BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524931.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 = 2,347,726 number of mapped reads = 2,168,408 (92.36%) number of supplementary alignments = 9,600 (0.41%) number of secondary alignments = 0 number of mapped bases = 126,041,564 bp number of sequenced bases = 126,001,398 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 141,501 duplication rate = 5.04% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8642 >>>>>>> ACTG content number of A's = 32,045,157 bp (25.43%) number of C's = 23,630,380 bp (18.75%) number of T's = 40,585,161 bp (32.21%) number of G's = 29,739,682 bp (23.6%) number of N's = 1,018 bp (0%) GC percentage = 42.36% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 637,841 number of insertions = 8,330 mapped reads with insertion percentage = 0.38% number of deletions = 24,006 mapped reads with deletion percentage = 1.1% homopolymer indels = 42.5% >>>>>>> Coverage mean coverageData = 0.0407X std coverageData = 0.3528X There is a 3.39% of reference with a coverageData >= 1X There is a 0.49% 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 12973873 0.052051517255798534 0.6423252717661003 chr2 243199373 11137583 0.04579610079833553 0.4453140924173154 chr3 198022430 8149676 0.041155317607202375 0.2389733679937464 chr4 191154276 5670483 0.029664431885374095 0.25817473936252777 chr5 180915260 7655460 0.04231517009676243 0.24104069904844794 chr6 171115067 8240729 0.04815899116586852 0.2726719041024388 chr7 159138663 7618162 0.04787122033317573 0.4431829042218335 chr8 146364022 9386001 0.06412778818007611 0.42183279256359923 chr9 141213431 4646843 0.03290652289299592 0.2878526541074004 chr10 135534747 5864704 0.04327085216014754 0.40015774170945323 chr11 135006516 6101553 0.04519450750066019 0.30685232815099334 chr12 133851895 4014492 0.029992044565375783 0.2126830707862902 chr13 115169878 3215194 0.027916969747940515 0.19490518956822248 chr14 107349540 2295825 0.021386444692729937 0.18347880692763643 chr15 102531392 3489038 0.034028973292394196 0.21691087428963834 chr16 90354753 3951254 0.043730449907820566 0.26419436544091623 chr17 81195210 2970136 0.036580187427312526 0.23394735679434359 chr18 78077248 3304175 0.04231930664359482 0.48949518459208835 chr19 59128983 2676985 0.045273652009201644 0.45477337277838586 chr20 63025520 2508097 0.03979494338166508 0.2422611446600134 chr21 48129895 1224222 0.025435792037360565 0.22670540325943855 chr22 51304566 2493116 0.04859442724844412 0.2596857204222371 chrMT 16571 7957 0.4801762114537445 0.7593179499045737 chrX 155270560 6086004 0.03919612320584147 0.257937273314868 chrY 59373566 360002 0.006063338018134198 0.21155815287735608