BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080679.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 = 1,376,687 number of mapped reads = 1,265,184 (91.9%) number of supplementary alignments = 10,523 (0.76%) number of secondary alignments = 0 number of mapped bases = 84,054,344 bp number of sequenced bases = 84,023,954 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 45,445 duplication rate = 3.16% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8514 >>>>>>> ACTG content number of A's = 22,888,175 bp (27.24%) number of C's = 15,326,787 bp (18.24%) number of T's = 26,881,474 bp (31.99%) number of G's = 18,923,414 bp (22.52%) number of N's = 4,104 bp (0%) GC percentage = 40.76% >>>>>>> Mismatches and indels general error rate = 0.0069 number of mismatches = 568,449 number of insertions = 6,264 mapped reads with insertion percentage = 0.49% number of deletions = 19,101 mapped reads with deletion percentage = 1.5% homopolymer indels = 48.13% >>>>>>> Coverage mean coverageData = 0.0272X std coverageData = 0.2181X There is a 2.38% of reference with a coverageData >= 1X There is a 0.27% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% 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 10292463 0.04129363031757501 0.25010214550270377 chr2 243199373 5580619 0.022946683337049557 0.3100981329484622 chr3 198022430 5230343 0.026412881611441695 0.18035958400827168 chr4 191154276 3680691 0.01925508064491322 0.15576311559048023 chr5 180915260 3937975 0.021766958740793894 0.16358337308211207 chr6 171115067 5032683 0.02941110381589016 0.2295067246233299 chr7 159138663 5249863 0.03298923656283326 0.35909452779435574 chr8 146364022 9928616 0.0678350858655688 0.31345325834207055 chr9 141213431 2580558 0.018274168269447402 0.16938914932396265 chr10 135534747 4004790 0.029548068584951133 0.19809330793365004 chr11 135006516 3485517 0.025817398324685305 0.19355619836037843 chr12 133851895 2727300 0.020375505329976836 0.1597555448105425 chr13 115169878 1774963 0.015411694714133499 0.13872160993495167 chr14 107349540 1588362 0.014796169597000601 0.13688265527140017 chr15 102531392 1492095 0.014552567471238467 0.139475849985296 chr16 90354753 2024323 0.02240416727164314 0.16764034692443214 chr17 81195210 1318796 0.01624228818424141 0.14345398445743188 chr18 78077248 2774014 0.03552909549270999 0.24855988700225204 chr19 59128983 1261164 0.021329032498326583 0.17733026816961478 chr20 63025520 2276226 0.03611594160587648 0.21354577359681973 chr21 48129895 1279090 0.026575790368958834 0.1837240099507219 chr22 51304566 767560 0.014960851632581786 0.1347688117702309 chrMT 16571 7994 0.482409027819685 0.8281023845679373 chrX 155270560 5598938 0.03605923750130095 0.21798284246087468 chrY 59373566 159401 0.0026847132611169085 0.059715775815809155