BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716885.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 = 851,275 number of mapped reads = 743,523 (87.34%) number of supplementary alignments = 3,262 (0.38%) number of secondary alignments = 0 number of mapped bases = 43,176,980 bp number of sequenced bases = 43,164,322 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 16,821 duplication rate = 1.68% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8149 >>>>>>> ACTG content number of A's = 11,221,433 bp (26%) number of C's = 8,433,327 bp (19.54%) number of T's = 13,485,197 bp (31.24%) number of G's = 10,023,248 bp (23.22%) number of N's = 1,117 bp (0%) GC percentage = 42.76% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 212,312 number of insertions = 3,420 mapped reads with insertion percentage = 0.46% number of deletions = 8,045 mapped reads with deletion percentage = 1.07% homopolymer indels = 41.68% >>>>>>> Coverage mean coverageData = 0.0139X std coverageData = 0.1582X There is a 1.31% of reference with a coverageData >= 1X There is a 0.06% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% 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 4849444 0.019456095958934442 0.2753573747361028 chr2 243199373 3717194 0.015284554208122896 0.18955774800494246 chr3 198022430 3949741 0.01994592733762534 0.14854402454670423 chr4 191154276 2046546 0.010706252786100375 0.11078299432532883 chr5 180915260 1926081 0.010646315849751977 0.10901196244142204 chr6 171115067 3063714 0.017904408148932904 0.16462297863916722 chr7 159138663 2493835 0.01567083041284568 0.19061435406816363 chr8 146364022 2870827 0.01961429428333146 0.15687597004087384 chr9 141213431 1573089 0.011139797318570923 0.1321109133003763 chr10 135534747 2255607 0.01664227845572324 0.1701458374801862 chr11 135006516 1448212 0.010726978540798727 0.12505338159790366 chr12 133851895 1935170 0.014457546529318842 0.1272058239977279 chr13 115169878 975598 0.008470947585791486 0.0967060150517709 chr14 107349540 963620 0.008976470695635957 0.10419629843393645 chr15 102531392 1294565 0.0126260355462647 0.11766339459200525 chr16 90354753 918791 0.010168706896913326 0.11292377586817026 chr17 81195210 924774 0.011389514233659843 0.11344511089412156 chr18 78077248 855119 0.010952217475697914 0.19914030819292747 chr19 59128983 907887 0.015354348306650226 0.1899893587877419 chr20 63025520 663804 0.010532305009145503 0.10826366229204187 chr21 48129895 392525 0.008155534102037829 0.09871692659043975 chr22 51304566 671298 0.013084566391225296 0.11950486596258156 chrMT 16571 7859 0.4742622654034156 0.7182111246787032 chrX 155270560 2369621 0.015261238189647799 0.13892524132137404 chrY 59373566 102059 0.001718929935924684 0.05169588124647086