BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524570.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 = 2,861,182 number of mapped reads = 2,607,960 (91.15%) number of supplementary alignments = 10,435 (0.36%) number of secondary alignments = 0 number of mapped bases = 151,141,370 bp number of sequenced bases = 151,093,571 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 144,813 duplication rate = 4.15% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8356 >>>>>>> ACTG content number of A's = 38,271,951 bp (25.33%) number of C's = 28,218,280 bp (18.68%) number of T's = 48,666,364 bp (32.21%) number of G's = 35,934,641 bp (23.78%) number of N's = 2,335 bp (0%) GC percentage = 42.46% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 770,668 number of insertions = 9,754 mapped reads with insertion percentage = 0.37% number of deletions = 28,858 mapped reads with deletion percentage = 1.1% homopolymer indels = 42.49% >>>>>>> Coverage mean coverageData = 0.0488X std coverageData = 0.4165X There is a 4.13% of reference with a coverageData >= 1X There is a 0.53% of reference with a coverageData >= 2X There is a 0.09% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 14789460 0.05933569970924967 0.8204857673978919 chr2 243199373 11916704 0.0489997315905909 0.483381323921613 chr3 198022430 8232275 0.04157243702140207 0.2398916561918808 chr4 191154276 8590630 0.04494082047110471 0.29211256161757315 chr5 180915260 8272925 0.045728176827095735 0.24683478712229925 chr6 171115067 6481155 0.03787600422118293 0.3065787993526702 chr7 159138663 7600893 0.047762704905972474 0.5396906952761698 chr8 146364022 13901478 0.09497879198755552 0.4337683041725017 chr9 141213431 6438659 0.045595230952217285 0.35013458069244413 chr10 135534747 7891621 0.05822581422607444 0.4215831481376226 chr11 135006516 5263865 0.03898971068922333 0.39699018063296027 chr12 133851895 6955479 0.05196399348698052 0.26522133720714536 chr13 115169878 3366122 0.029227451295902214 0.19902522796537633 chr14 107349540 3617687 0.03370006988385791 0.21947483134417725 chr15 102531392 3969654 0.03871647426770525 0.23889473327617702 chr16 90354753 4755333 0.052629583304820725 0.2917624727367043 chr17 81195210 5235744 0.06448340979720356 0.3166236095591351 chr18 78077248 3586651 0.04593721079923309 0.638457174943332 chr19 59128983 3120889 0.05278103633204718 0.5301572161543965 chr20 63025520 4314424 0.06845519084967486 0.30854133046902005 chr21 48129895 2093588 0.04349870283323909 0.27123300825032803 chr22 51304566 1241521 0.02419903522817053 0.17844171882213006 chrMT 16571 105987 6.395932653430692 4.26785826897279 chrX 155270560 8913673 0.05740736041655289 0.32200970070557866 chrY 59373566 484953 0.00816782673959654 0.22205522553933404