BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716536.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 = 1,635,347 number of mapped reads = 1,548,370 (94.68%) number of supplementary alignments = 31,387 (1.92%) number of secondary alignments = 0 number of mapped bases = 123,358,279 bp number of sequenced bases = 123,303,901 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 53,413 duplication rate = 2.35% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.5052 >>>>>>> ACTG content number of A's = 31,156,414 bp (25.27%) number of C's = 24,744,607 bp (20.07%) number of T's = 37,315,927 bp (30.26%) number of G's = 30,078,053 bp (24.39%) number of N's = 8,900 bp (0.01%) GC percentage = 44.46% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 763,087 number of insertions = 8,980 mapped reads with insertion percentage = 0.57% number of deletions = 28,457 mapped reads with deletion percentage = 1.81% homopolymer indels = 43.43% >>>>>>> Coverage mean coverageData = 0.0398X std coverageData = 0.399X There is a 3.48% of reference with a coverageData >= 1X There is a 0.35% 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 11821429 0.04742788183464546 0.8849325403624011 chr2 243199373 9902267 0.04071666336080562 0.4029471350419399 chr3 198022430 7791174 0.03934490653407293 0.2184429144094299 chr4 191154276 7784466 0.04072347301297095 0.2647845059036624 chr5 180915260 7195029 0.03977016090295534 0.22051405008843528 chr6 171115067 6940787 0.040562103160676086 0.24505295509449357 chr7 159138663 6628357 0.04165145587530794 0.4762402082712464 chr8 146364022 6116402 0.041788971882721286 0.43308235075088924 chr9 141213431 5029524 0.03561647050414064 0.31031672887932965 chr10 135534747 5750577 0.042428802408876004 0.3826625611948535 chr11 135006516 6810750 0.0504475650641929 0.39841419386607685 chr12 133851895 5358420 0.040032455274540565 0.22185289215525822 chr13 115169878 4404603 0.038244401022982766 0.21689203991665895 chr14 107349540 3594481 0.033483897555592695 0.2162440446404721 chr15 102531392 3506134 0.03419571247018669 0.2043457946918769 chr16 90354753 2722312 0.030129151036470656 0.2100450489575232 chr17 81195210 3731052 0.045951626949422265 0.2765787941921766 chr18 78077248 3246925 0.04158605846353601 0.5410039461488771 chr19 59128983 2217087 0.03749577428044044 0.6096398458150352 chr20 63025520 2548666 0.04043863501641875 0.23025773483608594 chr21 48129895 1644888 0.034176014720165085 0.23473502298496884 chr22 51304566 1383218 0.02696091416112944 0.18236153449431097 chrMT 16571 14038 0.8471425985154788 0.9939952884423789 chrX 155270560 6852025 0.04412958258152737 0.2685220080890634 chrY 59373566 363668 0.006125082667259703 0.20456826483459345