BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004120.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,748,930 number of mapped reads = 2,284,333 (83.1%) number of supplementary alignments = 13,401 (0.49%) number of secondary alignments = 0 number of mapped bases = 150,907,707 bp number of sequenced bases = 150,837,001 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 114,250 duplication rate = 3.76% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.538 >>>>>>> ACTG content number of A's = 41,295,773 bp (27.38%) number of C's = 26,731,613 bp (17.72%) number of T's = 49,184,271 bp (32.61%) number of G's = 33,609,412 bp (22.28%) number of N's = 15,932 bp (0.01%) GC percentage = 40% >>>>>>> Mismatches and indels general error rate = 0.0098 number of mismatches = 1,452,906 number of insertions = 13,793 mapped reads with insertion percentage = 0.6% number of deletions = 42,253 mapped reads with deletion percentage = 1.83% homopolymer indels = 47.46% >>>>>>> Coverage mean coverageData = 0.0487X std coverageData = 0.5082X There is a 4.11% of reference with a coverageData >= 1X There is a 0.54% 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% 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 12501466 0.0501562080360875 1.1606031091172708 chr2 243199373 12982372 0.053381601440230686 0.560803560804685 chr3 198022430 11211342 0.05661652571377899 0.27481646404306875 chr4 191154276 8340370 0.04363161617164138 0.2629860760785467 chr5 180915260 11872195 0.06562296071652551 0.29977893226609253 chr6 171115067 8476003 0.049533937300798886 0.2958012430768298 chr7 159138663 5208293 0.03272801782933164 0.4418542759328428 chr8 146364022 9835201 0.06719684841675094 0.6370498043351601 chr9 141213431 6452221 0.04569126997558752 0.4392472535615722 chr10 135534747 7858857 0.05798407547844539 0.43245326678944157 chr11 135006516 4772474 0.035349953034859445 0.3303763039468251 chr12 133851895 6428466 0.04802670892332156 0.26042638206706314 chr13 115169878 3986173 0.03461124618018611 0.21192351016098007 chr14 107349540 3863979 0.03599436942161094 0.2552541336573007 chr15 102531392 3556222 0.03468422627091613 0.22204732494901172 chr16 90354753 2866347 0.031723256440090095 0.2678692820853836 chr17 81195210 4371722 0.053842117041140725 0.30392673923257596 chr18 78077248 4477271 0.0573441189935383 0.9227715320500062 chr19 59128983 3096978 0.052376649197568646 0.7195235835504294 chr20 63025520 2534680 0.04021672490762472 0.2508907312552167 chr21 48129895 2774829 0.05765292028997778 0.29774838571870277 chr22 51304566 1954474 0.03809551765821389 0.22047467969307713 chrMT 16571 76547 4.61933498280128 3.416067737833341 chrX 155270560 10988278 0.07076858613764257 0.35483008353245166 chrY 59373566 420947 0.007089804914193633 0.14941606258743004