BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818957.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 2,508,129 number of mapped reads = 2,355,860 (93.93%) number of supplementary alignments = 23,814 (0.95%) number of secondary alignments = 0 number of mapped bases = 218,686,540 bp number of sequenced bases = 218,583,429 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 375,249 duplication rate = 13.31% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.4853 >>>>>>> ACTG content number of A's = 63,850,472 bp (29.21%) number of C's = 44,974,942 bp (20.58%) number of T's = 63,534,680 bp (29.07%) number of G's = 46,213,120 bp (21.14%) number of N's = 10,215 bp (0%) GC percentage = 41.72% >>>>>>> Mismatches and indels general error rate = 0.006 number of mismatches = 1,259,264 number of insertions = 27,205 mapped reads with insertion percentage = 1.13% number of deletions = 57,251 mapped reads with deletion percentage = 2.38% homopolymer indels = 42.95% >>>>>>> Coverage mean coverageData = 0.0706X std coverageData = 0.7054X There is a 5.23% of reference with a coverageData >= 1X There is a 1.17% of reference with a coverageData >= 2X There is a 0.32% of reference with a coverageData >= 3X There is a 0.1% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% 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 24047289 0.09647835140198106 1.3954424180521112 chr2 243199373 19592664 0.08056214848876275 0.9415885265659149 chr3 198022430 16107740 0.08134300745627654 0.36571510829661896 chr4 191154276 16289478 0.08521639348522865 0.4228954612103549 chr5 180915260 12741481 0.070427895358302 0.3648650880538566 chr6 171115067 12307672 0.071926290394989 0.42828336813882595 chr7 159138663 10789437 0.06779896724405683 0.6532403184331157 chr8 146364022 14250895 0.09736610681551236 0.5196640437675349 chr9 141213431 8438780 0.059759046573976383 0.8614159081860511 chr10 135534747 10484095 0.07735355864131284 0.8536312813880745 chr11 135006516 8650662 0.06407588504839277 0.5054015658911739 chr12 133851895 9297829 0.06946355895820526 0.35534502280297625 chr13 115169878 4639203 0.04028139197994114 0.24796589103801042 chr14 107349540 5569496 0.05188188044401494 0.3764706402838749 chr15 102531392 5788318 0.05645410529489349 0.30256615000988357 chr16 90354753 5460203 0.06043072244356642 0.5317600337359819 chr17 81195210 3787064 0.04664147059906613 0.38881016053800294 chr18 78077248 5746003 0.07359382082729145 1.1495156231988655 chr19 59128983 2244792 0.03796432622560073 1.2377128816552398 chr20 63025520 3824721 0.06068527479027543 0.32717416605989 chr21 48129895 2622885 0.054495963475507274 0.3614917219784732 chr22 51304566 1602079 0.03122683076590103 0.23678294548952777 chrMT 16571 370376 22.350853901394 17.234615776716677 chrX 155270560 13496550 0.08692278819629426 0.5924274733819972 chrY 59373566 536828 0.009041532051485673 0.4710955969491588