BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081125.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,225,416 number of mapped reads = 2,025,561 (91.02%) number of supplementary alignments = 13,234 (0.59%) number of secondary alignments = 0 number of mapped bases = 137,452,359 bp number of sequenced bases = 137,399,751 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 79,082 duplication rate = 3.16% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.2944 >>>>>>> ACTG content number of A's = 38,790,642 bp (28.23%) number of C's = 26,122,291 bp (19.01%) number of T's = 42,741,165 bp (31.11%) number of G's = 29,744,049 bp (21.65%) number of N's = 1,604 bp (0%) GC percentage = 40.66% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 1,175,875 number of insertions = 10,516 mapped reads with insertion percentage = 0.51% number of deletions = 29,447 mapped reads with deletion percentage = 1.44% homopolymer indels = 47.34% >>>>>>> Coverage mean coverageData = 0.0444X std coverageData = 0.3467X There is a 3.71% of reference with a coverageData >= 1X There is a 0.53% of reference with a coverageData >= 2X There is a 0.1% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 12617142 0.05062030316867295 0.4949938597073155 chr2 243199373 9493324 0.0390351499796013 0.37383518206530814 chr3 198022430 11707979 0.0591245092790751 0.28310666174968413 chr4 191154276 8435584 0.04412971646001788 0.262346868586789 chr5 180915260 7553907 0.04175384099716077 0.2380948139016044 chr6 171115067 10266233 0.0599960785452049 0.3869117218430017 chr7 159138663 6771656 0.042551922156088495 0.3704911801481485 chr8 146364022 10116802 0.06912082533506765 0.4182974869759101 chr9 141213431 6899222 0.04885669834054241 0.4300547277936354 chr10 135534747 6257605 0.046169747157162586 0.3320690207100256 chr11 135006516 6085407 0.04507491327307491 0.28675630384916495 chr12 133851895 6708510 0.050118901940088334 0.27245733231026686 chr13 115169878 3617186 0.03140739629853563 0.20322466368298137 chr14 107349540 3699473 0.03446193621323389 0.28019238633528226 chr15 102531392 3916927 0.03820222200826065 0.2300418738380301 chr16 90354753 3484434 0.03856392590658734 0.28655061643609536 chr17 81195210 3070090 0.03781122063727651 0.2283792378162988 chr18 78077248 3299019 0.04225326947998987 0.7469634785848638 chr19 59128983 2790392 0.04719161159934038 0.37808634748178627 chr20 63025520 2285542 0.036263754745696666 0.23412674347617954 chr21 48129895 2608081 0.05418837917680892 0.3221273248488576 chr22 51304566 1304712 0.02543071897343406 0.18172350828326705 chrMT 16571 143048 8.63243014905558 5.825660023173573 chrX 155270560 3960892 0.025509613670485893 0.20931543157589708 chrY 59373566 359192 0.0060496955833847 0.14660587576178954