BamQC report ----------------------------------- >>>>>>> Input bam file = SRR504711.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP013494//SRP013494.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 = 2,370,955 number of mapped reads = 2,139,336 (90.23%) number of secondary alignments = 0 number of mapped bases = 68,452,220 bp number of sequenced bases = 68,452,220 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 232,384 duplication rate = 7.32% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 8.1376 >>>>>>> ACTG content number of A's = 19,919,275 bp (29.1%) number of C's = 13,582,991 bp (19.84%) number of T's = 21,226,983 bp (31.01%) number of G's = 13,722,851 bp (20.05%) number of N's = 120 bp (0%) GC percentage = 39.89% >>>>>>> Mismatches and indels general error rate = 0.0004 number of mismatches = 28,437 >>>>>>> Coverage mean coverageData = 0.0221X std coverageData = 0.7334X There is a 1.19% of reference with a coverageData >= 1X There is a 0.29% of reference with a coverageData >= 2X There is a 0.15% of reference with a coverageData >= 3X There is a 0.1% of reference with a coverageData >= 4X There is a 0.07% of reference with a coverageData >= 5X There is a 0.05% of reference with a coverageData >= 6X There is a 0.04% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.02% 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 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% 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 4739834 0.019016337776747202 0.27767505766743594 chr2 243199373 5915454 0.02432347553790774 0.36366287232279254 chr3 198022430 6022740 0.030414433354847732 0.5625224853690695 chr4 191154276 5751714 0.03008938183522507 0.5717442082546836 chr5 180915260 4091748 0.022616931263841424 0.3511482985677115 chr6 171115067 3482572 0.020352222986886364 0.29450753440817673 chr7 159138663 3518556 0.02211000101213619 0.32926651260120754 chr8 146364022 3379216 0.02308775034892113 0.35534542630368715 chr9 141213431 2516312 0.017819211545111457 0.2899712545704332 chr10 135534747 2155808 0.015905943292903332 0.21841458659610685 chr11 135006516 2591578 0.019195947549672344 0.2797715229678267 chr12 133851895 3425572 0.02559225627698435 0.4587347031370904 chr13 115169878 1994552 0.017318347771454617 0.29989272816525236 chr14 107349540 2179240 0.020300413024592373 0.3229655683683 chr15 102531392 3219198 0.031397193944270256 3.4395111357408767 chr16 90354753 1350450 0.014946087008837266 0.29385948889765384 chr17 81195210 1205256 0.01484392983280664 0.22992605613158096 chr18 78077248 2145414 0.02747809451480667 0.6940947483350898 chr19 59128983 990688 0.016754693717630827 0.2950305429743174 chr20 63025520 977218 0.01550511602284281 0.275501537619339 chr21 48129895 695536 0.014451226207744687 0.29742114592964214 chr22 51304566 280032 0.005458227636113324 0.09494005140826198 chrMT 16571 96 0.005793253273791563 0.10289510460556535 chrX 155270560 5611598 0.03614077259720065 0.6183502400254249 chrY 59373566 211838 0.0035678840647705074 0.08084017322902147