BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238047.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,997,996 number of mapped reads = 1,714,118 (85.79%) number of supplementary alignments = 20,086 (1.01%) number of secondary alignments = 0 number of mapped bases = 113,995,798 bp number of sequenced bases = 113,944,505 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 126,259 duplication rate = 5.68% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 40.9423 >>>>>>> ACTG content number of A's = 30,967,178 bp (27.18%) number of C's = 21,748,622 bp (19.09%) number of T's = 35,450,542 bp (31.11%) number of G's = 25,771,629 bp (22.62%) number of N's = 6,534 bp (0.01%) GC percentage = 41.7% >>>>>>> Mismatches and indels general error rate = 0.0077 number of mismatches = 866,299 number of insertions = 8,100 mapped reads with insertion percentage = 0.47% number of deletions = 28,848 mapped reads with deletion percentage = 1.66% homopolymer indels = 45.72% >>>>>>> Coverage mean coverageData = 0.0368X std coverageData = 0.3845X There is a 2.58% of reference with a coverageData >= 1X There is a 0.7% of reference with a coverageData >= 2X There is a 0.22% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 12264693 0.049206268577360934 0.5302818312832464 chr2 243199373 3893236 0.016008412982216034 0.480642609144534 chr3 198022430 12326366 0.062247322184663625 0.34077589316566986 chr4 191154276 6896070 0.036075938997043415 0.28298859077455263 chr5 180915260 1686957 0.009324569967176899 0.13009584198938393 chr6 171115067 15640615 0.09140407840298481 0.4318493620431367 chr7 159138663 5732544 0.036022320986823925 0.33077059454893026 chr8 146364022 3562570 0.024340476240807322 0.3501587140978492 chr9 141213431 8645553 0.06122330531010184 0.5019835625303344 chr10 135534747 1389866 0.01025468398889622 0.4401470493938796 chr11 135006516 5907152 0.043754569594255735 0.443741713115202 chr12 133851895 7243189 0.054113458759773254 0.3215206652254942 chr13 115169878 2538226 0.022038974461707776 0.19968381035842142 chr14 107349540 4723600 0.044002051615684615 0.32706659771948243 chr15 102531392 414170 0.004039445792367668 0.08785254201406494 chr16 90354753 1775435 0.01964960271652782 0.23835209436650942 chr17 81195210 2613997 0.0321939804084502 0.2683553668855496 chr18 78077248 8715774 0.1116301383983206 0.8917772769927659 chr19 59128983 963958 0.016302631147909308 0.4026317902694702 chr20 63025520 1855071 0.02943364846493928 0.23853180251352216 chr21 48129895 823059 0.017100785281164647 0.23368615859610548 chr22 51304566 1935673 0.037729059047103136 0.26223885119134555 chrMT 16571 40805 2.462434373302758 2.5701513465877235 chrX 155270560 2105326 0.013559080356250405 0.21964009863799053 chrY 59373566 301893 0.005084636486210042 0.15951478920711215