BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080996.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 = 3,526,304 number of mapped reads = 3,035,248 (86.07%) number of supplementary alignments = 20,636 (0.59%) number of secondary alignments = 0 number of mapped bases = 195,479,813 bp number of sequenced bases = 195,409,951 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 133,960 duplication rate = 3.62% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.9536 >>>>>>> ACTG content number of A's = 54,712,020 bp (28%) number of C's = 39,012,988 bp (19.96%) number of T's = 58,024,755 bp (29.69%) number of G's = 43,657,608 bp (22.34%) number of N's = 2,580 bp (0%) GC percentage = 42.31% >>>>>>> Mismatches and indels general error rate = 0.0074 number of mismatches = 1,428,168 number of insertions = 13,015 mapped reads with insertion percentage = 0.43% number of deletions = 39,609 mapped reads with deletion percentage = 1.29% homopolymer indels = 46.44% >>>>>>> Coverage mean coverageData = 0.0631X std coverageData = 0.398X There is a 5.04% of reference with a coverageData >= 1X There is a 0.91% of reference with a coverageData >= 2X There is a 0.2% of reference with a coverageData >= 3X There is a 0.06% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 15351406 0.06159024173504466 0.49692762804233004 chr2 243199373 16076158 0.06610279377652836 0.44541062163208195 chr3 198022430 14068280 0.07104387114126415 0.3193285393675824 chr4 191154276 12716706 0.06652587776796581 0.3242566018148466 chr5 180915260 11805041 0.06525177035922786 0.30778522738339553 chr6 171115067 11486161 0.06712536307512885 0.4270556331487461 chr7 159138663 11030338 0.06931274771360874 0.6052552702818899 chr8 146364022 9396435 0.06419907619100547 0.42615750161557736 chr9 141213431 7983253 0.056533241515815874 0.38292866028914996 chr10 135534747 9572376 0.0706267301329009 0.3867575323339655 chr11 135006516 9159826 0.06784728820051915 0.4225163707573563 chr12 133851895 8109456 0.060585290929202014 0.3006884664970986 chr13 115169878 6371690 0.05532427498099807 0.2836519161683779 chr14 107349540 6291052 0.05860343695930136 0.304344632294124 chr15 102531392 6293808 0.061384205141777455 0.3067219898922215 chr16 90354753 5791088 0.06409278768101995 0.3348936200771608 chr17 81195210 5398003 0.06648179122881756 0.3581955239296101 chr18 78077248 5184959 0.066408065509686 0.6551572444267494 chr19 59128983 3349915 0.056654365254345744 0.4434939330203573 chr20 63025520 3852880 0.061132062059940165 0.30965658920948386 chr21 48129895 2691591 0.05592347542000663 0.3053059906064169 chr22 51304566 2250543 0.043866329558269725 0.2524382273763427 chrMT 16571 75691 4.567678474443305 2.839340752895837 chrX 155270560 10685950 0.0688214816768871 0.3513863115054184 chrY 59373566 487207 0.008205789761726624 0.17021371599498264