BamQC report ----------------------------------- >>>>>>> Input bam file = SRR054604.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 4,347,881 number of mapped reads = 3,244,785 (74.63%) number of supplementary alignments = 115 (0%) number of secondary alignments = 0 number of mapped bases = 151,540,550 bp number of sequenced bases = 151,508,188 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 429,065 duplication rate = 10.64% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7332 >>>>>>> ACTG content number of A's = 46,499,819 bp (30.69%) number of C's = 29,797,736 bp (19.67%) number of T's = 44,892,657 bp (29.63%) number of G's = 30,283,373 bp (19.99%) number of N's = 34,603 bp (0.02%) GC percentage = 39.66% >>>>>>> Mismatches and indels general error rate = 0.0075 number of mismatches = 1,120,048 number of insertions = 7,151 mapped reads with insertion percentage = 0.22% number of deletions = 22,445 mapped reads with deletion percentage = 0.69% homopolymer indels = 44.55% >>>>>>> Coverage mean coverageData = 0.049X std coverageData = 0.4433X There is a 3.04% of reference with a coverageData >= 1X There is a 0.89% of reference with a coverageData >= 2X There is a 0.38% of reference with a coverageData >= 3X There is a 0.2% of reference with a coverageData >= 4X There is a 0.11% of reference with a coverageData >= 5X There is a 0.07% of reference with a coverageData >= 6X There is a 0.04% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% 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 11187634 0.044885079744696 0.42199561759522036 chr2 243199373 14553978 0.0598438138243062 0.5276288289111847 chr3 198022430 11345941 0.057296241642929034 0.4446150067689396 chr4 191154276 8988891 0.047024273733745826 0.4073706513448792 chr5 180915260 9146745 0.05055817292582174 0.3851216691419167 chr6 171115067 8911875 0.052081182307575524 0.4466721634334091 chr7 159138663 7471384 0.04694889261448677 0.42721207559575664 chr8 146364022 9418415 0.06434924970837437 0.4823699715157966 chr9 141213431 6631235 0.04695895392556534 0.41769201049554133 chr10 135534747 4573002 0.03374044000687145 0.33757507828472577 chr11 135006516 6316094 0.046783623391925766 0.6498190685308178 chr12 133851895 8183705 0.06114000104369086 0.4714467726854541 chr13 115169878 5137570 0.044608625876984956 0.49435804421889684 chr14 107349540 3215728 0.029955675636802914 0.3202475893940221 chr15 102531392 4573056 0.04460152067378545 0.34815166872684733 chr16 90354753 4288271 0.0474603809718787 0.41005133518425885 chr17 81195210 3105791 0.03825091406254137 0.341577810383983 chr18 78077248 5468193 0.07003567799930653 0.539087222475745 chr19 59128983 2939801 0.049718443491578404 0.45021452368893256 chr20 63025520 3260320 0.05173015629224479 0.42048004631087343 chr21 48129895 1756929 0.036503902616035214 0.33988068708648916 chr22 51304566 2300791 0.04484573556279572 0.3844580608624173 chrMT 16571 11328 0.6836038863074045 1.51204875031345 chrX 155270560 8411430 0.0541727292024966 0.49281269852440646 chrY 59373566 342443 0.005767600349286752 0.13210833601879085