BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082920.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 = 1,963,180 number of mapped reads = 1,744,120 (88.84%) number of supplementary alignments = 19,195 (0.98%) number of secondary alignments = 0 number of mapped bases = 115,858,597 bp number of sequenced bases = 115,814,287 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 91,407 duplication rate = 4.45% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1774 >>>>>>> ACTG content number of A's = 31,154,032 bp (26.9%) number of C's = 21,884,072 bp (18.9%) number of T's = 36,250,288 bp (31.3%) number of G's = 26,520,979 bp (22.9%) number of N's = 4,916 bp (0%) GC percentage = 41.8% >>>>>>> Mismatches and indels general error rate = 0.0075 number of mismatches = 851,895 number of insertions = 9,328 mapped reads with insertion percentage = 0.53% number of deletions = 26,980 mapped reads with deletion percentage = 1.53% homopolymer indels = 47.65% >>>>>>> Coverage mean coverageData = 0.0374X std coverageData = 0.3008X There is a 3.05% of reference with a coverageData >= 1X There is a 0.51% of reference with a coverageData >= 2X There is a 0.11% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% 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 12081157 0.048469917352783644 0.4772805402037945 chr2 243199373 13367565 0.05496545831966434 0.4466724928134636 chr3 198022430 8068695 0.04074636898456402 0.24030042734924276 chr4 191154276 5489771 0.02871905936333854 0.20729091933743146 chr5 180915260 7036015 0.03889121901601888 0.23491366497849475 chr6 171115067 7583024 0.04431534950689059 0.31308192974298693 chr7 159138663 3981052 0.02501624636622717 0.24121992602233538 chr8 146364022 10136196 0.06925333057600727 0.3542001824031282 chr9 141213431 4010917 0.02840322603591439 0.26830740154627186 chr10 135534747 3830533 0.028262368763635203 0.22317193734435106 chr11 135006516 4476142 0.03315500712573014 0.25773475908619586 chr12 133851895 3561124 0.0266049576660831 0.19554000463389962 chr13 115169878 2781322 0.024149734707542194 0.1862244441394593 chr14 107349540 2217625 0.02065798325731065 0.17921990851250974 chr15 102531392 2183921 0.021300022923711012 0.18380817952885964 chr16 90354753 4115168 0.04554456587358498 0.26329402361000265 chr17 81195210 3662819 0.04511126949483843 0.2823298248724595 chr18 78077248 3413452 0.04371890771559981 0.5205820390637237 chr19 59128983 2116855 0.0358006326609744 0.32806247535539124 chr20 63025520 2525411 0.040069657497470865 0.24487986272948295 chr21 48129895 2316549 0.04813118748752724 0.2657756600054236 chr22 51304566 1818156 0.03543848319465367 0.224631781199948 chrMT 16571 10157 0.6129382656448011 1.0216889960183284 chrX 155270560 4862721 0.03131772694063833 0.22606679997541113 chrY 59373566 212250 0.003574823179729511 0.07712088999721067