BamQC report ----------------------------------- >>>>>>> Input bam file = SRR2046422.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP058890/SRP058890.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 = 7,794,098 number of mapped reads = 7,747,206 (99.4%) number of supplementary alignments = 54,729 (0.7%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 3,877,228 number of mapped paired reads (second in pair) = 3,869,978 number of mapped paired reads (both in pair) = 7,714,162 number of mapped paired reads (singletons) = 33,044 number of mapped bases = 750,397,521 bp number of sequenced bases = 750,182,628 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 5,674,110 duplication rate = 42.35% >>>>>>> Insert size mean insert size = 16,331.4473 std insert size = 1,206,434.3291 median insert size = 140 >>>>>>> Mapping quality mean mapping quality = 53.1243 >>>>>>> ACTG content number of A's = 218,425,877 bp (29.12%) number of C's = 157,095,249 bp (20.94%) number of T's = 219,754,243 bp (29.29%) number of G's = 154,837,226 bp (20.64%) number of N's = 70,033 bp (0.01%) GC percentage = 41.58% >>>>>>> Mismatches and indels general error rate = 0.0043 number of mismatches = 3,094,392 number of insertions = 65,834 mapped reads with insertion percentage = 0.83% number of deletions = 78,369 mapped reads with deletion percentage = 0.98% homopolymer indels = 48.83% >>>>>>> Coverage mean coverageData = 0.2424X std coverageData = 16.6909X There is a 2.33% of reference with a coverageData >= 1X There is a 1.18% of reference with a coverageData >= 2X There is a 0.29% of reference with a coverageData >= 3X There is a 0.22% of reference with a coverageData >= 4X There is a 0.14% of reference with a coverageData >= 5X There is a 0.12% of reference with a coverageData >= 6X There is a 0.11% of reference with a coverageData >= 7X There is a 0.1% of reference with a coverageData >= 8X There is a 0.09% of reference with a coverageData >= 9X There is a 0.09% of reference with a coverageData >= 10X There is a 0.09% of reference with a coverageData >= 11X There is a 0.08% of reference with a coverageData >= 12X There is a 0.08% of reference with a coverageData >= 13X There is a 0.08% of reference with a coverageData >= 14X There is a 0.08% of reference with a coverageData >= 15X There is a 0.07% of reference with a coverageData >= 16X There is a 0.07% of reference with a coverageData >= 17X There is a 0.07% of reference with a coverageData >= 18X There is a 0.07% of reference with a coverageData >= 19X There is a 0.07% of reference with a coverageData >= 20X There is a 0.07% of reference with a coverageData >= 21X There is a 0.06% of reference with a coverageData >= 22X There is a 0.06% of reference with a coverageData >= 23X There is a 0.06% of reference with a coverageData >= 24X There is a 0.06% of reference with a coverageData >= 25X There is a 0.06% of reference with a coverageData >= 26X There is a 0.06% of reference with a coverageData >= 27X There is a 0.06% of reference with a coverageData >= 28X There is a 0.06% of reference with a coverageData >= 29X There is a 0.06% of reference with a coverageData >= 30X There is a 0.06% of reference with a coverageData >= 31X There is a 0.05% of reference with a coverageData >= 32X There is a 0.05% of reference with a coverageData >= 33X There is a 0.05% of reference with a coverageData >= 34X There is a 0.05% of reference with a coverageData >= 35X There is a 0.05% of reference with a coverageData >= 36X There is a 0.05% of reference with a coverageData >= 37X There is a 0.05% of reference with a coverageData >= 38X There is a 0.05% of reference with a coverageData >= 39X There is a 0.05% of reference with a coverageData >= 40X There is a 0.05% of reference with a coverageData >= 41X There is a 0.05% of reference with a coverageData >= 42X There is a 0.05% of reference with a coverageData >= 43X There is a 0.05% of reference with a coverageData >= 44X There is a 0.05% of reference with a coverageData >= 45X There is a 0.05% of reference with a coverageData >= 46X There is a 0.05% of reference with a coverageData >= 47X There is a 0.05% of reference with a coverageData >= 48X There is a 0.05% of reference with a coverageData >= 49X There is a 0.05% of reference with a coverageData >= 50X There is a 0.04% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 103284722 0.41438100168263975 21.994903322236258 chr2 243199373 116242970 0.47797397076348547 28.683619577475753 chr3 198022430 31372246 0.15842773972625224 12.093908827389862 chr4 191154276 16252351 0.08502216816745443 4.514248809785017 chr5 180915260 40541204 0.22408946597429094 11.447927858920501 chr6 171115067 54044568 0.31583757612647867 19.908520481349353 chr7 159138663 46761649 0.29384216329629465 18.02615377134052 chr8 146364022 81120150 0.554235589399149 28.267955397912992 chr9 141213431 12264444 0.08685040731005254 4.6848104763561205 chr10 135534747 27755646 0.2047862014306929 14.102241578007987 chr11 135006516 20911099 0.15488955362717455 9.98076284760114 chr12 133851895 17547461 0.13109609692115304 6.413094401687972 chr13 115169878 10085531 0.08757090981723537 6.0162845595936805 chr14 107349540 51609123 0.48075774707558133 24.651090862407248 chr15 102531392 10222214 0.09969838310592721 5.2084619509352414 chr16 90354753 22942860 0.253919791026378 15.3135638130401 chr17 81195210 27838008 0.3428528357768888 15.47196882027938 chr18 78077248 9933672 0.12722876707949543 7.266160484580127 chr19 59128983 8545241 0.1445186533987909 5.914426218150961 chr20 63025520 11611659 0.1842374168432089 13.528667489130502 chr21 48129895 4793989 0.09960522456988531 12.26056126097062 chr22 51304566 2945169 0.057405592320964184 4.478661454141436 chrMT 16571 40601 2.4501237100959505 2.3025035012363957 chrX 155270560 21378213 0.13768362141541834 19.770847369544207 chrY 59373566 352731 0.00594087611311741 1.4092390281263287