BamQC report ----------------------------------- >>>>>>> Input bam file = SRR2971297.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 10,025,682 number of mapped reads = 8,671,365 (86.49%) number of secondary alignments = 0 number of mapped bases = 341,760,764 bp number of sequenced bases = 341,725,885 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 622,905 duplication rate = 5.15% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 36.5473 >>>>>>> ACTG content number of A's = 98,033,488 bp (28.69%) number of C's = 70,281,944 bp (20.57%) number of T's = 101,058,635 bp (29.57%) number of G's = 72,349,327 bp (21.17%) number of N's = 2,491 bp (0%) GC percentage = 41.74% >>>>>>> Mismatches and indels general error rate = 0.0033 number of mismatches = 1,124,700 number of insertions = 12,869 mapped reads with insertion percentage = 0.15% number of deletions = 28,067 mapped reads with deletion percentage = 0.32% homopolymer indels = 38.44% >>>>>>> Coverage mean coverageData = 0.1104X std coverageData = 1.2894X There is a 8.85% of reference with a coverageData >= 1X There is a 1.49% of reference with a coverageData >= 2X There is a 0.28% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% 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 31008225 0.12440580840117546 3.0612428465126906 chr2 243199373 29253259 0.1202850921823717 0.9512139244524781 chr3 198022430 23455495 0.11844867775837313 0.4236079527576138 chr4 191154276 22770353 0.11912029108885851 0.4570470877215808 chr5 180915260 21426934 0.1184362999561231 0.46115881406370246 chr6 171115067 20344349 0.11889279744138487 0.5902859614187042 chr7 159138663 19375904 0.12175484973126864 1.588659996956483 chr8 146364022 17935350 0.12253933552058306 2.179630287261983 chr9 141213431 14414264 0.10207431331372438 0.9540604973840929 chr10 135534747 16058536 0.1184827976253204 1.0477179446875495 chr11 135006516 15805332 0.11707088271206109 0.9182611750468133 chr12 133851895 15661483 0.11700606106473128 0.4835365114054362 chr13 115169878 11053047 0.09597168280407486 0.35776681103025654 chr14 107349540 10375581 0.09665230982824892 0.5400629630373404 chr15 102531392 9249320 0.09020964038018717 0.35627076436249094 chr16 90354753 8760779 0.09695980243562838 0.5009754835021201 chr17 81195210 8257028 0.10169353586252194 0.4749209503674133 chr18 78077248 9149738 0.1171882748736226 1.9080704416669871 chr19 59128983 6649735 0.11246151485473714 2.6543790715511144 chr20 63025520 6512323 0.10332835016672612 0.4342006882004019 chr21 48129895 4237098 0.0880346404246259 0.4884049927013152 chr22 51304566 3318416 0.0646807147730282 0.40140523560126 chrMT 16571 40099 2.4198298231850823 2.8995801761944753 chrX 155270560 13397349 0.08628389696024796 0.573841145822927 chrY 59373566 3250767 0.05475108232508723 0.47195092233445013