BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081126.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 = 1,948,358 number of mapped reads = 1,799,806 (92.38%) number of supplementary alignments = 10,062 (0.52%) number of secondary alignments = 0 number of mapped bases = 122,628,708 bp number of sequenced bases = 122,583,127 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 63,337 duplication rate = 2.97% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.8042 >>>>>>> ACTG content number of A's = 34,211,383 bp (27.91%) number of C's = 23,188,472 bp (18.92%) number of T's = 38,346,225 bp (31.28%) number of G's = 26,835,636 bp (21.89%) number of N's = 1,411 bp (0%) GC percentage = 40.81% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 1,004,179 number of insertions = 8,778 mapped reads with insertion percentage = 0.48% number of deletions = 26,200 mapped reads with deletion percentage = 1.44% homopolymer indels = 48.79% >>>>>>> Coverage mean coverageData = 0.0396X std coverageData = 0.2927X There is a 3.42% of reference with a coverageData >= 1X There is a 0.41% of reference with a coverageData >= 2X There is a 0.06% 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% 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 10026601 0.04022698503126297 0.40214996240057843 chr2 243199373 9731691 0.040015279973604205 0.3197341879686465 chr3 198022430 8473653 0.042791379744203724 0.23195267726663168 chr4 191154276 7671000 0.040129889639507726 0.2328738190697274 chr5 180915260 7392887 0.040863811046121815 0.2277316937060499 chr6 171115067 7333501 0.04285713192047548 0.2647479738794909 chr7 159138663 6845485 0.04301585089979045 0.45720097438030766 chr8 146364022 5844324 0.039930058768130876 0.3001745813494384 chr9 141213431 5170956 0.036618018296007554 0.275457148265073 chr10 135534747 5314151 0.03920877205016659 0.26979886516442153 chr11 135006516 5513149 0.04083616971494917 0.2944292600162657 chr12 133851895 5887259 0.04398338178178202 0.23788554698094913 chr13 115169878 3635602 0.031567299220374274 0.1983067079296236 chr14 107349540 3810917 0.03550007759697899 0.22205914347717673 chr15 102531392 3920234 0.03823447554481656 0.22500574453619715 chr16 90354753 3856978 0.04268705155997715 0.25143822278231 chr17 81195210 3143606 0.038716643506433446 0.2421061212782463 chr18 78077248 3010783 0.03856159223234917 0.49776537832653855 chr19 59128983 2425745 0.04102463592177799 0.3332452430595324 chr20 63025520 3111204 0.04936419405980308 0.2560079984043351 chr21 48129895 1643537 0.03414794484799936 0.21881122711581916 chr22 51304566 1725239 0.03362739682857857 0.20708351328178884 chrMT 16571 52216 3.151047009836461 2.497294920535297 chrX 155270560 6809655 0.043856704065471264 0.2562348997833748 chrY 59373566 278335 0.00468786058765613 0.10518895274695343