BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708512.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP051114/SRP051114.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 = 3,431,004 number of mapped reads = 2,385,020 (69.51%) number of supplementary alignments = 459 (0.01%) number of secondary alignments = 0 number of mapped bases = 114,463,723 bp number of sequenced bases = 114,442,958 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 119,182 duplication rate = 3.8% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.1446 >>>>>>> ACTG content number of A's = 33,273,622 bp (29.07%) number of C's = 21,060,004 bp (18.4%) number of T's = 36,819,197 bp (32.17%) number of G's = 23,288,409 bp (20.35%) number of N's = 1,726 bp (0%) GC percentage = 38.75% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 555,754 number of insertions = 5,473 mapped reads with insertion percentage = 0.23% number of deletions = 13,634 mapped reads with deletion percentage = 0.57% homopolymer indels = 48.58% >>>>>>> Coverage mean coverageData = 0.037X std coverageData = 0.403X There is a 3.13% of reference with a coverageData >= 1X There is a 0.41% of reference with a coverageData >= 2X There is a 0.07% 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 9093431 0.03648308262389444 0.8250559525578113 chr2 243199373 9986467 0.041062881358662054 0.3274059945642346 chr3 198022430 8110160 0.04095576445557203 0.23490849984274506 chr4 191154276 8005977 0.04188228046753189 0.24056101372741265 chr5 180915260 7435108 0.04109718549999596 0.2361923761546368 chr6 171115067 6953930 0.04063891112522546 0.2852384920629567 chr7 159138663 6550879 0.04116459744292309 0.4715376401251636 chr8 146364022 6283226 0.04292876018397472 0.859732298096185 chr9 141213431 4806937 0.03404022525307809 0.25485079246322995 chr10 135534747 5431630 0.04007555346674311 0.30034610295585873 chr11 135006516 5228667 0.03872899734706138 0.32049394652179153 chr12 133851895 5260919 0.0393040307722203 0.23211513318016325 chr13 115169878 4007740 0.03479850868644664 0.21942929734607944 chr14 107349540 3673966 0.034224329233269186 0.22471123338205345 chr15 102531392 3158185 0.0308021274108909 0.2019906997298984 chr16 90354753 2937977 0.03251602049091983 0.21453458055233451 chr17 81195210 2790239 0.03436457643252601 0.27739767327940434 chr18 78077248 3139216 0.04020654006657612 0.4221147257501201 chr19 59128983 1933659 0.032702388945197995 0.5218406806527415 chr20 63025520 2251359 0.03572138714603228 0.22010586187000583 chr21 48129895 1559151 0.03239464785867495 0.24227257813466985 chr22 51304566 1158857 0.02258779462241236 0.19673976308267035 chrMT 16571 211622 12.770623378190816 8.918407854116383 chrX 155270560 3701467 0.023838820443489093 0.20234654937542967 chrY 59373566 792954 0.013355337289325017 0.14080203921157322