BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525032.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 = 1,095,937 number of mapped reads = 1,006,261 (91.82%) number of supplementary alignments = 5,520 (0.5%) number of secondary alignments = 0 number of mapped bases = 58,736,271 bp number of sequenced bases = 58,716,446 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 28,148 duplication rate = 2.07% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.5045 >>>>>>> ACTG content number of A's = 14,605,372 bp (24.87%) number of C's = 11,523,232 bp (19.63%) number of T's = 19,264,976 bp (32.81%) number of G's = 13,322,191 bp (22.69%) number of N's = 675 bp (0%) GC percentage = 42.31% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 296,311 number of insertions = 3,794 mapped reads with insertion percentage = 0.38% number of deletions = 11,979 mapped reads with deletion percentage = 1.18% homopolymer indels = 42.95% >>>>>>> Coverage mean coverageData = 0.019X std coverageData = 0.1908X There is a 1.76% 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 4773311 0.01915064837491418 0.31966009920695815 chr2 243199373 4994836 0.020538029923292605 0.21700232128562075 chr3 198022430 3838404 0.019383682949451735 0.14741486161714565 chr4 191154276 3783229 0.019791495535260745 0.16398532063803611 chr5 180915260 3548115 0.01961202719991669 0.14854515884000774 chr6 171115067 3313247 0.019362684175555388 0.17561133610816848 chr7 159138663 3217421 0.02021772044170058 0.21806031248804947 chr8 146364022 3028291 0.020690132442520607 0.19735833171041242 chr9 141213431 2447710 0.017333407896590235 0.16376886560905232 chr10 135534747 2842616 0.020973337560441237 0.19708099771841087 chr11 135006516 2711725 0.020085882373262635 0.18626520511811293 chr12 133851895 2661770 0.01988593437545281 0.15035412591945801 chr13 115169878 1798567 0.01561664413675944 0.13325584528488146 chr14 107349540 1756944 0.016366572227510243 0.13870616802352817 chr15 102531392 1686762 0.016451176240736106 0.13968406861938193 chr16 90354753 1721049 0.01904768640117914 0.15171497154852284 chr17 81195210 1608931 0.019815590106854825 0.1618610239226582 chr18 78077248 1592443 0.02039573679646086 0.2730082944902923 chr19 59128983 1168880 0.019768308885001456 0.22414437269518636 chr20 63025520 1253398 0.019887150474918732 0.15157158358551523 chr21 48129895 778345 0.01617175769861954 0.14414780676100583 chr22 51304566 712937 0.013896170566962792 0.12447641447143076 chrMT 16571 3507 0.21163478365819804 0.4711709890068604 chrX 155270560 3306859 0.02129739855385335 0.16303918017126867 chrY 59373566 186974 0.003149111845497035 0.09945799706879793