BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3083637.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 = 1,809,054 number of mapped reads = 1,414,364 (78.18%) number of supplementary alignments = 9,074 (0.5%) number of secondary alignments = 0 number of mapped bases = 87,480,149 bp number of sequenced bases = 87,450,716 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 40,598 duplication rate = 2.33% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.9276 >>>>>>> ACTG content number of A's = 25,906,669 bp (29.62%) number of C's = 16,416,939 bp (18.77%) number of T's = 26,074,136 bp (29.82%) number of G's = 19,041,031 bp (21.77%) number of N's = 11,941 bp (0.01%) GC percentage = 40.55% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 771,302 number of insertions = 6,566 mapped reads with insertion percentage = 0.46% number of deletions = 18,429 mapped reads with deletion percentage = 1.29% homopolymer indels = 46.66% >>>>>>> Coverage mean coverageData = 0.0283X std coverageData = 0.2412X There is a 2.57% of reference with a coverageData >= 1X There is a 0.2% of reference with a coverageData >= 2X There is a 0.02% 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 6758775 0.027116381788272456 0.40796236397593183 chr2 243199373 7816673 0.03214100802801001 0.2476772045112939 chr3 198022430 6271645 0.03167138692318845 0.1911229306518132 chr4 191154276 5944522 0.031098033088205676 0.19673887808956717 chr5 180915260 5503349 0.030419484790835224 0.18772705309924392 chr6 171115067 5018724 0.029329527130419204 0.19604979518418522 chr7 159138663 4432780 0.027854827459496752 0.24488903251159208 chr8 146364022 4577015 0.031271448662431534 0.34242302898375143 chr9 141213431 3541095 0.025076191229997095 0.22581791065642193 chr10 135534747 4318205 0.03186050142551268 0.25790029551422566 chr11 135006516 4213709 0.031211152800950732 0.21750877521752093 chr12 133851895 3913650 0.029238659639447016 0.185472166129464 chr13 115169878 2683609 0.02330130974003463 0.16364659862157588 chr14 107349540 2778434 0.02588212301608372 0.1801680815870677 chr15 102531392 2432142 0.023720949775069864 0.1651607758443458 chr16 90354753 2278672 0.025219171369988694 0.18443891751539787 chr17 81195210 2044246 0.025176928540489026 0.18562957334037977 chr18 78077248 2219416 0.02842589943743919 0.3597818689868229 chr19 59128983 1597595 0.027018814106780763 0.29169107632405494 chr20 63025520 1757890 0.027891717513794413 0.1827052395208879 chr21 48129895 1089923 0.02264544728385549 0.17138031437207513 chr22 51304566 954761 0.01860966916667807 0.14663987991895916 chrMT 16571 7431 0.4484340112244282 0.6866303308105814 chrX 155270560 5096418 0.03282282230449868 0.20529494978763038 chrY 59373566 229470 0.0038648512369966123 0.09994934052710765