BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716787.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 = 1,735,429 number of mapped reads = 1,480,475 (85.31%) number of supplementary alignments = 32,109 (1.85%) number of secondary alignments = 0 number of mapped bases = 109,312,928 bp number of sequenced bases = 109,275,179 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 41,770 duplication rate = 1.94% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.0578 >>>>>>> ACTG content number of A's = 29,017,589 bp (26.55%) number of C's = 22,970,915 bp (21.02%) number of T's = 32,065,905 bp (29.34%) number of G's = 25,207,600 bp (23.07%) number of N's = 13,170 bp (0.01%) GC percentage = 44.09% >>>>>>> Mismatches and indels general error rate = 0.0074 number of mismatches = 784,291 number of insertions = 9,552 mapped reads with insertion percentage = 0.64% number of deletions = 22,212 mapped reads with deletion percentage = 1.48% homopolymer indels = 38.52% >>>>>>> Coverage mean coverageData = 0.0353X std coverageData = 0.2908X There is a 3.12% of reference with a coverageData >= 1X There is a 0.3% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 8779725 0.03522448596025765 0.3593188753697381 chr2 243199373 8888929 0.0365499667632778 0.3976451690332385 chr3 198022430 7468894 0.03771741413333833 0.21395449682683546 chr4 191154276 6977064 0.036499649110648194 0.22445402346050525 chr5 180915260 6539718 0.036147962311194756 0.21136056313222154 chr6 171115067 6318793 0.03692715732624527 0.2356691410008793 chr7 159138663 5907510 0.03712177725157839 0.3447873638836183 chr8 146364022 5409848 0.036961597024164856 0.3496993040905875 chr9 141213431 4586721 0.03248077018962878 0.3075009048724029 chr10 135534747 5292561 0.03904947710567534 0.29833748599905263 chr11 135006516 5004454 0.03706824046922298 0.3200258621040159 chr12 133851895 4891402 0.03654338999085519 0.21380748548201362 chr13 115169878 3521286 0.03057471329439109 0.19243522422803885 chr14 107349540 3399638 0.03166886416094564 0.22712484184384388 chr15 102531392 3226833 0.03147165894324345 0.1968496533009395 chr16 90354753 3226530 0.0357095768940899 0.23291038589043928 chr17 81195210 2983125 0.0367401599183006 0.2308941835186041 chr18 78077248 3088896 0.039562050137832726 0.5577521691685281 chr19 59128983 2220145 0.03754749172668841 0.32049481781659794 chr20 63025520 2344585 0.037200565739084736 0.21900701250441196 chr21 48129895 1419207 0.029487016333611366 0.20363048932808872 chr22 51304566 1282046 0.02498892593692343 0.17492082197072886 chrMT 16571 14390 0.8683845271860479 1.2138296530580484 chrX 155270560 6247563 0.04023662309197571 0.2734528065885957 chrY 59373566 273065 0.004599100549224212 0.12573771992555116