BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR9716363.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.result/quality.files/genome_results.txt
>>>>>>> Reference
number of bases = 3,095,693,983 bp
number of contigs = 25
>>>>>>> Globals
number of windows = 424
number of reads = 1,595,972
number of mapped reads = 1,466,109 (91.86%)
number of supplementary alignments = 7,921 (0.5%)
number of secondary alignments = 0
number of mapped bases = 85,655,820 bp
number of sequenced bases = 85,633,116 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 57,120
duplication rate = 3.06%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 44.9515
>>>>>>> ACTG content
number of A's = 20,835,070 bp (24.33%)
number of C's = 16,502,537 bp (19.27%)
number of T's = 26,876,665 bp (31.39%)
number of G's = 21,418,208 bp (25.01%)
number of N's = 636 bp (0%)
GC percentage = 44.28%
>>>>>>> Mismatches and indels
general error rate = 0.0049
number of mismatches = 413,292
number of insertions = 4,663
mapped reads with insertion percentage = 0.32%
number of deletions = 14,192
mapped reads with deletion percentage = 0.96%
homopolymer indels = 44.97%
>>>>>>> Coverage
mean coverageData = 0.0277X
std coverageData = 0.2494X
There is a 2.46% of reference with a coverageData >= 1X
There is a 0.23% of reference with a coverageData >= 2X
There is a 0.03% of reference with a coverageData >= 3X
There is a 0.01% of reference with a coverageData >= 4X
There is a 0% of reference with a coverageData >= 5X
There is a 0% of reference with a coverageData >= 6X
There is a 0% of reference with a coverageData >= 7X
There is a 0% of reference with a coverageData >= 8X
There is a 0% of reference with a coverageData >= 9X
There is a 0% of reference with a coverageData >= 10X
There is a 0% of reference with a coverageData >= 11X
There is a 0% of reference with a coverageData >= 12X
There is a 0% of reference with a coverageData >= 13X
There is a 0% of reference with a coverageData >= 14X
There is a 0% of reference with a coverageData >= 15X
There is a 0% of reference with a coverageData >= 16X
There is a 0% of reference with a coverageData >= 17X
There is a 0% of reference with a coverageData >= 18X
There is a 0% of reference with a coverageData >= 19X
There is a 0% of reference with a coverageData >= 20X
There is a 0% of reference with a coverageData >= 21X
There is a 0% of reference with a coverageData >= 22X
There is a 0% of reference with a coverageData >= 23X
There is a 0% of reference with a coverageData >= 24X
There is a 0% of reference with a coverageData >= 25X
There is a 0% of reference with a coverageData >= 26X
There is a 0% of reference with a coverageData >= 27X
There is a 0% of reference with a coverageData >= 28X
There is a 0% of reference with a coverageData >= 29X
There is a 0% of reference with a coverageData >= 30X
There is a 0% of reference with a coverageData >= 31X
There is a 0% of reference with a coverageData >= 32X
There is a 0% of reference with a coverageData >= 33X
There is a 0% of reference with a coverageData >= 34X
There is a 0% of reference with a coverageData >= 35X
There is a 0% of reference with a coverageData >= 36X
There is a 0% of reference with a coverageData >= 37X
There is a 0% of reference with a coverageData >= 38X
There is a 0% of reference with a coverageData >= 39X
There is a 0% of reference with a coverageData >= 40X
There is a 0% of reference with a coverageData >= 41X
There is a 0% of reference with a coverageData >= 42X
There is a 0% of reference with a coverageData >= 43X
There is a 0% of reference with a coverageData >= 44X
There is a 0% of reference with a coverageData >= 45X
There is a 0% of reference with a coverageData >= 46X
There is a 0% of reference with a coverageData >= 47X
There is a 0% of reference with a coverageData >= 48X
There is a 0% of reference with a coverageData >= 49X
There is a 0% of reference with a coverageData >= 50X
There is a 0% of reference with a coverageData >= 51X
>>>>>>> Coverage per contig
chr1 249250621 10065381 0.040382571403904347 0.40291031182293346
chr2 243199373 8738800 0.035932658428358695 0.34303990037026355
chr3 198022430 5371334 0.027124876712198712 0.18066960588156505
chr4 191154276 3562953 0.018639148830759088 0.16773920707665838
chr5 180915260 6094487 0.03368697035286023 0.201847138409868
chr6 171115067 3166450 0.018504799463392667 0.16411667036834388
chr7 159138663 5732991 0.036025129857978004 0.3838090609147007
chr8 146364022 3789692 0.02589223736964539 0.22886087099835828
chr9 141213431 2630807 0.018630005526882213 0.19446755655559952
chr10 135534747 3816941 0.028162084516968923 0.21834538675972984
chr11 135006516 3707861 0.027464311426272196 0.22992543327883577
chr12 133851895 3423164 0.02557426624404533 0.1776832392755352
chr13 115169878 2482120 0.021551815831566654 0.16161072525698233
chr14 107349540 1852006 0.017252109324362264 0.15208150620913877
chr15 102531392 3717102 0.0362533066945975 0.20939196570830326
chr16 90354753 2535303 0.028059431472298973 0.1910943430243484
chr17 81195210 3231580 0.039800131066844956 0.2344152607313055
chr18 78077248 2711924 0.03473385742284359 0.38847453527422643
chr19 59128983 1368403 0.023142677762612626 0.29527866931013036
chr20 63025520 2174493 0.03450178594321792 0.20654939208592046
chr21 48129895 1060865 0.02204170609555662 0.1685810314734019
chr22 51304566 1018469 0.019851429987732476 0.15485400513370484
chrMT 16571 9582 0.5782390923903205 0.8122094221194491
chrX 155270560 3195416 0.020579664296953654 0.17417231075067863
chrY 59373566 197696 0.003329697259551498 0.08414442230353661