bam-stats-txt

TXT

A TXT-type anvi’o artifact. This artifact is typically generated, used, and/or exported by anvi’o (and not provided by the user)..

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Provided by

anvi-profile-blitz

Required or used by

There are no anvi’o tools that use or require this artifact directly, which means it is most likely an end-product for the user.

Description

A collection of TAB-delimited text files generated from the profiling of BAM files.

Example outputs

The number of columns and their content for files that are considered artifact bam-stats-txt will be variable and depend on the user parameters set for anvi-profile-blitz.

The column names may be one of these:

  • gene_callers_id: Unique number assigned by the gene caller during the creation of the contigs-db.
  • contig: Contig name as appears in the bam-file and contigs-db
  • sample: The name of the bam-file without its prefix. I.e., the value SAMPLE-01 will appear in the sample column if the BAM file path was /path/to/SAMPLE-01.bam.
  • length: Depending on the context, the length of the gene or contig.
  • num_mapped_reads: The actual number of short reads mapping to a gene or contig in a given sample. Useful for those who wish to do TPM/RPKM normalizations.
  • detection: Proportion of nucleotides that have at least 1X coverage.
  • mean_cov: Mean covearge.
  • q2q3_cov: Mean of the coverage (inner quartiles).
  • median_cov: Median coverage.
  • min_cov: Minimum coverage value observed for the gene or the contig.
  • max_cov: Minimum coverage value observed for the gene or the contig.
  • std_cov: Standard deviation of coverage.

Contig mode, default output

12-column TAB delimited file, where each row represents a single contig x sample pair (so the values in the first column are not unique):

contig sample length gc_content num_mapped_reads detection mean_cov q2q3_cov median_cov min_cov max_cov std_cov
contig_878 SAMPLE-01 27538 0.608 11877 0.9995 63.61 65.2 65.0 0 107 15.21
contig_6515 SAMPLE-01 12315 0.446 7669 0.9985 91.51 92.5 92.0 0 195 23.98
contig_1720 SAMPLE-01 16856 0.312 4237 0.9993 37.85 38.25 38.0 0 56 7.961
contig_878 SAMPLE-02 27538 0.608 1594 0.9999 9.262 9.161 9.0 0 21 3.42
contig_6515 SAMPLE-02 12315 0.446 2562 0.9918 33.05 33.47 33.0 0 56 8.503
contig_1720 SAMPLE-02 16856 0.312 926 0.9986 8.93 8.751 9.0 0 19 3.306
contig_878 SAMPLE-03 27538 0.608 6395 1.0 37.32 37.21 37.0 0 75 11.46
contig_6515 SAMPLE-03 12315 0.446 300 0.9276 3.953 3.682 4.0 0 15 2.644
contig_1720 SAMPLE-03 16856 0.312 18175 1.0 178.1 178.1 178.0 1 269 29.13

Contig mode, minimal output:

7-column TAB delimited file, where each row represents a single contig x sample pair:

contig sample length gc_content num_mapped_reads detection mean_cov
contig_878 SAMPLE-01 27538 0.608 11877 0.9995 63.61
contig_6515 SAMPLE-01 12315 0.446 7669 0.9985 91.51
contig_1720 SAMPLE-01 16856 0.312 4237 0.9993 37.85
contig_878 SAMPLE-02 27538 0.608 1594 0.9999 9.262
contig_6515 SAMPLE-02 12315 0.446 2562 0.9918 33.05
contig_1720 SAMPLE-02 16856 0.312 926 0.9986 8.93
contig_878 SAMPLE-03 27538 0.608 6395 1.0 37.32
contig_6515 SAMPLE-03 12315 0.446 300 0.9276 3.953
contig_1720 SAMPLE-03 16856 0.312 18175 1.0 178.1

