BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3083786.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 = 3,059,544 number of mapped reads = 2,272,796 (74.29%) number of supplementary alignments = 13,381 (0.44%) number of secondary alignments = 0 number of mapped bases = 144,329,828 bp number of sequenced bases = 144,279,910 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 89,522 duplication rate = 3.11% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.9493 >>>>>>> ACTG content number of A's = 40,505,058 bp (28.07%) number of C's = 27,910,197 bp (19.34%) number of T's = 43,453,840 bp (30.12%) number of G's = 32,409,205 bp (22.46%) number of N's = 1,610 bp (0%) GC percentage = 41.81% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 1,240,529 number of insertions = 11,154 mapped reads with insertion percentage = 0.49% number of deletions = 31,469 mapped reads with deletion percentage = 1.37% homopolymer indels = 45.3% >>>>>>> Coverage mean coverageData = 0.0466X std coverageData = 0.3587X There is a 4.03% of reference with a coverageData >= 1X There is a 0.46% of reference with a coverageData >= 2X There is a 0.07% 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% 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 11536519 0.04628481547494319 0.5474364117033006 chr2 243199373 12092845 0.04972399743810195 0.46523652357422546 chr3 198022430 9863572 0.049810377541574455 0.2502114913242571 chr4 191154276 9498001 0.04968761985737635 0.261309077836016 chr5 180915260 8982074 0.04964796225592026 0.2517790475137965 chr6 171115067 8174122 0.04776973847662404 0.29449924228522983 chr7 159138663 8064478 0.05067579334884823 0.47381116824718555 chr8 146364022 7013129 0.04791566195140497 0.3693693184338657 chr9 141213431 6198128 0.0438919156351353 0.3406833131530746 chr10 135534747 6669794 0.04921095252422613 0.35295003433655864 chr11 135006516 6655756 0.04929951677295339 0.33403972081408223 chr12 133851895 6707811 0.05011367975029416 0.2556526696489812 chr13 115169878 4572243 0.03969998995744356 0.22328218412451056 chr14 107349540 4407404 0.04105657089913939 0.252778790195505 chr15 102531392 4138995 0.04036807575966588 0.231404750055716 chr16 90354753 4012186 0.044404813989143435 0.2661715564224432 chr17 81195210 3807263 0.046890241431729776 0.274775395190079 chr18 78077248 3981907 0.050999581850016025 0.7197432983928733 chr19 59128983 2872868 0.04858646055184139 0.4406372984155146 chr20 63025520 2911534 0.04619611230498376 0.25293651339043316 chr21 48129895 1943503 0.040380370661519206 0.23984758285738894 chr22 51304566 1667775 0.0325073405747161 0.20204867799186071 chrMT 16571 6684 0.4033552591877376 0.7598635671042963 chrX 155270560 8191711 0.05275765734341397 0.29885828683693505 chrY 59373566 359526 0.0060553209824048635 0.12452588839141296