BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084829.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 = 1,477,262 number of mapped reads = 1,363,924 (92.33%) number of supplementary alignments = 11,051 (0.75%) number of secondary alignments = 0 number of mapped bases = 93,101,793 bp number of sequenced bases = 93,063,422 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 49,754 duplication rate = 2.84% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.6941 >>>>>>> ACTG content number of A's = 26,217,447 bp (28.17%) number of C's = 17,122,651 bp (18.4%) number of T's = 29,690,213 bp (31.9%) number of G's = 20,019,851 bp (21.51%) number of N's = 13,260 bp (0.01%) GC percentage = 39.91% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 762,439 number of insertions = 7,827 mapped reads with insertion percentage = 0.57% number of deletions = 22,838 mapped reads with deletion percentage = 1.66% homopolymer indels = 48.68% >>>>>>> Coverage mean coverageData = 0.0301X std coverageData = 0.2842X There is a 2.67% of reference with a coverageData >= 1X There is a 0.25% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% 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 7402852 0.02970043553071027 0.4456292390290591 chr2 243199373 6855639 0.028189377774423784 0.3804000256629383 chr3 198022430 7445449 0.03759901845462658 0.2134521847659408 chr4 191154276 5375032 0.028118816447506516 0.18656776177743598 chr5 180915260 5473351 0.030253672354670358 0.19683702528705388 chr6 171115067 5196319 0.030367395993247046 0.2007224416055407 chr7 159138663 4983045 0.031312598120797334 0.3273446580730831 chr8 146364022 5995489 0.040962860394749195 0.3817434443690561 chr9 141213431 5964713 0.04223899212533119 0.3412062318553052 chr10 135534747 2845990 0.02099823154574524 0.19946731112298074 chr11 135006516 3695047 0.027369397488933054 0.2553055624155211 chr12 133851895 4015680 0.030000920046742707 0.19222145913805008 chr13 115169878 2894465 0.02513213567874058 0.17270763819668306 chr14 107349540 1963221 0.018288117489837403 0.16215164241580596 chr15 102531392 2616019 0.02551432248184049 0.18151134243218847 chr16 90354753 1921247 0.021263375043480005 0.18004457178206887 chr17 81195210 2390206 0.02943777102122157 0.20428476611830396 chr18 78077248 3790349 0.0485461398434535 0.5659897509199552 chr19 59128983 1983147 0.033539338905930444 0.3154911930415755 chr20 63025520 1817446 0.028836668067157557 0.19215988868482495 chr21 48129895 784368 0.016296898216794364 0.15253744445724574 chr22 51304566 902658 0.017594106536248644 0.1428184052821785 chrMT 16571 9423 0.5686440166556032 0.9076970993719249 chrX 155270560 6544412 0.04214844076043778 0.24376233910198697 chrY 59373566 236226 0.003978639248314646 0.12556932052750622