BamQC report ----------------------------------- >>>>>>> Input bam file = SRR960891.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 222,129,622 number of mapped reads = 218,676,956 (98.45%) number of supplementary alignments = 387,977 (0.17%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 109,612,832 number of mapped paired reads (second in pair) = 109,064,124 number of mapped paired reads (both in pair) = 217,421,790 number of mapped paired reads (singletons) = 1,255,166 number of mapped bases = 21,519,374,704 bp number of sequenced bases = 21,513,067,445 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 31,347,880 duplication rate = 9.64% >>>>>>> Insert size mean insert size = 15,544.6961 std insert size = 1,174,558.5368 median insert size = 163 >>>>>>> Mapping quality mean mapping quality = 53.6359 >>>>>>> ACTG content number of A's = 6,573,687,099 bp (30.56%) number of C's = 4,189,259,793 bp (19.47%) number of T's = 6,561,835,702 bp (30.5%) number of G's = 4,185,691,904 bp (19.46%) number of N's = 2,592,947 bp (0.01%) GC percentage = 38.93% >>>>>>> Mismatches and indels general error rate = 0.0121 number of mismatches = 254,761,836 number of insertions = 2,545,616 mapped reads with insertion percentage = 1.13% number of deletions = 2,708,058 mapped reads with deletion percentage = 1.2% homopolymer indels = 40.91% >>>>>>> Coverage mean coverageData = 6.9514X std coverageData = 94.457X There is a 89.36% of reference with a coverageData >= 1X There is a 85.14% of reference with a coverageData >= 2X There is a 78.9% of reference with a coverageData >= 3X There is a 71.2% of reference with a coverageData >= 4X There is a 62.64% of reference with a coverageData >= 5X There is a 53.86% of reference with a coverageData >= 6X There is a 45.36% of reference with a coverageData >= 7X There is a 37.5% of reference with a coverageData >= 8X There is a 30.46% of reference with a coverageData >= 9X There is a 24.36% of reference with a coverageData >= 10X There is a 19.2% of reference with a coverageData >= 11X There is a 14.92% of reference with a coverageData >= 12X There is a 11.46% of reference with a coverageData >= 13X There is a 8.7% of reference with a coverageData >= 14X There is a 6.55% of reference with a coverageData >= 15X There is a 4.88% of reference with a coverageData >= 16X There is a 3.62% of reference with a coverageData >= 17X There is a 2.68% of reference with a coverageData >= 18X There is a 1.98% of reference with a coverageData >= 19X There is a 1.47% of reference with a coverageData >= 20X There is a 1.09% of reference with a coverageData >= 21X There is a 0.82% of reference with a coverageData >= 22X There is a 0.63% of reference with a coverageData >= 23X There is a 0.49% of reference with a coverageData >= 24X There is a 0.39% of reference with a coverageData >= 25X There is a 0.32% of reference with a coverageData >= 26X There is a 0.27% of reference with a coverageData >= 27X There is a 0.23% of reference with a coverageData >= 28X There is a 0.2% of reference with a coverageData >= 29X There is a 0.18% of reference with a coverageData >= 30X There is a 0.16% of reference with a coverageData >= 31X There is a 0.15% of reference with a coverageData >= 32X There is a 0.14% of reference with a coverageData >= 33X There is a 0.13% of reference with a coverageData >= 34X There is a 0.12% of reference with a coverageData >= 35X There is a 0.12% of reference with a coverageData >= 36X There is a 0.11% of reference with a coverageData >= 37X There is a 0.1% of reference with a coverageData >= 38X There is a 0.1% of reference with a coverageData >= 39X There is a 0.1% of reference with a coverageData >= 40X There is a 0.09% of reference with a coverageData >= 41X There is a 0.09% of reference with a coverageData >= 42X There is a 0.08% of reference with a coverageData >= 43X There is a 0.08% of reference with a coverageData >= 44X There is a 0.08% of reference with a coverageData >= 45X There is a 0.08% of reference with a coverageData >= 46X There is a 0.07% of reference with a coverageData >= 47X There is a 0.07% of reference with a coverageData >= 48X There is a 0.07% of reference with a coverageData >= 49X There is a 0.07% of reference with a coverageData >= 50X There is a 0.07% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1823632632 7.316461739126419 234.70838688867175 chr2 243199373 2261301163 9.298137306464191 50.69240426197378 chr3 198022430 1413739224 7.1392883321349 14.14661736591004 chr4 191154276 1199707553 6.276121979086672 77.00234137648515 chr5 180915260 1162708039 6.426810203849029 8.144273099042747 chr6 171115067 1317878614 7.701709949364073 27.551191460767846 chr7 159138663 1115229930 7.0079131555855785 59.00813502023789 chr8 146364022 1229897058 8.40300123755823 95.6438848231236 chr9 141213431 1089531712 7.7154963538843555 77.236125280259 chr10 135534747 956723482 7.058879757233029 222.63095730190327 chr11 135006516 954100977 7.067073540361563 36.65210481387771 chr12 133851895 1087359471 8.123601619536279 7.877367653821277 chr13 115169878 604589993 5.249549652210277 4.697224241846102 chr14 107349540 427611005 3.9833520013220363 6.797708635147351 chr15 102531392 525471528 5.124981898226838 4.604279776086192 chr16 90354753 583595371 6.458933831626987 85.63983198313787 chr17 81195210 459544876 5.659753524869263 24.471977278471673 chr18 78077248 679449905 8.702277838993506 80.55906437229764 chr19 59128983 374665789 6.336415239883291 102.78227330373412 chr20 63025520 416730682 6.612094307194927 22.50768582191935 chr21 48129895 269201414 5.5932267045253266 30.995715383986926 chr22 51304566 247565965 4.825417780553879 6.157967812239128 chrMT 16571 8498108 512.8301249170237 109.55761463051891 chrX 155270560 1250605409 8.054362713704387 25.706584074238094 chrY 59373566 60034804 1.0111369089739364 66.22341262252124