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 by

There are no anvi’o tools that 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 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 (for contig-level stats)
  • bin: Genome name as it appears in the collection being worked on (for genome-level stats)
  • gene_callers_id: Gene ID number as it appears in the contigs-db (for gene-level stats)
  • 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, contig or genome.
  • num_mapped_reads: The actual number of short reads mapping to a gene, contig or genome 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 coverage.
  • q2q3_cov: Mean of the coverage (inner quartiles).
  • median_cov: Median coverage.
  • min_cov: Minimum coverage value observed for the gene, contig, or genome.
  • max_cov: Maximum coverage value observed for the gene, contig, or genome.
  • std_cov: Standard deviation of coverage.

These files can also contain distribution of coverage (discov) scores and related data values. You can see a fuller description of these in discov-stats, but here is a quick overview of the related columns:

  • num_windows: The number of non-overlapping windows the contig (or genome) was divided into when computing discov.
  • actual_prop_windows_covered: The proportion of windows that contain bases with at least some reads mapping to them (the observed spread).
  • expected_prop_windows_covered: The proportion of windows we would expect to be covered if the same reads were placed randomly along the sequence (the expected spread), which depends on the number of mapped reads and their total aligned length.
  • normalized_spread: The observed spread divided by the expected spread, capped at 1. Also known as the Spread (S) metric.
  • window_depth_evenness: 1 / (1 + CV), where CV is the coefficient of variation of the mean coverage depths of the covered windows. Also known as the Evenness (E) metric. It is set to 0 when fewer than 3 windows are covered.
  • spread_evenness_score: The geometric or linear combination of S and E (C).
  • discov: The overall distribution of coverage score for the contig (or genome), computed as min(1, C + detection^2).

Contig mode, default output

19-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 num_windows actual_prop_windows_covered expected_prop_windows_covered normalized_spread window_depth_evenness spread_evenness_score discov
contig_878 SAMPLE-01 27538 0.608 11877 0.9995 63.61 65.2 65.0 0 107 15.21 92 1.0 1.0 1.0 0.8684 0.9319 1.0
contig_6515 SAMPLE-01 12315 0.446 7669 0.9985 91.51 92.5 92.0 0 195 23.98 41 1.0 1.0 1.0 0.8321 0.9122 1.0
contig_1720 SAMPLE-01 16856 0.312 4237 0.9993 37.85 38.25 38.0 0 56 7.961 57 1.0 1.0 1.0 0.8481 0.9209 1.0
contig_878 SAMPLE-02 27538 0.608 1594 0.9999 9.262 9.161 9.0 0 21 3.42 92 1.0 1.0 1.0 0.7851 0.8861 1.0
contig_6515 SAMPLE-02 12315 0.446 2562 0.9918 33.05 33.47 33.0 0 56 8.503 41 1.0 1.0 1.0 0.8324 0.9124 1.0
contig_1720 SAMPLE-02 16856 0.312 926 0.9986 8.93 8.751 9.0 0 19 3.306 57 1.0 1.0 1.0 0.7848 0.8859 1.0
contig_878 SAMPLE-03 27538 0.608 6395 1.0 37.32 37.21 37.0 0 75 11.46 92 1.0 1.0 1.0 0.8119 0.901 1.0
contig_6515 SAMPLE-03 12315 0.446 300 0.9276 3.953 3.682 4.0 0 15 2.644 41 1.0 1.0 1.0 0.6796 0.8244 1.0
contig_1720 SAMPLE-03 16856 0.312 18175 1.0 178.1 178.1 178.0 1 269 29.13 57 1.0 1.0 1.0 0.8659 0.9305 1.0

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

Genome mode, default output

19-column TAB delimited file, where each row represents a single bin/genome x sample pair:

bin sample length gc_content num_mapped_reads detection mean_cov q2q3_cov median_cov min_cov max_cov std_cov num_windows actual_prop_windows_covered expected_prop_windows_covered normalized_spread window_depth_evenness spread_evenness_score discov
Bin_1 SAMPLE-01 27538 0.608 11877 0.9995 63.61 65.2 65.0 0 107 15.21 3 1.0 1.0 1.0 0.9701 0.9849 1.0
Bin_2 SAMPLE-01 16856 0.312 4237 0.9993 37.85 38.25 38.0 0 56 7.961 2 1.0 1.0 1.0 0.0 0.0 0.9987
Bin_3 SAMPLE-01 12315 0.446 7669 0.9985 91.51 92.5 92.0 0 195 23.98 2 1.0 1.0 1.0 0.0 0.0 0.9971
Bin_1 SAMPLE-02 27538 0.608 1594 0.9999 9.262 9.161 9.0 0 21 3.42 3 1.0 1.0 1.0 0.9281 0.9634 1.0
Bin_2 SAMPLE-02 16856 0.312 926 0.9986 8.93 8.751 9.0 0 19 3.306 2 1.0 1.0 1.0 0.0 0.0 0.9973
Bin_3 SAMPLE-02 12315 0.446 2562 0.9918 33.05 33.47 33.0 0 56 8.503 2 1.0 1.0 1.0 0.0 0.0 0.9837
Bin_1 SAMPLE-03 27538 0.608 6395 1.0 37.32 37.21 37.0 0 75 11.46 3 1.0 1.0 1.0 0.9435 0.9713 1.0
Bin_2 SAMPLE-03 16856 0.312 18175 1.0 178.1 178.1 178.0 1 269 29.13 2 1.0 1.0 1.0 0.0 0.0 1.0
Bin_3 SAMPLE-03 12315 0.446 300 0.9276 3.953 3.682 4.0 0 15 2.644 2 1.0 1.0 1.0 0.0 0.0 0.8605

Genome mode, minimal output

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

bin sample length gc_content num_mapped_reads detection mean_cov
Bin_2 SAMPLE-01 16856 0.312 4237 0.9993 37.85
Bin_3 SAMPLE-01 12315 0.446 7669 0.9985 91.51
Bin_1 SAMPLE-01 27538 0.608 11877 0.9995 63.61
Bin_2 SAMPLE-02 16856 0.312 926 0.9986 8.93
Bin_3 SAMPLE-02 12315 0.446 2562 0.9918 33.05
Bin_1 SAMPLE-02 27538 0.608 1594 0.9999 9.262
Bin_2 SAMPLE-03 16856 0.312 18175 1.0 178.1
Bin_3 SAMPLE-03 12315 0.446 300 0.9276 3.953
Bin_1 SAMPLE-03 27538 0.608 6395 1.0 37.32

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 corresponding modes.

Edit this file to update this information.

Copyleft, The anvi'o Project