Gene mode, default output

12-column TAB delimited file, where each row represents a single gene x sample pair:

gene_callers_id contig sample length num_mapped_reads detection mean_cov q2q3_cov median_cov min_cov max_cov std_cov
0 contig_878 SAMPLE-01 933 385 0.9871 53.97 58.9 59.0 0 85 21.18
1 contig_878 SAMPLE-01 564 326 1.0 66.97 66.88 66.0 35 103 20.6
2 contig_878 SAMPLE-01 444 318 1.0 81.72 81.59 82.0 70 95 4.88
3 contig_878 SAMPLE-01 1218 522 1.0 54.45 57.1 58.0 15 87 17.8
4 contig_878 SAMPLE-01 3381 1476 1.0 60.89 60.96 61.0 19 95 13.66
5 contig_878 SAMPLE-01 942 472 1.0 64.34 63.98 63.0 38 92 10.49
6 contig_878 SAMPLE-01 588 320 1.0 67.51 66.18 66.0 51 92 9.591
7 contig_878 SAMPLE-01 1854 852 1.0 62.63 63.03 63.0 31 85 10.14
8 contig_878 SAMPLE-01 285 195 1.0 67.43 68.41 70.0 51 80 8.741
9 contig_878 SAMPLE-01 1215 567 1.0 60.96 63.68 64.0 16 83 13.94
10 contig_878 SAMPLE-01 2250 1018 1.0 62.36 62.91 62.0 9 107 18.65
11 contig_878 SAMPLE-01 741 433 1.0 70.23 70.42 71.0 44 94 11.49
12 contig_878 SAMPLE-01 963 470 1.0 63.49 65.79 65.0 24 88 13.8
13 contig_878 SAMPLE-01 684 310 1.0 56.33 57.69 58.0 26 85 13.38
14 contig_878 SAMPLE-01 1569 724 1.0 61.79 63.8 64.0 10 95 18.3
15 contig_878 SAMPLE-01 1584 775 1.0 65.69 66.14 67.0 44 88 8.792
16 contig_878 SAMPLE-01 831 456 1.0 67.95 67.82 67.0 48 91 8.154
17 contig_878 SAMPLE-01 192 179 1.0 81.12 81.14 82.0 69 91 5.041
18 contig_878 SAMPLE-01 1467 675 1.0 60.06 60.98 62.0 25 91 14.24
19 contig_878 SAMPLE-01 801 456 1.0 68.31 67.72 68.0 58 86 5.945
20 contig_878 SAMPLE-01 360 252 1.0 71.42 72.38 74.0 53 87 8.963
(…) (…) (…) (…) (…) (…) (…) (…) (…) (…) (…) (…)
0 contig_878 SAMPLE-02 933 58 1.0 8.17 7.548 8.0 1 21 4.7
1 contig_878 SAMPLE-02 564 41 1.0 8.151 8.28 8.0 2 14 3.13
2 contig_878 SAMPLE-02 444 42 1.0 10.84 10.31 10.0 7 15 2.128
3 contig_878 SAMPLE-02 1218 83 1.0 9.86 10.55 11.0 1 15 3.041
4 contig_878 SAMPLE-02 3381 224 1.0 10.17 9.925 10.0 3 18 2.796
5 contig_878 SAMPLE-02 942 78 1.0 11.07 10.98 11.0 6 17 2.34
6 contig_878 SAMPLE-02 588 47 1.0 10.09 9.296 9.0 5 18 3.169
7 contig_878 SAMPLE-02 1854 121 1.0 9.417 9.186 9.0 2 16 2.75
8 contig_878 SAMPLE-02 285 30 1.0 10.33 10.0 10.0 7 15 2.217
9 contig_878 SAMPLE-02 1215 79 1.0 9.386 8.685 9.0 3 20 3.965
10 contig_878 SAMPLE-02 2250 115 0.9991 7.619 7.98 8.0 0 14 2.97
11 contig_878 SAMPLE-02 741 58 1.0 10.82 11.18 11.0 3 16 3.067
12 contig_878 SAMPLE-02 963 46 1.0 6.849 7.004 7.0 2 12 2.912
13 contig_878 SAMPLE-02 684 36 1.0 7.281 7.029 8.0 2 14 3.168
14 contig_878 SAMPLE-02 1569 74 1.0 6.505 6.345 6.0 1 13 2.363
15 contig_878 SAMPLE-02 1584 102 1.0 9.199 9.064 9.0 4 15 2.398
16 contig_878 SAMPLE-02 831 60 1.0 10.59 10.73 11.0 6 15 2.31
17 contig_878 SAMPLE-02 192 16 1.0 8.208 8.854 9.0 3 11 2.857
18 contig_878 SAMPLE-02 1467 108 1.0 10.67 10.36 11.0 4 20 3.894
19 contig_878 SAMPLE-02 801 68 1.0 10.85 10.74 11.0 5 19 2.706
20 contig_878 SAMPLE-02 360 34 1.0 10.32 10.24 10.0 6 15 1.886
(…) (…) (…) (…) (…) (…) (…) (…) (…) (…) (…) (…)

