BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472485.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 13,267,396 number of mapped reads = 13,120,089 (98.89%) number of supplementary alignments = 50,756 (0.38%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,585,100 number of mapped paired reads (second in pair) = 6,534,989 number of mapped paired reads (both in pair) = 13,037,162 number of mapped paired reads (singletons) = 82,927 number of mapped bases = 1,296,619,558 bp number of sequenced bases = 1,296,441,419 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 7,766,866 duplication rate = 44.31% >>>>>>> Insert size mean insert size = 27,428.3914 std insert size = 1,593,168.917 median insert size = 254 >>>>>>> Mapping quality mean mapping quality = 55.1435 >>>>>>> ACTG content number of A's = 364,018,475 bp (28.08%) number of C's = 285,859,432 bp (22.05%) number of T's = 362,664,194 bp (27.97%) number of G's = 283,701,687 bp (21.88%) number of N's = 197,631 bp (0.02%) GC percentage = 43.93% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 8,282,153 number of insertions = 76,256 mapped reads with insertion percentage = 0.58% number of deletions = 71,378 mapped reads with deletion percentage = 0.54% homopolymer indels = 45.27% >>>>>>> Coverage mean coverageData = 0.4188X std coverageData = 14.5568X There is a 4.61% of reference with a coverageData >= 1X There is a 1.91% of reference with a coverageData >= 2X There is a 0.86% of reference with a coverageData >= 3X There is a 0.6% of reference with a coverageData >= 4X There is a 0.45% of reference with a coverageData >= 5X There is a 0.4% of reference with a coverageData >= 6X There is a 0.36% of reference with a coverageData >= 7X There is a 0.34% of reference with a coverageData >= 8X There is a 0.32% of reference with a coverageData >= 9X There is a 0.31% of reference with a coverageData >= 10X There is a 0.29% of reference with a coverageData >= 11X There is a 0.28% of reference with a coverageData >= 12X There is a 0.27% of reference with a coverageData >= 13X There is a 0.26% of reference with a coverageData >= 14X There is a 0.26% of reference with a coverageData >= 15X There is a 0.25% of reference with a coverageData >= 16X There is a 0.24% of reference with a coverageData >= 17X There is a 0.24% of reference with a coverageData >= 18X There is a 0.23% of reference with a coverageData >= 19X There is a 0.22% of reference with a coverageData >= 20X There is a 0.22% of reference with a coverageData >= 21X There is a 0.21% of reference with a coverageData >= 22X There is a 0.21% of reference with a coverageData >= 23X There is a 0.21% of reference with a coverageData >= 24X There is a 0.2% of reference with a coverageData >= 25X There is a 0.2% of reference with a coverageData >= 26X There is a 0.19% of reference with a coverageData >= 27X There is a 0.19% of reference with a coverageData >= 28X There is a 0.19% of reference with a coverageData >= 29X There is a 0.18% of reference with a coverageData >= 30X There is a 0.18% of reference with a coverageData >= 31X There is a 0.18% of reference with a coverageData >= 32X There is a 0.17% of reference with a coverageData >= 33X There is a 0.17% of reference with a coverageData >= 34X There is a 0.17% of reference with a coverageData >= 35X There is a 0.16% of reference with a coverageData >= 36X There is a 0.16% of reference with a coverageData >= 37X There is a 0.16% of reference with a coverageData >= 38X There is a 0.16% of reference with a coverageData >= 39X There is a 0.15% of reference with a coverageData >= 40X There is a 0.15% of reference with a coverageData >= 41X There is a 0.15% of reference with a coverageData >= 42X There is a 0.15% of reference with a coverageData >= 43X There is a 0.15% of reference with a coverageData >= 44X There is a 0.14% of reference with a coverageData >= 45X There is a 0.14% of reference with a coverageData >= 46X There is a 0.14% of reference with a coverageData >= 47X There is a 0.14% of reference with a coverageData >= 48X There is a 0.14% of reference with a coverageData >= 49X There is a 0.13% of reference with a coverageData >= 50X There is a 0.13% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 109454257 0.4391333372044036 14.350920191210857 chr2 243199373 84487744 0.3474011588015073 9.856798611853145 chr3 198022430 128602999 0.6494365259531458 14.499431740918125 chr4 191154276 82606880 0.43214769624091487 21.773619080710542 chr5 180915260 99858519 0.551962941102923 17.01503080171734 chr6 171115067 67566279 0.3948587356132701 11.145383188087994 chr7 159138663 46307479 0.290988237094841 9.317021811881792 chr8 146364022 66450855 0.45401085657512197 13.408848090902863 chr9 141213431 81000196 0.5736012178614937 16.508556359685404 chr10 135534747 33372246 0.24622649718009212 10.245233352215273 chr11 135006516 69273717 0.5131138781479259 19.16869308153524 chr12 133851895 69109600 0.5163139453498211 19.648895827503367 chr13 115169878 35755266 0.3104567498109184 13.147477468133863 chr14 107349540 44918616 0.41843324153974015 22.057235090097738 chr15 102531392 27014935 0.26347964728694995 7.004494495025183 chr16 90354753 61273931 0.6781483980150994 18.63668839369193 chr17 81195210 53721753 0.6616369734125942 18.10027875106129 chr18 78077248 27254712 0.3490736763672818 11.823363846318376 chr19 59128983 17545419 0.2967312832016745 9.354810318637323 chr20 63025520 25973949 0.412117964278597 10.65005585563314 chr21 48129895 5469594 0.11364234224903254 3.9786836146221956 chr22 51304566 8617999 0.16797723227987155 4.963958647661988 chrMT 16571 2402 0.14495202462132642 0.49338299925256424 chrX 155270560 48212290 0.31050503070253627 11.443961962488515 chrY 59373566 2767921 0.04661874275835142 1.821351008951687