BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524741.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 = 2,208,511 number of mapped reads = 2,016,157 (91.29%) number of supplementary alignments = 7,001 (0.32%) number of secondary alignments = 0 number of mapped bases = 115,331,354 bp number of sequenced bases = 115,293,551 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 100,145 duplication rate = 3.8% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.4022 >>>>>>> ACTG content number of A's = 28,599,704 bp (24.81%) number of C's = 22,333,066 bp (19.37%) number of T's = 36,413,286 bp (31.58%) number of G's = 27,933,710 bp (24.23%) number of N's = 13,785 bp (0.01%) GC percentage = 43.6% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 589,740 number of insertions = 7,565 mapped reads with insertion percentage = 0.37% number of deletions = 23,515 mapped reads with deletion percentage = 1.16% homopolymer indels = 43.74% >>>>>>> Coverage mean coverageData = 0.0373X std coverageData = 0.3113X There is a 3.22% of reference with a coverageData >= 1X There is a 0.37% of reference with a coverageData >= 2X There is a 0.06% 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 9190365 0.03687198436308008 0.4216394435432999 chr2 243199373 9699032 0.039880990976074594 0.5270492631883957 chr3 198022430 7549543 0.03812468617822739 0.22569999832947882 chr4 191154276 7366390 0.03853636002367009 0.2594709032558466 chr5 180915260 6833895 0.037774010882221876 0.22014646966297394 chr6 171115067 6551330 0.03828610837641784 0.2486059240227128 chr7 159138663 6399886 0.040215783388855036 0.38368463552215937 chr8 146364022 5740069 0.03921775940264883 0.28298905015833 chr9 141213431 4893478 0.03465306356022183 0.2632807596778881 chr10 135534747 5550588 0.04095324721416273 0.3591003684366158 chr11 135006516 5184213 0.03839972435108243 0.2735652887001138 chr12 133851895 5262480 0.03931569291566623 0.22891732774040732 chr13 115169878 3536907 0.030710347717829482 0.19869687281641277 chr14 107349540 3441793 0.03206155331452748 0.21052413616239732 chr15 102531392 3326039 0.03243922602747849 0.20787171552724762 chr16 90354753 3509988 0.03884674445405213 0.24785873118993063 chr17 81195210 3346909 0.041220522737732926 0.2455071080392974 chr18 78077248 3012524 0.03858389066172004 0.42740427876018555 chr19 59128983 2582903 0.04368252029634942 0.3633080732109308 chr20 63025520 2541024 0.0403173825459909 0.24381882210852304 chr21 48129895 1528135 0.031750225093987845 0.23479742475160328 chr22 51304566 1488902 0.029020847774055822 0.19619477475935496 chrMT 16571 34743 2.0966145676181283 1.9960116494288476 chrX 155270560 6376873 0.04106942745617714 0.25060503680147467 chrY 59373566 383345 0.00645649277660028 0.16896855615514664