Gene mode, minimal output:

6-column TAB delimited file, where each row represents a single gene x sample pair:

gene_callers_id contig sample length detection mean_cov
0 contig_878 SAMPLE-01 933 0.9871 53.97
1 contig_878 SAMPLE-01 564 1.0 66.97
2 contig_878 SAMPLE-01 444 1.0 81.72
3 contig_878 SAMPLE-01 1218 1.0 54.45
4 contig_878 SAMPLE-01 3381 1.0 60.89
5 contig_878 SAMPLE-01 942 1.0 64.34
6 contig_878 SAMPLE-01 588 1.0 67.51
7 contig_878 SAMPLE-01 1854 1.0 62.63
8 contig_878 SAMPLE-01 285 1.0 67.43
9 contig_878 SAMPLE-01 1215 1.0 60.96
10 contig_878 SAMPLE-01 2250 1.0 62.36
11 contig_878 SAMPLE-01 741 1.0 70.23
12 contig_878 SAMPLE-01 963 1.0 63.49
13 contig_878 SAMPLE-01 684 1.0 56.33
14 contig_878 SAMPLE-01 1569 1.0 61.79
15 contig_878 SAMPLE-01 1584 1.0 65.69
16 contig_878 SAMPLE-01 831 1.0 67.95
17 contig_878 SAMPLE-01 192 1.0 81.12
18 contig_878 SAMPLE-01 1467 1.0 60.06
19 contig_878 SAMPLE-01 801 1.0 68.31
20 contig_878 SAMPLE-01 360 1.0 71.42
(…) (…) (…) (…) (…) (…)
0 contig_878 SAMPLE-02 933 1.0 8.17
1 contig_878 SAMPLE-02 564 1.0 8.151
2 contig_878 SAMPLE-02 444 1.0 10.84
3 contig_878 SAMPLE-02 1218 1.0 9.86
4 contig_878 SAMPLE-02 3381 1.0 10.17
5 contig_878 SAMPLE-02 942 1.0 11.07
6 contig_878 SAMPLE-02 588 1.0 10.09
7 contig_878 SAMPLE-02 1854 1.0 9.417
8 contig_878 SAMPLE-02 285 1.0 10.33
9 contig_878 SAMPLE-02 1215 1.0 9.386
10 contig_878 SAMPLE-02 2250 0.9991 7.619
11 contig_878 SAMPLE-02 741 1.0 10.82
12 contig_878 SAMPLE-02 963 1.0 6.849
13 contig_878 SAMPLE-02 684 1.0 7.281
14 contig_878 SAMPLE-02 1569 1.0 6.505
15 contig_878 SAMPLE-02 1584 1.0 9.199
16 contig_878 SAMPLE-02 831 1.0 10.59
17 contig_878 SAMPLE-02 192 1.0 8.208
18 contig_878 SAMPLE-02 1467 1.0 10.67
19 contig_878 SAMPLE-02 801 1.0 10.85
20 contig_878 SAMPLE-02 360 1.0 10.32
(…) (…) (…) (…) (…) (…)

Reproducing these output files

Examples above generated by running anvi-profile-blitz in the mini-test output directory. To reproduce them, you can run this command to generate the necessary files,

anvi-self-test --suite mini -o TEST

then go into the directory,

cd TEST

and run anvi-profile-blitz in coresponding modes.

Edit this file to update this information.

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