39,576,837 201,105,948 OK
Chr: 4 193,574,945 60,069,053 59,694,025 36,805,092 37,006,775 193,574,945 OK
Chr: 5 182,045,439 55,211,290 54,881,762 35,973,332 35,979,055 182,045,439 OK
Chr: 6 172,126,628 52,011,787 51,932,667 34,034,070 34,148,104 172,126,628 OK
Chr: 7 160,567,428 47,705,013 47,481,945 32,683,324 32,697,146 160,567,428 OK
Chr: 8 146,259,331 43,699,677 43,714,844 29,380,618 29,464,192 146,259,331 OK
Chr: 9 150,617,247 44,170,480 44,172,441 31,061,036 31,213,290 150,617,247 OK
Chr: 10 134,758,134 39,425,966 39,354,993 27,914,190 28,062,985 134,758,134 OK
Chr: 11 135,127,769 39,530,773 39,447,258 28,031,551 28,118,187 135,127,769 OK
Chr: 12 133,324,548 39,435,295 39,526,705 27,244,633 27,117,915 133,324,548 OK
Chr: 13 113,566,686 34,882,690 35,164,669 22,166,973 21,352,354 113,566,686 OK
Chr: 14 101,161,492 29,904,472 29,713,014 20,750,663 20,793,343 101,161,492 OK
Chr: 15 99,753,195 29,739,684 28,001,629 22,070,765 19,941,117 99,753,195 OK
Chr: 16 96,330,374 28,260,390 26,134,354 21,357,467 20,578,163 96,330,374 OK
Chr: 17 84,276,897 23,103,987 23,009,049 19,018,268 19,145,593 84,276,897 OK
Chr: 18 80,542,538 24,309,092 24,176,845 15,890,714 16,165,887 80,542,538 OK
Chr: 19 61,707,364 16,263,646 16,032,707 14,615,256 14,795,755 61,707,364 OK
Chr: 20 66,210,255 18,636,660 18,627,634 14,290,517 14,655,444 66,210,255 OK
Chr: 21 45,090,682 13,184,375 13,128,223 9,454,120 9,323,964 45,090,682 OK
Chr: 22 51,324,926 13,839,754 13,953,165 11,749,204 11,782,803 51,324,926 OK
Chr: X 154,259,566 46,694,728 46,615,932 30,499,835 30,449,071 154,259,566 OK
Chr: Y 62,460,029 17,929,049 21,954,563 9,203,003 13,373,414 62,460,029 OK
Chr: M 16,569 4,093 5,124 5,183 2,169 16,569 OK
3,117,292,070
Totals: 3,117,292,070 922,993,979 923,878,813 633,696,734 636,722,544 3,117,292,070 OK

Discussion

The audit column is OK when the file length matches the count of bases in the file. All chromosomes pass.

It appears to be structurally complete.

Test Setup

This is the first and simplest audit that uses the genome data. Here are the steps followed to get access to this data. This is common to all other genome work in other audits.

These steps will not be noted in other audits, as they are based upon this audit.

  • The source github repository is https://github.com/marbl/CHM13.

  • July 24, 2022, the file chm13v2.0.fa.gz was downloaded from that page.

  • An unzipped form was added to our local revision control system

  • Code was written and added to our internal repository to break-up that single master file into an individual file for each chromosome. This to facilitate parallel CPU processing in all future testing.

  • Code was written to count the base pairs in each chromosome. That code also checks that the total count of bases match the expected length from the file itself. This testing meta data generated when the single file was broken up by chromosome.

  • Output is included into this page for inspection.

Phil Stone 2022-08-29 2022-08-24 2022-07-25