BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006439.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP030642/SRP030642.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 = 1,359,907 number of mapped reads = 1,281,561 (94.24%) number of supplementary alignments = 3,669 (0.27%) number of secondary alignments = 0 number of mapped bases = 71,564,799 bp number of sequenced bases = 71,545,337 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 28,959 duplication rate = 1.88% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.4399 >>>>>>> ACTG content number of A's = 20,287,549 bp (28.36%) number of C's = 14,885,989 bp (20.81%) number of T's = 20,627,146 bp (28.83%) number of G's = 15,743,155 bp (22%) number of N's = 1,498 bp (0%) GC percentage = 42.81% >>>>>>> Mismatches and indels general error rate = 0.0038 number of mismatches = 266,125 number of insertions = 4,456 mapped reads with insertion percentage = 0.35% number of deletions = 11,886 mapped reads with deletion percentage = 0.92% homopolymer indels = 45.26% >>>>>>> Coverage mean coverageData = 0.0231X std coverageData = 0.2277X There is a 1.99% of reference with a coverageData >= 1X There is a 0.25% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% 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 5574104 0.022363450801592986 0.2212563632522816 chr2 243199373 6396385 0.02630099297172119 0.2009753845549 chr3 198022430 4705207 0.02376098000615385 0.17420881437400312 chr4 191154276 4710228 0.02464097638077424 0.1823402294395191 chr5 180915260 4252430 0.023505092936881057 0.17370352429988203 chr6 171115067 4003340 0.02339560197817063 0.17633347747928743 chr7 159138663 3993800 0.02509635260665725 0.2017337315096582 chr8 146364022 3782862 0.02584557289632284 0.631741354182891 chr9 141213431 3159605 0.022374677660795594 0.1805742267024165 chr10 135534747 3258342 0.024040639556437877 0.19891131617060762 chr11 135006516 3423444 0.02535762051662751 0.19014830615368383 chr12 133851895 3141955 0.023473369577621594 0.1752119860299004 chr13 115169878 2270957 0.01971832426530833 0.1587180290759579 chr14 107349540 2189274 0.020393883383198474 0.16454429361759076 chr15 102531392 2220125 0.02165312453770256 0.16724810266728096 chr16 90354753 2145586 0.023746243874962505 0.18370116103219916 chr17 81195210 1934577 0.023826245415215996 0.18308818974781293 chr18 78077248 1996292 0.025568165517309217 0.2403012776484949 chr19 59128983 1471105 0.024879592466523565 0.2060868506479461 chr20 63025520 1652911 0.026226058904393015 0.1886752679352268 chr21 48129895 1394991 0.028983877899588187 0.20142198479661197 chr22 51304566 923972 0.018009547142451218 0.15794299782575308 chrMT 16571 49407 2.9815340051897894 2.569816885365436 chrX 155270560 2278806 0.014676355904171403 0.13892739664199416 chrY 59373566 635094 0.010696578339256227 0.14800553435239996