BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1695983.sorted.bam outfile = /seu_share/home/tujing/220232460/out/SRP050588/SRP050588.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 = 12,426,334 number of mapped reads = 11,282,656 (90.8%) number of supplementary alignments = 170,957 (1.38%) number of secondary alignments = 0 number of mapped bases = 1,494,676,793 bp number of sequenced bases = 1,484,589,590 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,232,500 duplication rate = 16.8% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 51.0842 >>>>>>> ACTG content number of A's = 429,309,713 bp (28.92%) number of C's = 314,268,649 bp (21.17%) number of T's = 421,269,898 bp (28.38%) number of G's = 319,741,330 bp (21.54%) number of N's = 0 bp (0%) GC percentage = 42.71% >>>>>>> Mismatches and indels general error rate = 0.0168 number of mismatches = 15,585,995 number of insertions = 8,510,108 mapped reads with insertion percentage = 46.05% number of deletions = 9,096,027 mapped reads with deletion percentage = 48.68% homopolymer indels = 37.06% >>>>>>> Coverage mean coverageData = 0.4828X std coverageData = 1.462X There is a 20.37% of reference with a coverageData >= 1X There is a 10.53% of reference with a coverageData >= 2X There is a 5.89% of reference with a coverageData >= 3X There is a 3.53% of reference with a coverageData >= 4X There is a 2.23% of reference with a coverageData >= 5X There is a 1.47% of reference with a coverageData >= 6X There is a 1.01% of reference with a coverageData >= 7X There is a 0.71% of reference with a coverageData >= 8X There is a 0.51% of reference with a coverageData >= 9X There is a 0.37% of reference with a coverageData >= 10X There is a 0.28% of reference with a coverageData >= 11X There is a 0.21% of reference with a coverageData >= 12X There is a 0.16% of reference with a coverageData >= 13X There is a 0.12% of reference with a coverageData >= 14X There is a 0.1% of reference with a coverageData >= 15X There is a 0.08% of reference with a coverageData >= 16X There is a 0.06% of reference with a coverageData >= 17X There is a 0.05% of reference with a coverageData >= 18X There is a 0.04% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% 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 158323694 0.6351987945498438 1.9627733211379361 chr2 243199373 127159086 0.5228594318785518 1.4580833298956328 chr3 198022430 93369592 0.47151018195262023 1.345144953301315 chr4 191154276 45640292 0.23876155404444105 0.8744576244819627 chr5 180915260 133576362 0.7383366223501544 1.7577953578126775 chr6 171115067 70598487 0.4125790220448559 1.2738400974707627 chr7 159138663 85569010 0.5377009482604488 1.4214645291847354 chr8 146364022 87677321 0.5990360185647262 1.6456024286175364 chr9 141213431 57436970 0.4067387187837678 1.2927304213330717 chr10 135534747 51136982 0.3772979485474673 1.316860887098475 chr11 135006516 87675884 0.649419647270951 1.6826700464531466 chr12 133851895 78499010 0.5864617008223904 1.5284712770595983 chr13 115169878 29702980 0.2579058041547982 0.9201975342639449 chr14 107349540 32516055 0.3028988759523329 1.0519940673778496 chr15 102531392 53163184 0.5185064102123962 1.4556993267624214 chr16 90354753 58506492 0.6475198045198574 1.7153671358770028 chr17 81195210 44513314 0.5482258620921111 1.5750896046036533 chr18 78077248 27919961 0.357594071450879 1.4302977675068747 chr19 59128983 22639263 0.38287928950173217 1.583645622832 chr20 63025520 45184381 0.7169219865222849 1.796391007803788 chr21 48129895 12978063 0.26964660945136076 1.088469890079606 chr22 51304566 11227461 0.218839410901556 0.869845925435925 chrMT 16571 215333 12.99456882505582 7.348831133534505 chrX 155270560 77480598 0.4990037905447111 1.410432377803833 chrY 59373566 1967018 0.033129524340848926 0.579670200639713