BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472768.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 = 16,054,514 number of mapped reads = 15,887,652 (98.96%) number of supplementary alignments = 52,220 (0.33%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,974,014 number of mapped paired reads (second in pair) = 7,913,638 number of mapped paired reads (both in pair) = 15,790,222 number of mapped paired reads (singletons) = 97,430 number of mapped bases = 1,566,028,733 bp number of sequenced bases = 1,565,799,371 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 9,933,161 duplication rate = 47.35% >>>>>>> Insert size mean insert size = 21,979.3908 std insert size = 1,484,465.6241 median insert size = 257 >>>>>>> Mapping quality mean mapping quality = 55.0227 >>>>>>> ACTG content number of A's = 432,097,187 bp (27.6%) number of C's = 352,723,948 bp (22.53%) number of T's = 429,636,953 bp (27.44%) number of G's = 351,039,363 bp (22.42%) number of N's = 301,920 bp (0.02%) GC percentage = 44.95% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 10,057,532 number of insertions = 90,186 mapped reads with insertion percentage = 0.56% number of deletions = 91,085 mapped reads with deletion percentage = 0.57% homopolymer indels = 45.7% >>>>>>> Coverage mean coverageData = 0.5059X std coverageData = 16.9497X There is a 4.34% of reference with a coverageData >= 1X There is a 1.86% of reference with a coverageData >= 2X There is a 0.87% of reference with a coverageData >= 3X There is a 0.63% of reference with a coverageData >= 4X There is a 0.49% of reference with a coverageData >= 5X There is a 0.44% of reference with a coverageData >= 6X There is a 0.4% of reference with a coverageData >= 7X There is a 0.38% of reference with a coverageData >= 8X There is a 0.36% of reference with a coverageData >= 9X There is a 0.35% of reference with a coverageData >= 10X There is a 0.34% of reference with a coverageData >= 11X There is a 0.32% of reference with a coverageData >= 12X There is a 0.31% of reference with a coverageData >= 13X There is a 0.3% of reference with a coverageData >= 14X There is a 0.3% of reference with a coverageData >= 15X There is a 0.29% of reference with a coverageData >= 16X There is a 0.28% of reference with a coverageData >= 17X There is a 0.27% of reference with a coverageData >= 18X There is a 0.27% of reference with a coverageData >= 19X There is a 0.26% of reference with a coverageData >= 20X There is a 0.26% of reference with a coverageData >= 21X There is a 0.25% of reference with a coverageData >= 22X There is a 0.25% of reference with a coverageData >= 23X There is a 0.24% of reference with a coverageData >= 24X There is a 0.24% of reference with a coverageData >= 25X There is a 0.23% of reference with a coverageData >= 26X There is a 0.23% of reference with a coverageData >= 27X There is a 0.22% of reference with a coverageData >= 28X There is a 0.22% of reference with a coverageData >= 29X There is a 0.22% of reference with a coverageData >= 30X There is a 0.21% of reference with a coverageData >= 31X There is a 0.21% of reference with a coverageData >= 32X There is a 0.21% of reference with a coverageData >= 33X There is a 0.2% of reference with a coverageData >= 34X There is a 0.2% of reference with a coverageData >= 35X There is a 0.2% of reference with a coverageData >= 36X There is a 0.19% of reference with a coverageData >= 37X There is a 0.19% of reference with a coverageData >= 38X There is a 0.19% of reference with a coverageData >= 39X There is a 0.19% of reference with a coverageData >= 40X There is a 0.18% of reference with a coverageData >= 41X There is a 0.18% of reference with a coverageData >= 42X There is a 0.18% of reference with a coverageData >= 43X There is a 0.18% of reference with a coverageData >= 44X There is a 0.17% of reference with a coverageData >= 45X There is a 0.17% of reference with a coverageData >= 46X There is a 0.17% of reference with a coverageData >= 47X There is a 0.17% of reference with a coverageData >= 48X There is a 0.17% of reference with a coverageData >= 49X There is a 0.16% of reference with a coverageData >= 50X There is a 0.16% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 154780642 0.6209839774080242 20.764424375897363 chr2 243199373 83715283 0.34422491294827473 11.467218593692419 chr3 198022430 156672121 0.7911837108553814 18.79505723902895 chr4 191154276 67941167 0.35542582892574165 16.107891576357453 chr5 180915260 71409402 0.39471187781506106 12.103769029438762 chr6 171115067 85458053 0.49941863389505026 15.708156135724987 chr7 159138663 59936576 0.37663113959930655 10.59846080957818 chr8 146364022 56995479 0.38940907896067517 12.251655465341988 chr9 141213431 142752621 1.0108997422490216 25.836618808502465 chr10 135534747 50174570 0.3701970978704081 17.40785838765976 chr11 135006516 58907127 0.436328028789366 14.23756647980814 chr12 133851895 97278601 0.7267629718652844 23.193286856524807 chr13 115169878 40710919 0.3534858220480185 15.863639934090358 chr14 107349540 67974521 0.6332073803017694 21.62893213657512 chr15 102531392 36907827 0.35996611652361066 11.01208225016079 chr16 90354753 86997898 0.9628480529408342 31.303841018693817 chr17 81195210 42912299 0.5285077654211375 12.057042556916416 chr18 78077248 26725346 0.3422936474400327 15.359045250124124 chr19 59128983 42798783 0.7238207191894371 17.417678546939182 chr20 63025520 30752272 0.4879336497342664 15.393804755895678 chr21 48129895 12703093 0.2639335282156755 12.228956156848282 chr22 51304566 11464331 0.2234563488949502 8.079447629102159 chrMT 16571 4833 0.291654094502444 0.8237848218435919 chrX 155270560 72916908 0.46961193416189134 14.338218793415468 chrY 59373566 7138061 0.12022287830917887 4.550194916557632