BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524966.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 = 1,308,756 number of mapped reads = 1,211,933 (92.6%) number of supplementary alignments = 2,826 (0.22%) number of secondary alignments = 0 number of mapped bases = 70,278,145 bp number of sequenced bases = 70,257,360 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 36,461 duplication rate = 2.16% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.1035 >>>>>>> ACTG content number of A's = 17,933,624 bp (25.53%) number of C's = 13,503,257 bp (19.22%) number of T's = 22,050,776 bp (31.39%) number of G's = 16,768,857 bp (23.87%) number of N's = 846 bp (0%) GC percentage = 43.09% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 336,292 number of insertions = 5,059 mapped reads with insertion percentage = 0.42% number of deletions = 12,226 mapped reads with deletion percentage = 1% homopolymer indels = 42% >>>>>>> Coverage mean coverageData = 0.0227X std coverageData = 0.2264X There is a 2.07% of reference with a coverageData >= 1X There is a 0.14% 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 7007003 0.0281122790061173 0.42265003498349546 chr2 243199373 6422684 0.026409130586039792 0.24878144476030367 chr3 198022430 4416610 0.022303584497978333 0.1618016883650866 chr4 191154276 4551247 0.02380928690289931 0.17416958208928 chr5 180915260 2969964 0.016416326627173405 0.14109185877928065 chr6 171115067 5027872 0.029382988232123358 0.23226550128977347 chr7 159138663 4386506 0.027564049598682378 0.3099973825453698 chr8 146364022 4250584 0.029041180625659493 0.22404817809293628 chr9 141213431 1867148 0.013222170063979254 0.17128956593048522 chr10 135534747 3786827 0.027939897951039818 0.22697245810144007 chr11 135006516 2817310 0.020867955736299425 0.20510574774479726 chr12 133851895 4106839 0.030681963822775913 0.19048017040212245 chr13 115169878 1325934 0.011512854081516002 0.11994876925260495 chr14 107349540 1702367 0.015858167626987503 0.14017392953980434 chr15 102531392 1723917 0.01681355306285123 0.15085766162937034 chr16 90354753 1969463 0.02179700496774088 0.16547722435193685 chr17 81195210 1592538 0.019613693960518114 0.18664840132243565 chr18 78077248 1334806 0.01709596629225456 0.26577594928772025 chr19 59128983 1893127 0.03201690446798316 0.2721296845202889 chr20 63025520 1552344 0.02463040368409495 0.17080766806022302 chr21 48129895 815699 0.0169478657703284 0.14630851728750133 chr22 51304566 752328 0.014663957979880387 0.1291849671042673 chrMT 16571 28612 1.7266308611429606 1.6781851651241377 chrX 155270560 3782015 0.024357579440687276 0.18674562745503842 chrY 59373566 194401 0.003274201182391504 0.07848523055809696