BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524660.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 = 2,728,753 number of mapped reads = 2,521,954 (92.42%) number of supplementary alignments = 11,203 (0.41%) number of secondary alignments = 0 number of mapped bases = 149,846,715 bp number of sequenced bases = 149,801,823 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 135,922 duplication rate = 3.94% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.0109 >>>>>>> ACTG content number of A's = 37,946,473 bp (25.33%) number of C's = 27,095,456 bp (18.09%) number of T's = 46,460,834 bp (31.01%) number of G's = 38,278,741 bp (25.55%) number of N's = 20,319 bp (0.01%) GC percentage = 43.64% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 746,748 number of insertions = 10,515 mapped reads with insertion percentage = 0.41% number of deletions = 27,985 mapped reads with deletion percentage = 1.1% homopolymer indels = 42.56% >>>>>>> Coverage mean coverageData = 0.0484X std coverageData = 0.4365X There is a 4.19% of reference with a coverageData >= 1X There is a 0.46% of reference with a coverageData >= 2X There is a 0.07% 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 12081750 0.04847229648426834 0.8510145997931955 chr2 243199373 12678177 0.052130796406288434 0.5806405458332442 chr3 198022430 10025683 0.05062902722686516 0.25311346270164164 chr4 191154276 9653508 0.05050113553306022 0.30156128802049437 chr5 180915260 8953764 0.04949148015485261 0.2528527805330411 chr6 171115067 8590293 0.050201850430856565 0.29909260753991085 chr7 159138663 8257131 0.05188639168094557 0.5405929310896276 chr8 146364022 7685373 0.05250862127852704 0.47394554968814556 chr9 141213431 6314433 0.04471552709458635 0.3475183976125496 chr10 135534747 7319728 0.05400628371704564 0.4545016137957024 chr11 135006516 6854107 0.05076871252643835 0.35084128707262086 chr12 133851895 6740117 0.05035503606430077 0.25749373091155814 chr13 115169878 4672551 0.04057094685817068 0.2264687774716167 chr14 107349540 4537812 0.04227136883865548 0.24593108808306896 chr15 102531392 4287907 0.041820430956404066 0.22999362799564682 chr16 90354753 4311147 0.04771356079076438 0.2798160167938167 chr17 81195210 4055018 0.0499415913820532 0.2764096774864599 chr18 78077248 3986426 0.051057460426883895 0.6957860396722803 chr19 59128983 3118752 0.05274489500352137 0.6060410421613637 chr20 63025520 3185062 0.050536068563972185 0.2619987419250779 chr21 48129895 1993201 0.041412951347597995 0.28683201258519114 chr22 51304566 1777219 0.03464056201157612 0.20960510294873008 chrMT 16571 28559 1.7234325025647215 1.659931491244675 chrX 155270560 8254068 0.053159259553131 0.297211609244526 chrY 59373566 484929 0.008167422519307667 0.29766855738958875