BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1777271.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP052908/SRP052908.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 = 3,658,004 number of mapped reads = 3,572,603 (97.67%) number of supplementary alignments = 52,463 (1.43%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,795,676 number of mapped paired reads (second in pair) = 1,776,927 number of mapped paired reads (both in pair) = 3,546,182 number of mapped paired reads (singletons) = 26,421 number of mapped bases = 267,072,604 bp number of sequenced bases = 267,026,296 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 62,894 duplication rate = 1.68% >>>>>>> Insert size mean insert size = 226,906.0912 std insert size = 4,606,525.0725 median insert size = 166 >>>>>>> Mapping quality mean mapping quality = 52.7413 >>>>>>> ACTG content number of A's = 80,328,707 bp (30.08%) number of C's = 53,550,782 bp (20.05%) number of T's = 78,724,162 bp (29.48%) number of G's = 54,407,896 bp (20.38%) number of N's = 14,749 bp (0.01%) GC percentage = 40.43% >>>>>>> Mismatches and indels general error rate = 0.0057 number of mismatches = 1,447,774 number of insertions = 55,519 mapped reads with insertion percentage = 1.54% number of deletions = 24,165 mapped reads with deletion percentage = 0.67% homopolymer indels = 50.09% >>>>>>> Coverage mean coverageData = 0.0863X std coverageData = 0.3694X There is a 7.16% of reference with a coverageData >= 1X There is a 1.24% of reference with a coverageData >= 2X There is a 0.15% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% 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 22198397 0.08906054841885429 0.4388886451024804 chr2 243199373 25586942 0.10520973670437876 0.3765488635478375 chr3 198022430 18392245 0.09287960459832757 0.3459100187229638 chr4 191154276 17169912 0.0898222752809359 0.33898411005648493 chr5 180915260 18361246 0.10149086373366183 0.35975037701154317 chr6 171115067 13036273 0.07618424974815338 0.32515220695948965 chr7 159138663 18395257 0.11559263257100508 0.4013598214150771 chr8 146364022 13548744 0.09256881448639065 0.3504434070420606 chr9 141213431 9657786 0.0683914124287512 0.33438519426535945 chr10 135534747 11854316 0.0874632982492674 0.3793841402043431 chr11 135006516 15611209 0.11563300396552711 0.3904787260314789 chr12 133851895 12337980 0.09217635656185517 0.3426038187623091 chr13 115169878 12198575 0.10591810299564614 0.3702592036220415 chr14 107349540 5426373 0.05054863765601604 0.2537629133589836 chr15 102531392 9753338 0.09512538364835621 0.3519263503253144 chr16 90354753 6541891 0.07240228967257539 0.3175235845874094 chr17 81195210 5949413 0.07327295538739292 0.3179646051396563 chr18 78077248 5907146 0.07565771273085854 0.3550948268754658 chr19 59128983 4399831 0.07441073356529741 0.3535684920268699 chr20 63025520 6601336 0.10474068282181567 0.36735358469576695 chr21 48129895 2358447 0.04900170673549153 0.25903850576873777 chr22 51304566 1825399 0.03557965971293861 0.21372737857432342 chrMT 16571 784337 47.33190513547764 13.651606618338226 chrX 155270560 8909903 0.057383080218168854 0.2715091362826428 chrY 59373566 266308 0.004485295695394142 0.10026828126593727