BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472576.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 6,285,174 number of mapped reads = 5,778,703 (91.94%) number of supplementary alignments = 169,555 (2.7%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,918,019 number of mapped paired reads (second in pair) = 2,860,684 number of mapped paired reads (both in pair) = 5,630,770 number of mapped paired reads (singletons) = 147,933 number of mapped bases = 471,056,218 bp number of sequenced bases = 470,852,363 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 772,935 duplication rate = 11.64% >>>>>>> Insert size mean insert size = 242,083.6987 std insert size = 4,735,202.4894 median insert size = 132 >>>>>>> Mapping quality mean mapping quality = 50.3281 >>>>>>> ACTG content number of A's = 120,688,096 bp (25.63%) number of C's = 94,233,265 bp (20.01%) number of T's = 140,137,397 bp (29.76%) number of G's = 115,482,690 bp (24.53%) number of N's = 310,915 bp (0.07%) GC percentage = 44.54% >>>>>>> Mismatches and indels general error rate = 0.0124 number of mismatches = 5,756,245 number of insertions = 46,536 mapped reads with insertion percentage = 0.79% number of deletions = 108,921 mapped reads with deletion percentage = 1.85% homopolymer indels = 42.73% >>>>>>> Coverage mean coverageData = 0.1522X std coverageData = 1.4903X There is a 9.25% of reference with a coverageData >= 1X There is a 3.66% of reference with a coverageData >= 2X There is a 1.05% of reference with a coverageData >= 3X There is a 0.45% of reference with a coverageData >= 4X There is a 0.18% of reference with a coverageData >= 5X There is a 0.09% of reference with a coverageData >= 6X There is a 0.05% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% 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% 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 31060610 0.12461597838907691 1.8285988974011733 chr2 243199373 46309033 0.19041592265947166 2.248795953106923 chr3 198022430 24709752 0.12478259154783627 0.49216544426462133 chr4 191154276 23857389 0.12480698574590086 0.7834568527941128 chr5 180915260 22435874 0.12401316505860258 0.5264602508615561 chr6 171115067 30599156 0.1788221022056462 0.884567956991225 chr7 159138663 39694508 0.2494334641984519 2.8413206538805666 chr8 146364022 22223213 0.15183521671739794 1.3132699306563147 chr9 141213431 16454177 0.11651991516302723 1.7102400990039681 chr10 135534747 17990095 0.13273419103368378 1.314151411358086 chr11 135006516 17316240 0.12826225365300145 1.2413699344758793 chr12 133851895 24028531 0.1795158073779979 0.6172902736104787 chr13 115169878 22385313 0.19436777557409585 0.6479102775256051 chr14 107349540 11911976 0.11096438792378617 2.6484816582214514 chr15 102531392 11122018 0.10847427098229584 0.4673817986686359 chr16 90354753 17431909 0.19292741578298597 0.8399484336672932 chr17 81195210 18531874 0.22823851308470045 1.3321911628872458 chr18 78077248 10757316 0.1377778581540169 2.948876892342929 chr19 59128983 10561783 0.17862277455372436 1.3431644762272228 chr20 63025520 16685995 0.2647498188035577 0.917722814147108 chr21 48129895 7232239 0.15026500681125524 0.6810594149536553 chr22 51304566 5304744 0.10339711284176929 0.4675629144562682 chrMT 16571 20384 1.2301007784684086 1.6611243730007308 chrX 155270560 21396620 0.1378021693230191 0.7471849107897955 chrY 59373566 1035469 0.01743989909583669 0.6171215086470685