BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472708.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 15,524,482 number of mapped reads = 15,166,450 (97.69%) number of supplementary alignments = 49,403 (0.32%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,618,106 number of mapped paired reads (second in pair) = 7,548,344 number of mapped paired reads (both in pair) = 15,065,060 number of mapped paired reads (singletons) = 101,390 number of mapped bases = 1,495,742,392 bp number of sequenced bases = 1,495,513,062 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 9,091,697 duplication rate = 46.43% >>>>>>> Insert size mean insert size = 24,200.6693 std insert size = 1,489,437.2159 median insert size = 248 >>>>>>> Mapping quality mean mapping quality = 55.2563 >>>>>>> ACTG content number of A's = 414,793,693 bp (27.74%) number of C's = 334,953,049 bp (22.4%) number of T's = 412,055,240 bp (27.55%) number of G's = 333,423,911 bp (22.29%) number of N's = 287,169 bp (0.02%) GC percentage = 44.69% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 9,660,589 number of insertions = 90,667 mapped reads with insertion percentage = 0.59% number of deletions = 86,505 mapped reads with deletion percentage = 0.56% homopolymer indels = 44.81% >>>>>>> Coverage mean coverageData = 0.4832X std coverageData = 14.6425X There is a 4.54% of reference with a coverageData >= 1X There is a 1.9% of reference with a coverageData >= 2X There is a 0.87% of reference with a coverageData >= 3X There is a 0.64% of reference with a coverageData >= 4X There is a 0.49% of reference with a coverageData >= 5X There is a 0.45% of reference with a coverageData >= 6X There is a 0.41% of reference with a coverageData >= 7X There is a 0.39% of reference with a coverageData >= 8X There is a 0.37% of reference with a coverageData >= 9X There is a 0.35% of reference with a coverageData >= 10X There is a 0.34% of reference with a coverageData >= 11X There is a 0.33% of reference with a coverageData >= 12X There is a 0.32% of reference with a coverageData >= 13X There is a 0.31% of reference with a coverageData >= 14X There is a 0.3% of reference with a coverageData >= 15X There is a 0.29% of reference with a coverageData >= 16X There is a 0.29% of reference with a coverageData >= 17X There is a 0.28% of reference with a coverageData >= 18X There is a 0.27% of reference with a coverageData >= 19X There is a 0.27% of reference with a coverageData >= 20X There is a 0.26% of reference with a coverageData >= 21X There is a 0.26% of reference with a coverageData >= 22X There is a 0.25% of reference with a coverageData >= 23X There is a 0.25% of reference with a coverageData >= 24X There is a 0.24% of reference with a coverageData >= 25X There is a 0.24% of reference with a coverageData >= 26X There is a 0.23% of reference with a coverageData >= 27X There is a 0.23% of reference with a coverageData >= 28X There is a 0.22% of reference with a coverageData >= 29X There is a 0.22% of reference with a coverageData >= 30X There is a 0.22% of reference with a coverageData >= 31X There is a 0.21% of reference with a coverageData >= 32X There is a 0.21% of reference with a coverageData >= 33X There is a 0.21% of reference with a coverageData >= 34X There is a 0.2% of reference with a coverageData >= 35X There is a 0.2% of reference with a coverageData >= 36X There is a 0.2% of reference with a coverageData >= 37X There is a 0.19% of reference with a coverageData >= 38X There is a 0.19% of reference with a coverageData >= 39X There is a 0.19% of reference with a coverageData >= 40X There is a 0.19% of reference with a coverageData >= 41X There is a 0.18% of reference with a coverageData >= 42X There is a 0.18% of reference with a coverageData >= 43X There is a 0.18% of reference with a coverageData >= 44X There is a 0.18% of reference with a coverageData >= 45X There is a 0.17% of reference with a coverageData >= 46X There is a 0.17% of reference with a coverageData >= 47X There is a 0.17% of reference with a coverageData >= 48X There is a 0.17% of reference with a coverageData >= 49X There is a 0.17% of reference with a coverageData >= 50X There is a 0.16% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 187231338 0.7511770171276725 23.316859655766677 chr2 243199373 83285472 0.3424575934247988 11.778053724971791 chr3 198022430 160893532 0.8125015534856329 16.57326382573659 chr4 191154276 58076865 0.3038219506007807 11.994875395113398 chr5 180915260 60863624 0.336420620350102 10.641098016763559 chr6 171115067 104293775 0.6094949838636945 13.821645413846108 chr7 159138663 75851776 0.4766395203408238 14.335537172405648 chr8 146364022 66597625 0.45501363033054665 12.059935458388296 chr9 141213431 92220286 0.6530560538536876 16.595669619547092 chr10 135534747 43933530 0.3241495702943246 10.213202392869382 chr11 135006516 54297447 0.4021838990349177 11.265939502677847 chr12 133851895 66257813 0.4950084046251269 16.825692908905243 chr13 115169878 52381018 0.4548152599414927 17.179456185815077 chr14 107349540 71325561 0.6644235364213018 20.226605851459112 chr15 102531392 34627497 0.33772580596584506 10.490573461104022 chr16 90354753 59019730 0.6532000591048044 15.481167982888255 chr17 81195210 72466127 0.8924926359572196 20.260530341091076 chr18 78077248 16424771 0.2103656496704392 7.561745602645777 chr19 59128983 41450505 0.7010183990480607 21.518016887841966 chr20 63025520 20385431 0.323447248035399 8.31263257657177 chr21 48129895 5589147 0.1161263077760714 4.419310900198391 chr22 51304566 19584718 0.38173440547182486 11.132198460132047 chrMT 16571 11611 0.7006819141874359 2.154574948454735 chrX 155270560 44729876 0.28807699283109434 7.497207390449932 chrY 59373566 3943317 0.06641536403590784 3.7483482056444295