BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716343.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 = 1,656,415 number of mapped reads = 1,474,191 (89%) number of supplementary alignments = 8,807 (0.53%) number of secondary alignments = 0 number of mapped bases = 85,158,624 bp number of sequenced bases = 85,134,490 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 71,153 duplication rate = 3.81% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6517 >>>>>>> ACTG content number of A's = 21,079,432 bp (24.76%) number of C's = 17,069,645 bp (20.05%) number of T's = 27,440,318 bp (32.23%) number of G's = 19,543,976 bp (22.96%) number of N's = 1,119 bp (0%) GC percentage = 43.01% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 428,423 number of insertions = 5,761 mapped reads with insertion percentage = 0.39% number of deletions = 15,235 mapped reads with deletion percentage = 1.02% homopolymer indels = 41.55% >>>>>>> Coverage mean coverageData = 0.0275X std coverageData = 0.2505X There is a 2.4% of reference with a coverageData >= 1X There is a 0.26% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% 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 6884282 0.02761991914956954 0.3799991863815062 chr2 243199373 7225691 0.02971097709203387 0.3573653400937389 chr3 198022430 5647902 0.028521526576560038 0.19001289014847658 chr4 191154276 5344961 0.02796150372278358 0.21843020586085035 chr5 180915260 5048932 0.027907717679536818 0.18782405013003625 chr6 171115067 4918426 0.028743383538516805 0.2055610920301923 chr7 159138663 4632752 0.029111417129349643 0.31065056839238575 chr8 146364022 4235955 0.02894123119956351 0.26288434573364255 chr9 141213431 3486207 0.024687502989712076 0.20176735076832347 chr10 135534747 4139085 0.030538921506231904 0.26716094495014814 chr11 135006516 3910632 0.028966246340287754 0.22941026754727886 chr12 133851895 3844004 0.02871833827978304 0.1940837981421426 chr13 115169878 2579039 0.022393346635306847 0.16897408915314233 chr14 107349540 2600752 0.024226950576593062 0.18035428407604553 chr15 102531392 2464708 0.02403856957291675 0.1764633605185676 chr16 90354753 2529181 0.027991676320558365 0.19901553341697092 chr17 81195210 2395675 0.02950512721132195 0.20347477176111786 chr18 78077248 2212829 0.02834153427128989 0.33000134223577415 chr19 59128983 1838606 0.031094835505626743 0.28553200422309866 chr20 63025520 1887702 0.02995139111902607 0.20068344876307773 chr21 48129895 1143619 0.023761094845521687 0.19348029544513456 chr22 51304566 1126331 0.02195381596250127 0.16627495248619734 chrMT 16571 14026 0.8464184418562549 1.1094668531984186 chrX 155270560 4769052 0.030714463836544418 0.2121371298565496 chrY 59373566 278275 0.004686850036933945 0.13922104226193074