BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525033.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 = 2,205,317 number of mapped reads = 2,013,377 (91.3%) number of supplementary alignments = 7,730 (0.35%) number of secondary alignments = 0 number of mapped bases = 116,165,643 bp number of sequenced bases = 116,135,344 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 70,325 duplication rate = 2.58% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.5951 >>>>>>> ACTG content number of A's = 30,375,443 bp (26.16%) number of C's = 21,185,788 bp (18.24%) number of T's = 35,858,260 bp (30.88%) number of G's = 28,712,439 bp (24.72%) number of N's = 3,414 bp (0%) GC percentage = 42.97% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 561,599 number of insertions = 7,096 mapped reads with insertion percentage = 0.35% number of deletions = 18,307 mapped reads with deletion percentage = 0.9% homopolymer indels = 41.74% >>>>>>> Coverage mean coverageData = 0.0375X std coverageData = 0.3124X There is a 3.31% of reference with a coverageData >= 1X There is a 0.33% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 9209441 0.036948517773201454 0.557478370211403 chr2 243199373 9853420 0.040515811691669124 0.33719743642132544 chr3 198022430 7874458 0.0397654851523638 0.2202720793794813 chr4 191154276 7554857 0.03952230187097672 0.24606536946160268 chr5 180915260 7044226 0.03893660490552317 0.21917626463718834 chr6 171115067 6648719 0.03885525171199565 0.2407342643202409 chr7 159138663 6312135 0.039664371190550975 0.3419014245654814 chr8 146364022 5872858 0.04012501104950505 0.34461296243815814 chr9 141213431 5011284 0.03548730432022433 0.29579571195099386 chr10 135534747 5637308 0.04159308313756619 0.31910591177203484 chr11 135006516 5526118 0.04093223174502185 0.30049849615783497 chr12 133851895 5281166 0.039455294973597496 0.2258052103486083 chr13 115169878 3743145 0.03250107636651313 0.1976998343064522 chr14 107349540 3528901 0.032872996009111914 0.22219887166130184 chr15 102531392 3241676 0.03161642436298924 0.19634032750395397 chr16 90354753 3305194 0.03658018964425701 0.2297024114635124 chr17 81195210 2984817 0.036760998586000335 0.2270488490929722 chr18 78077248 3124081 0.040012693582642665 0.5451781733078442 chr19 59128983 2190591 0.03704766916082423 0.41737661819619665 chr20 63025520 2367307 0.03756108636628464 0.22413364364269564 chr21 48129895 1562089 0.032455691000364745 0.23098485952259357 chr22 51304566 1279441 0.02493815072911834 0.17357635314833442 chrMT 16571 4984 0.300766399131012 0.6053779192571153 chrX 155270560 6656521 0.04287046430437296 0.26754353302852163 chrY 59373566 350906 0.005910138528650949 0.1505221419526991