BamQC report ----------------------------------- >>>>>>> Input bam file = SRR504638.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 395,619,616 number of mapped reads = 369,241,814 (93.33%) number of supplementary alignments = 2,277,263 (0.58%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 185,998,458 number of mapped paired reads (second in pair) = 183,243,356 number of mapped paired reads (both in pair) = 364,044,040 number of mapped paired reads (singletons) = 5,197,774 number of mapped bases = 35,193,507,849 bp number of sequenced bases = 35,185,049,641 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 96,719,223 duplication rate = 23.28% >>>>>>> Insert size mean insert size = 45,528.7737 std insert size = 2,032,824.0507 median insert size = 349 >>>>>>> Mapping quality mean mapping quality = 53.795 >>>>>>> ACTG content number of A's = 9,327,897,010 bp (26.51%) number of C's = 8,073,912,239 bp (22.95%) number of T's = 9,290,012,996 bp (26.4%) number of G's = 8,339,733,579 bp (23.7%) number of N's = 153,493,817 bp (0.44%) GC percentage = 46.65% >>>>>>> Mismatches and indels general error rate = 0.0157 number of mismatches = 325,514,355 number of insertions = 136,644,088 mapped reads with insertion percentage = 33.78% number of deletions = 3,941,917 mapped reads with deletion percentage = 1.04% homopolymer indels = 20.11% >>>>>>> Coverage mean coverageData = 11.3685X std coverageData = 26.388X There is a 72.39% of reference with a coverageData >= 1X There is a 64.08% of reference with a coverageData >= 2X There is a 57.55% of reference with a coverageData >= 3X There is a 52.1% of reference with a coverageData >= 4X There is a 47.42% of reference with a coverageData >= 5X There is a 43.34% of reference with a coverageData >= 6X There is a 39.76% of reference with a coverageData >= 7X There is a 36.6% of reference with a coverageData >= 8X There is a 33.79% of reference with a coverageData >= 9X There is a 31.28% of reference with a coverageData >= 10X There is a 29.03% of reference with a coverageData >= 11X There is a 27% of reference with a coverageData >= 12X There is a 25.17% of reference with a coverageData >= 13X There is a 23.52% of reference with a coverageData >= 14X There is a 22.02% of reference with a coverageData >= 15X There is a 20.65% of reference with a coverageData >= 16X There is a 19.4% of reference with a coverageData >= 17X There is a 18.26% of reference with a coverageData >= 18X There is a 17.21% of reference with a coverageData >= 19X There is a 16.25% of reference with a coverageData >= 20X There is a 15.36% of reference with a coverageData >= 21X There is a 14.54% of reference with a coverageData >= 22X There is a 13.78% of reference with a coverageData >= 23X There is a 13.08% of reference with a coverageData >= 24X There is a 12.42% of reference with a coverageData >= 25X There is a 11.82% of reference with a coverageData >= 26X There is a 11.25% of reference with a coverageData >= 27X There is a 10.72% of reference with a coverageData >= 28X There is a 10.23% of reference with a coverageData >= 29X There is a 9.77% of reference with a coverageData >= 30X There is a 9.33% of reference with a coverageData >= 31X There is a 8.93% of reference with a coverageData >= 32X There is a 8.54% of reference with a coverageData >= 33X There is a 8.18% of reference with a coverageData >= 34X There is a 7.84% of reference with a coverageData >= 35X There is a 7.52% of reference with a coverageData >= 36X There is a 7.22% of reference with a coverageData >= 37X There is a 6.94% of reference with a coverageData >= 38X There is a 6.67% of reference with a coverageData >= 39X There is a 6.41% of reference with a coverageData >= 40X There is a 6.17% of reference with a coverageData >= 41X There is a 5.94% of reference with a coverageData >= 42X There is a 5.72% of reference with a coverageData >= 43X There is a 5.52% of reference with a coverageData >= 44X There is a 5.32% of reference with a coverageData >= 45X There is a 5.13% of reference with a coverageData >= 46X There is a 4.95% of reference with a coverageData >= 47X There is a 4.78% of reference with a coverageData >= 48X There is a 4.62% of reference with a coverageData >= 49X There is a 4.47% of reference with a coverageData >= 50X There is a 4.32% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 2971072308 11.92001968171626 24.82891782870235 chr2 243199373 1959770069 8.058285861616922 16.809708515207653 chr3 198022430 1733819109 8.75567029957162 17.501203163276635 chr4 191154276 1346896984 7.0461253192159825 12.517937838842004 chr5 180915260 2377979132 13.144160044874047 22.287042290277903 chr6 171115067 921550266 5.3855588649011255 12.132500798293423 chr7 159138663 1802438341 11.326212669010546 19.087255070932628 chr8 146364022 2044483306 13.968482678072348 37.24619926517838 chr9 141213431 969773880 6.867433735817948 15.487077029594014 chr10 135534747 2032213483 14.994040480261493 25.183257369410807 chr11 135006516 1558319825 11.542552694271437 21.558979517543015 chr12 133851895 1685359942 12.591229597459192 25.979948407291293 chr13 115169878 453684185 3.939260793521028 7.594680498007969 chr14 107349540 1061571982 9.888929025685625 18.148589860096717 chr15 102531392 1435435329 13.999959436813263 26.44711283263884 chr16 90354753 2099629641 23.23762249673794 37.483784073952606 chr17 81195210 1570447081 19.34162225825883 34.06740177310085 chr18 78077248 475078447 6.084723260225565 53.75029178756692 chr19 59128983 1852219774 31.3250741011392 64.67206484925147 chr20 63025520 1775572952 28.172285639214085 40.27525257730599 chr21 48129895 534580000 11.107026100929579 21.744348695710574 chr22 51304566 725595648 14.142905877032465 30.16755615541066 chrMT 16571 421412 25.430692173073442 22.361324506954766 chrX 155270560 1756551961 11.312846176377544 20.510658282749464 chrY 59373566 49042792 0.826003814559496 29.87180643556891