BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716360.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 = 1,028,214 number of mapped reads = 914,144 (88.91%) number of supplementary alignments = 5,353 (0.52%) number of secondary alignments = 0 number of mapped bases = 52,998,118 bp number of sequenced bases = 52,983,811 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 33,677 duplication rate = 3.01% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7064 >>>>>>> ACTG content number of A's = 12,818,391 bp (24.19%) number of C's = 10,728,167 bp (20.25%) number of T's = 16,918,725 bp (31.93%) number of G's = 12,518,096 bp (23.63%) number of N's = 432 bp (0%) GC percentage = 43.87% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 259,380 number of insertions = 3,783 mapped reads with insertion percentage = 0.41% number of deletions = 9,171 mapped reads with deletion percentage = 1% homopolymer indels = 42.41% >>>>>>> Coverage mean coverageData = 0.0171X std coverageData = 0.1729X There is a 1.55% of reference with a coverageData >= 1X There is a 0.13% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0% 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 6274436 0.025173201072987497 0.24383222092352716 chr2 243199373 5362486 0.022049752570702557 0.2401515903989848 chr3 198022430 3310442 0.016717510233562934 0.14023298760882894 chr4 191154276 2223982 0.011634487318504975 0.12796456868179065 chr5 180915260 3762604 0.020797604359079493 0.15682354538158008 chr6 171115067 1975132 0.011542712366760783 0.12316795114269198 chr7 159138663 3565044 0.022402123612160797 0.25401724206379894 chr8 146364022 2291837 0.015658472407925495 0.15501962488005622 chr9 141213431 1437928 0.01018265748390463 0.13174346230844688 chr10 135534747 2389830 0.017632600147916313 0.16352990216429283 chr11 135006516 2284037 0.016917976018283442 0.16273940145562718 chr12 133851895 2125046 0.015876099475468763 0.1370895535441728 chr13 115169878 1489303 0.012931358666543 0.12250841571019193 chr14 107349540 1150841 0.010720502388738694 0.11470638886477151 chr15 102531392 2307307 0.02250342022080418 0.16368630655111446 chr16 90354753 1583073 0.017520638897657106 0.14826012168538774 chr17 81195210 2100304 0.02586733872601598 0.18395954485801277 chr18 78077248 1660483 0.02126718144573948 0.2470238071435651 chr19 59128983 871569 0.014740131755690776 0.18265033344086626 chr20 63025520 1440524 0.022856201741770634 0.16578087953473156 chr21 48129895 670014 0.013920952871391055 0.13380510307034651 chr22 51304566 643188 0.012536661941551168 0.12176390501506783 chrMT 16571 5629 0.33968981956429906 0.656159472133243 chrX 155270560 1939872 0.012493495225366611 0.12886478428097112 chrY 59373566 133207 0.002243540500835001 0.07202946735640836