BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472769.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 = 12,852,902 number of mapped reads = 12,726,198 (99.01%) number of supplementary alignments = 73,626 (0.57%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,386,768 number of mapped paired reads (second in pair) = 6,339,430 number of mapped paired reads (both in pair) = 12,649,002 number of mapped paired reads (singletons) = 77,196 number of mapped bases = 1,252,028,562 bp number of sequenced bases = 1,251,863,151 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 7,683,519 duplication rate = 45.61% >>>>>>> Insert size mean insert size = 39,323.5387 std insert size = 1,954,230.2184 median insert size = 228 >>>>>>> Mapping quality mean mapping quality = 55.1393 >>>>>>> ACTG content number of A's = 337,503,052 bp (26.96%) number of C's = 290,339,627 bp (23.19%) number of T's = 336,061,070 bp (26.84%) number of G's = 287,715,522 bp (22.98%) number of N's = 243,880 bp (0.02%) GC percentage = 46.18% >>>>>>> Mismatches and indels general error rate = 0.0059 number of mismatches = 7,236,064 number of insertions = 69,130 mapped reads with insertion percentage = 0.54% number of deletions = 67,051 mapped reads with deletion percentage = 0.52% homopolymer indels = 44.95% >>>>>>> Coverage mean coverageData = 0.4044X std coverageData = 14.9423X There is a 3.72% of reference with a coverageData >= 1X There is a 1.64% of reference with a coverageData >= 2X There is a 0.76% of reference with a coverageData >= 3X There is a 0.56% of reference with a coverageData >= 4X There is a 0.44% of reference with a coverageData >= 5X There is a 0.39% of reference with a coverageData >= 6X There is a 0.36% of reference with a coverageData >= 7X There is a 0.34% of reference with a coverageData >= 8X There is a 0.32% of reference with a coverageData >= 9X There is a 0.31% of reference with a coverageData >= 10X There is a 0.3% of reference with a coverageData >= 11X There is a 0.28% of reference with a coverageData >= 12X There is a 0.28% of reference with a coverageData >= 13X There is a 0.27% of reference with a coverageData >= 14X There is a 0.26% of reference with a coverageData >= 15X There is a 0.25% of reference with a coverageData >= 16X There is a 0.24% of reference with a coverageData >= 17X There is a 0.24% of reference with a coverageData >= 18X There is a 0.23% of reference with a coverageData >= 19X There is a 0.23% of reference with a coverageData >= 20X There is a 0.22% of reference with a coverageData >= 21X There is a 0.22% of reference with a coverageData >= 22X There is a 0.21% of reference with a coverageData >= 23X There is a 0.21% of reference with a coverageData >= 24X There is a 0.2% of reference with a coverageData >= 25X There is a 0.2% of reference with a coverageData >= 26X There is a 0.19% of reference with a coverageData >= 27X There is a 0.19% of reference with a coverageData >= 28X There is a 0.19% of reference with a coverageData >= 29X There is a 0.18% of reference with a coverageData >= 30X There is a 0.18% of reference with a coverageData >= 31X There is a 0.18% of reference with a coverageData >= 32X There is a 0.17% of reference with a coverageData >= 33X There is a 0.17% of reference with a coverageData >= 34X There is a 0.17% of reference with a coverageData >= 35X There is a 0.17% of reference with a coverageData >= 36X There is a 0.16% of reference with a coverageData >= 37X There is a 0.16% of reference with a coverageData >= 38X There is a 0.16% of reference with a coverageData >= 39X There is a 0.16% of reference with a coverageData >= 40X There is a 0.15% of reference with a coverageData >= 41X There is a 0.15% of reference with a coverageData >= 42X There is a 0.15% of reference with a coverageData >= 43X There is a 0.15% of reference with a coverageData >= 44X There is a 0.15% of reference with a coverageData >= 45X There is a 0.14% of reference with a coverageData >= 46X There is a 0.14% of reference with a coverageData >= 47X There is a 0.14% of reference with a coverageData >= 48X There is a 0.14% of reference with a coverageData >= 49X There is a 0.14% of reference with a coverageData >= 50X There is a 0.13% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 154358293 0.619289502191451 25.828601352048096 chr2 243199373 76225656 0.31342866990039486 9.47269017287347 chr3 198022430 137516912 0.6944511891910427 15.591448770052743 chr4 191154276 47631889 0.24918034791960395 10.662404967264171 chr5 180915260 67875069 0.37517602992693927 11.933238189325225 chr6 171115067 99153983 0.5794579328306607 20.75457742666847 chr7 159138663 45899270 0.28842312191601105 9.239985993889682 chr8 146364022 48942461 0.3343886040518892 11.128293652130145 chr9 141213431 73286662 0.5189779858829434 16.149131826727366 chr10 135534747 34051061 0.25123491764071393 11.515798763809622 chr11 135006516 48414468 0.35860838005774476 11.850247198593875 chr12 133851895 56610081 0.4229307399794377 13.23906398697801 chr13 115169878 30394549 0.26391057738204776 10.41903005791816 chr14 107349540 43497517 0.40519518760862877 14.814108971014907 chr15 102531392 28843366 0.2813125369447827 10.432817309499454 chr16 90354753 47564633 0.5264209288469861 16.585837390466228 chr17 81195210 40826241 0.5028158803949149 12.60020709112676 chr18 78077248 29955406 0.3836637018763776 14.575444314757807 chr19 59128983 19095644 0.32294896734482986 7.966538778415345 chr20 63025520 53682790 0.8517627462653223 35.09635252555843 chr21 48129895 5123797 0.10645768082394529 4.267850309571425 chr22 51304566 10416273 0.20302818661403355 6.422907424608917 chrMT 16571 1630 0.09836461287791926 0.42407051995329575 chrX 155270560 50048593 0.3223315031516599 10.905847393843752 chrY 59373566 2612318 0.04399799735794882 2.32923798114375