BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080761.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 = 6,003,006 number of mapped reads = 4,388,387 (73.1%) number of supplementary alignments = 28,011 (0.47%) number of secondary alignments = 0 number of mapped bases = 281,533,418 bp number of sequenced bases = 281,432,528 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 650,401 duplication rate = 10.89% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1501 >>>>>>> ACTG content number of A's = 87,021,529 bp (30.92%) number of C's = 56,601,385 bp (20.11%) number of T's = 73,543,338 bp (26.13%) number of G's = 64,175,649 bp (22.8%) number of N's = 90,627 bp (0.03%) GC percentage = 42.92% >>>>>>> Mismatches and indels general error rate = 0.008 number of mismatches = 2,214,714 number of insertions = 19,962 mapped reads with insertion percentage = 0.45% number of deletions = 53,801 mapped reads with deletion percentage = 1.21% homopolymer indels = 43.44% >>>>>>> Coverage mean coverageData = 0.0909X std coverageData = 0.6037X There is a 5.48% of reference with a coverageData >= 1X There is a 1.89% of reference with a coverageData >= 2X There is a 0.8% of reference with a coverageData >= 3X There is a 0.38% of reference with a coverageData >= 4X There is a 0.19% of reference with a coverageData >= 5X There is a 0.11% of reference with a coverageData >= 6X There is a 0.06% of reference with a coverageData >= 7X There is a 0.04% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% 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 33625721 0.1349072707024469 0.8740582739671495 chr2 243199373 20439929 0.08404597737182488 0.5625495345634387 chr3 198022430 17198205 0.08684978262310991 0.4651872414545148 chr4 191154276 15207202 0.07955460018064152 0.5046860809283169 chr5 180915260 22352525 0.12355245765337872 0.5606279756218651 chr6 171115067 19665404 0.11492502878194823 0.7039227765663894 chr7 159138663 18772411 0.11796260346864923 0.8343091675644009 chr8 146364022 12513813 0.08549787597391934 0.838049144427975 chr9 141213431 10106604 0.07156970784174205 0.44412992446926614 chr10 135534747 12715511 0.0938173515017518 0.7167045054127703 chr11 135006516 11834621 0.08765962822120378 0.5197739371568671 chr12 133851895 10488298 0.07835748608564712 0.44079686746254193 chr13 115169878 10889614 0.09455262251819005 0.4880696311139639 chr14 107349540 7264098 0.06766771427245985 0.4475043721149588 chr15 102531392 6210833 0.06057494079471778 0.3830015780041203 chr16 90354753 7591940 0.08402369269937576 0.49438548346072386 chr17 81195210 8226961 0.1013232307669381 0.5291010296996123 chr18 78077248 4338748 0.05556994017002238 0.5033677260114614 chr19 59128983 5269942 0.08912620736263974 0.8764879417481405 chr20 63025520 4967227 0.07881294751713275 0.4656938728877198 chr21 48129895 3754682 0.07801143135674823 0.5088967939160328 chr22 51304566 1962312 0.038248291584807484 0.30205154399892303 chrMT 16571 65175 3.9330758554100536 4.140475008542453 chrX 155270560 15333505 0.09875345976726045 0.5100885183092861 chrY 59373566 738137 0.012432081307024745 0.33457929634355577