BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716654.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 = 1,015,601 number of mapped reads = 775,903 (76.4%) number of supplementary alignments = 22,126 (2.18%) number of secondary alignments = 0 number of mapped bases = 57,662,844 bp number of sequenced bases = 57,643,123 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 12,646 duplication rate = 0.99% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.9555 >>>>>>> ACTG content number of A's = 15,140,029 bp (26.27%) number of C's = 11,697,201 bp (20.29%) number of T's = 17,410,191 bp (30.2%) number of G's = 13,388,374 bp (23.23%) number of N's = 7,328 bp (0.01%) GC percentage = 43.52% >>>>>>> Mismatches and indels general error rate = 0.0077 number of mismatches = 435,499 number of insertions = 4,464 mapped reads with insertion percentage = 0.57% number of deletions = 11,457 mapped reads with deletion percentage = 1.46% homopolymer indels = 40.07% >>>>>>> Coverage mean coverageData = 0.0186X std coverageData = 0.1868X There is a 1.73% of reference with a coverageData >= 1X There is a 0.1% of reference with a coverageData >= 2X There is a 0.01% 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 4865060 0.019518747758706687 0.19626645778753515 chr2 243199373 5089016 0.02092528421115625 0.29610332636424724 chr3 198022430 4420906 0.022325279010059616 0.15984511630967996 chr4 191154276 2379622 0.012448698767272148 0.11931509057884943 chr5 180915260 3708866 0.02050057026698577 0.15227319827744773 chr6 171115067 4161639 0.02432070461685294 0.1739407007151527 chr7 159138663 3253213 0.02044263121652593 0.2311448034905373 chr8 146364022 4014765 0.027429999156486695 0.2559535440399424 chr9 141213431 2504802 0.01773770371743181 0.1828423977057907 chr10 135534747 2626821 0.019381162824615005 0.17036500612295177 chr11 135006516 2272101 0.016829565470751057 0.16004349784373284 chr12 133851895 2188447 0.0163497647904051 0.13540981439829342 chr13 115169878 2053852 0.01783323934753148 0.14004803267109567 chr14 107349540 1362142 0.012688848037914275 0.12725942536519794 chr15 102531392 1125783 0.010979886043095953 0.11069648240494101 chr16 90354753 1414391 0.015653753156737643 0.13976073297743602 chr17 81195210 1683407 0.020732836333571893 0.16486448786185018 chr18 78077248 1768433 0.022649786529361282 0.32227300048345575 chr19 59128983 976722 0.016518498212627807 0.1959611340343532 chr20 63025520 1133959 0.017992060993705407 0.14938576309307167 chr21 48129895 1266314 0.02631034204417026 0.17483661664348157 chr22 51304566 951863 0.018553182966210065 0.14597744108046357 chrMT 16571 4585 0.27668819021181584 0.5979032230147616 chrX 155270560 2314237 0.01490454468638485 0.1490629212191936 chrY 59373566 121898 0.002053068532215161 0.06155728909855096