BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084844.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,809,109 number of mapped reads = 2,509,142 (89.32%) number of supplementary alignments = 22,813 (0.81%) number of secondary alignments = 0 number of mapped bases = 174,061,478 bp number of sequenced bases = 173,996,598 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 133,226 duplication rate = 4.49% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.2758 >>>>>>> ACTG content number of A's = 50,771,691 bp (29.18%) number of C's = 31,819,990 bp (18.29%) number of T's = 55,971,050 bp (32.17%) number of G's = 35,406,515 bp (20.35%) number of N's = 27,352 bp (0.02%) GC percentage = 38.64% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 1,396,145 number of insertions = 13,615 mapped reads with insertion percentage = 0.54% number of deletions = 36,911 mapped reads with deletion percentage = 1.46% homopolymer indels = 48.78% >>>>>>> Coverage mean coverageData = 0.0562X std coverageData = 0.4567X There is a 4.45% of reference with a coverageData >= 1X There is a 0.87% of reference with a coverageData >= 2X There is a 0.18% of reference with a coverageData >= 3X There is a 0.04% 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 13702657 0.05497541769414488 0.6777087338054535 chr2 243199373 14571234 0.05991476795460324 0.3967484897248085 chr3 198022430 12802661 0.06465258001328435 0.30566682657638733 chr4 191154276 12273758 0.06420864998070983 0.31202819747711197 chr5 180915260 10898995 0.06024364666640061 0.29739595086947684 chr6 171115067 10149790 0.059315583238499975 0.29785153163372197 chr7 159138663 9515004 0.059790649365955774 0.3714123722778278 chr8 146364022 9399657 0.06422108979760068 1.2331184219795095 chr9 141213431 7031165 0.04979104997455943 0.35473495574024655 chr10 135534747 7778883 0.057394012769286386 0.3478412149903526 chr11 135006516 8147858 0.06035159073359096 0.34980848740878884 chr12 133851895 7725423 0.057716201926016814 0.29244058975721055 chr13 115169878 6295219 0.05466029060133241 0.28307181877660115 chr14 107349540 5328561 0.049637483309197226 0.28175653409211754 chr15 102531392 4781336 0.04663289853706463 0.2589874632917657 chr16 90354753 4188693 0.04635830281114265 0.2760663277077831 chr17 81195210 3967490 0.04886359675650817 0.28890998398901735 chr18 78077248 4512532 0.057795735833312156 0.5930810815402923 chr19 59128983 2524622 0.04269686153742912 0.48924828523263847 chr20 63025520 3569524 0.05663616896774513 0.2975139052959577 chr21 48129895 2225227 0.04623378048092563 0.2718939826402797 chr22 51304566 1494165 0.02912343123612039 0.20247671794154212 chrMT 16571 336380 20.299318085812565 10.491482992263371 chrX 155270560 10479042 0.06748891740971373 0.33102328426764566 chrY 59373566 361602 0.006090286037392465 0.11741777427604999