BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3085003.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 = 2,596,917 number of mapped reads = 2,425,954 (93.42%) number of supplementary alignments = 26,542 (1.02%) number of secondary alignments = 0 number of mapped bases = 169,800,052 bp number of sequenced bases = 169,732,960 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 95,773 duplication rate = 2.88% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.9903 >>>>>>> ACTG content number of A's = 50,202,270 bp (29.58%) number of C's = 31,576,560 bp (18.6%) number of T's = 53,723,950 bp (31.65%) number of G's = 34,205,171 bp (20.15%) number of N's = 25,009 bp (0.01%) GC percentage = 38.76% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 1,395,951 number of insertions = 14,192 mapped reads with insertion percentage = 0.58% number of deletions = 41,023 mapped reads with deletion percentage = 1.67% homopolymer indels = 47.78% >>>>>>> Coverage mean coverageData = 0.0549X std coverageData = 0.5268X There is a 4.56% of reference with a coverageData >= 1X There is a 0.67% of reference with a coverageData >= 2X There is a 0.11% 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 0.01% 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 12809108 0.05139047577337831 0.8674883064513101 chr2 243199373 14355229 0.05902658721081489 0.49731252920657865 chr3 198022430 11307848 0.05710387454592896 0.29291591123956884 chr4 191154276 13103796 0.06855089132298563 0.31998432015355077 chr5 180915260 10464346 0.05784114618081416 0.28120158402613943 chr6 171115067 9324462 0.05449234929148583 0.3480756241499388 chr7 159138663 9003437 0.056576050283896125 0.38864380863393366 chr8 146364022 10660502 0.07283553604450689 1.3071176399676376 chr9 141213431 7377832 0.052245965187263245 0.484239776050054 chr10 135534747 7797870 0.057534102306621045 0.6232013675418484 chr11 135006516 8021574 0.059416198844802426 0.4086246827696261 chr12 133851895 7292418 0.05448124585759507 0.2767120705224684 chr13 115169878 5401822 0.04690307998763357 0.246660982221045 chr14 107349540 5537930 0.05158783167585068 0.2918176266669867 chr15 102531392 3831605 0.0373700671107635 0.22130713026848103 chr16 90354753 4074839 0.04509822521456065 0.31892840509774256 chr17 81195210 4006623 0.04934555868505051 0.30245342491638705 chr18 78077248 5061970 0.06483284349366412 0.8932587574877014 chr19 59128983 2526658 0.042731294735781265 0.5303410589081603 chr20 63025520 3294762 0.05227663333836833 0.2738011737687359 chr21 48129895 2169060 0.045066792686749055 0.2820734591337049 chr22 51304566 1296839 0.025277262846351727 0.17984477840186847 chrMT 16571 21358 1.2888781606420856 1.3880551091939721 chrX 155270560 10587740 0.06818897284842665 0.34034811428548944 chrY 59373566 470424 0.007923121882219438 0.17470720723280195