BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124786.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 148,011 number of mapped reads = 138,719 (93.72%) number of supplementary alignments = 7,438 (5.03%) number of secondary alignments = 0 number of mapped bases = 17,768,705 bp number of sequenced bases = 17,747,636 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 14,447 duplication rate = 1.39% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 50.9604 >>>>>>> ACTG content number of A's = 5,119,475 bp (28.85%) number of C's = 3,447,307 bp (19.42%) number of T's = 5,198,697 bp (29.29%) number of G's = 3,982,157 bp (22.44%) number of N's = 0 bp (0%) GC percentage = 41.86% >>>>>>> Mismatches and indels general error rate = 0.0163 number of mismatches = 264,544 number of insertions = 6,718 mapped reads with insertion percentage = 4.57% number of deletions = 9,888 mapped reads with deletion percentage = 6.78% homopolymer indels = 40.15% >>>>>>> Coverage mean coverageData = 0.0057X std coverageData = 0.7142X There is a 0.5% of reference with a coverageData >= 1X There is a 0.01% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% 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 1682372 0.006749720394879177 1.0931476004063396 chr2 243199373 1696794 0.006976967000650943 0.6488632854989271 chr3 198022430 1080320 0.005455543596753156 0.07603588883516584 chr4 191154276 994138 0.0052007102367932385 0.10710692463195483 chr5 180915260 934744 0.005166750444379318 0.14308368443108968 chr6 171115067 860624 0.0050295045029553126 0.07496544401862294 chr7 159138663 964072 0.0060580627097514324 0.08889963713428786 chr8 146364022 960359 0.006561441718238653 0.11641545234500478 chr9 141213431 690346 0.004888670965016068 0.13862184256695925 chr10 135534747 994081 0.007334510315646216 0.516656603851332 chr11 135006516 720681 0.005338120124513101 0.07778012389481757 chr12 133851895 841515 0.006286911365730011 0.08134091572891794 chr13 115169878 412963 0.0035856858335822843 0.060554956279864174 chr14 107349540 524178 0.004882908673851793 0.2861756389337856 chr15 102531392 461046 0.004496632602042504 0.06981435750944179 chr16 90354753 573852 0.006351099205594641 0.14638270247662577 chr17 81195210 465117 0.005728379789891547 0.18083152766097668 chr18 78077248 346801 0.004441767722141026 0.09001081266869299 chr19 59128983 515125 0.008711886690153287 0.9088074681879266 chr20 63025520 392123 0.006221654339385062 0.08381758358784488 chr21 48129895 205623 0.004272251165310043 0.08526520948778146 chr22 51304566 181126 0.003530407020692856 0.1029124966473748 chrMT 16571 10830 0.6535513849496107 0.8755230892030051 chrX 155270560 598524 0.0038547165670040733 0.06567228580367127 chrY 59373566 661351 0.011138812177796428 4.227616521153566