BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525272.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 = 1,581,676 number of mapped reads = 1,451,234 (91.75%) number of supplementary alignments = 6,009 (0.38%) number of secondary alignments = 0 number of mapped bases = 83,646,901 bp number of sequenced bases = 83,619,201 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 48,237 duplication rate = 2.37% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.9945 >>>>>>> ACTG content number of A's = 21,560,651 bp (25.78%) number of C's = 14,284,756 bp (17.08%) number of T's = 26,883,741 bp (32.15%) number of G's = 20,888,371 bp (24.98%) number of N's = 1,682 bp (0%) GC percentage = 42.06% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 414,297 number of insertions = 4,833 mapped reads with insertion percentage = 0.33% number of deletions = 17,334 mapped reads with deletion percentage = 1.19% homopolymer indels = 44.95% >>>>>>> Coverage mean coverageData = 0.027X std coverageData = 0.2766X There is a 2.47% of reference with a coverageData >= 1X There is a 0.16% of reference with a coverageData >= 2X There is a 0.02% 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 8572614 0.034393551220079005 0.48819269743017824 chr2 243199373 6754163 0.02777212340921619 0.3498042768905725 chr3 198022430 6022775 0.030414610102502026 0.18994931727405232 chr4 191154276 4681275 0.02448951233505234 0.17379701514223936 chr5 180915260 3689833 0.020395366316804896 0.15494856816463828 chr6 171115067 5063291 0.029589977602615204 0.20721541915010203 chr7 159138663 6044587 0.03798314555401285 0.508933153106924 chr8 146364022 5482621 0.037458802546434536 0.27876434026235714 chr9 141213431 2675147 0.018943998322652467 0.1883638659681042 chr10 135534747 5159952 0.0380710637988648 0.29477997708397957 chr11 135006516 3751402 0.027786821785698107 0.22377419681249974 chr12 133851895 3626897 0.027096344059977635 0.1789484215741261 chr13 115169878 2596568 0.022545547890569093 0.16233555910571923 chr14 107349540 2405343 0.02240664468613466 0.1639525011708617 chr15 102531392 2168372 0.021148371807923956 0.1583213921126436 chr16 90354753 2055475 0.022748941607974957 0.17588663910411226 chr17 81195210 1357709 0.016721540593342882 0.14259753697817584 chr18 78077248 1717261 0.0219943843307592 0.3654955847595122 chr19 59128983 1472016 0.02489499946244636 0.3694192121666773 chr20 63025520 1421862 0.0225600994644709 0.16372786092915181 chr21 48129895 1126060 0.023396269615797 0.16892048209420704 chr22 51304566 842504 0.01642161830196556 0.13721995576900356 chrMT 16571 49266 2.973025164443908 2.409757017798204 chrX 155270560 4686344 0.03018179363815008 0.2012631607869027 chrY 59373566 223564 0.0037653793609095333 0.09546122682337849