BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081246.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 = 1,394,569 number of mapped reads = 1,163,901 (83.46%) number of supplementary alignments = 14,794 (1.06%) number of secondary alignments = 0 number of mapped bases = 76,299,213 bp number of sequenced bases = 76,272,923 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 29,291 duplication rate = 1.67% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.4998 >>>>>>> ACTG content number of A's = 22,312,142 bp (29.25%) number of C's = 14,964,643 bp (19.62%) number of T's = 21,936,730 bp (28.76%) number of G's = 17,054,295 bp (22.36%) number of N's = 5,113 bp (0.01%) GC percentage = 41.98% >>>>>>> Mismatches and indels general error rate = 0.0093 number of mismatches = 696,539 number of insertions = 6,236 mapped reads with insertion percentage = 0.53% number of deletions = 16,005 mapped reads with deletion percentage = 1.36% homopolymer indels = 44.1% >>>>>>> Coverage mean coverageData = 0.0246X std coverageData = 0.2818X There is a 2.3% of reference with a coverageData >= 1X There is a 0.1% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% 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 8044484 0.032274679869303116 0.5565760785979936 chr2 243199373 4965531 0.020417532079739367 0.283416539536438 chr3 198022430 4932155 0.02490705219605678 0.1658923152161718 chr4 191154276 3327153 0.017405590236443363 0.14289144149067923 chr5 180915260 4654937 0.025729930134141255 0.16851116482368328 chr6 171115067 5400445 0.03156031257025426 0.21771379490331388 chr7 159138663 5183046 0.03256937002166469 0.469598389617435 chr8 146364022 4682097 0.031989398323585286 0.30581014117383265 chr9 141213431 2296937 0.016265712005821883 0.22355319051450007 chr10 135534747 2438340 0.0179905157457519 0.2387355492758579 chr11 135006516 4196330 0.031082425680846397 0.3267420450872362 chr12 133851895 2297725 0.01716617459917172 0.1401864499421612 chr13 115169878 2237789 0.019430332295741426 0.143979487156961 chr14 107349540 2766374 0.025769779730774812 0.17552560031302716 chr15 102531392 1700246 0.01658268718325798 0.1393923507397907 chr16 90354753 2543469 0.028149808566241115 0.1865345660927642 chr17 81195210 1327170 0.016345422346958644 0.16822251862192855 chr18 78077248 1987437 0.025454752196183966 0.37501673432456084 chr19 59128983 2095635 0.035441756202706884 0.40287942416647365 chr20 63025520 1848456 0.029328690981050214 0.18033463062914368 chr21 48129895 1172965 0.024370819840766327 0.1719211632109858 chr22 51304566 542259 0.010569410137881294 0.10619612754437938 chrMT 16571 38235 2.307344155452296 2.0703082758260156 chrX 155270560 5415722 0.034879258502062464 0.21940200494074158 chrY 59373566 204276 0.003440520988751122 0.07542174684742309