BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081910.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 = 2,366,156 number of mapped reads = 2,198,729 (92.92%) number of supplementary alignments = 16,938 (0.72%) number of secondary alignments = 0 number of mapped bases = 150,732,379 bp number of sequenced bases = 150,678,363 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 75,352 duplication rate = 2.77% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.66 >>>>>>> ACTG content number of A's = 42,370,685 bp (28.12%) number of C's = 28,458,906 bp (18.89%) number of T's = 46,950,789 bp (31.16%) number of G's = 32,896,235 bp (21.83%) number of N's = 1,748 bp (0%) GC percentage = 40.72% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 1,218,231 number of insertions = 11,702 mapped reads with insertion percentage = 0.53% number of deletions = 32,464 mapped reads with deletion percentage = 1.46% homopolymer indels = 47.32% >>>>>>> Coverage mean coverageData = 0.0487X std coverageData = 0.3429X There is a 4.14% of reference with a coverageData >= 1X There is a 0.55% of reference with a coverageData >= 2X There is a 0.09% 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 0.01% 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 12384680 0.04968765955451722 0.47209019801800006 chr2 243199373 12791160 0.052595365860585504 0.4227179231280437 chr3 198022430 9789935 0.04943851562673986 0.25407169852333183 chr4 191154276 10133151 0.05301032868341381 0.2753006977749037 chr5 180915260 9384520 0.05187246227874862 0.2607237867328347 chr6 171115067 9526818 0.05567492195178815 0.3020826244125219 chr7 159138663 8260896 0.05191005029368633 0.4177167407694426 chr8 146364022 7731621 0.0528246005702139 0.47040410811744554 chr9 141213431 6333556 0.04485094622479642 0.34161093061429104 chr10 135534747 7154849 0.05278977648440219 0.35740513516100497 chr11 135006516 6721534 0.049786737700867716 0.31656774076701716 chr12 133851895 6880402 0.051403097430932895 0.2603324011441785 chr13 115169878 5016284 0.043555520654454456 0.2380645741509922 chr14 107349540 4620315 0.04303991428375008 0.24927027096681542 chr15 102531392 4382515 0.042743153238376005 0.23906492893309025 chr16 90354753 3911697 0.04329265334829702 0.2651989125936999 chr17 81195210 3602521 0.044368639480087554 0.2572744201609246 chr18 78077248 3991775 0.051125969501384066 0.5980042667538189 chr19 59128983 2576545 0.04357499265630867 0.4245566513918103 chr20 63025520 3013806 0.047818820058922164 0.2571404262190404 chr21 48129895 1944378 0.04039855063053846 0.24663126313869146 chr22 51304566 1512327 0.02947743481545093 0.19356995375196065 chrMT 16571 49867 3.0092933437933738 2.5131447025293987 chrX 155270560 8641578 0.05565496768994715 0.29172666919969276 chrY 59373566 375649 0.006326872803968015 0.13777438808019649