BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549107.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 10,598,511 number of mapped reads = 9,088,473 (85.75%) number of secondary alignments = 0 number of mapped bases = 360,912,696 bp number of sequenced bases = 360,875,806 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 512,763 duplication rate = 4.32% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.1171 >>>>>>> ACTG content number of A's = 106,027,096 bp (29.38%) number of C's = 74,433,934 bp (20.63%) number of T's = 106,664,677 bp (29.56%) number of G's = 73,748,625 bp (20.44%) number of N's = 1,474 bp (0%) GC percentage = 41.06% >>>>>>> Mismatches and indels general error rate = 0.0031 number of mismatches = 1,106,826 number of insertions = 8,758 mapped reads with insertion percentage = 0.1% number of deletions = 29,054 mapped reads with deletion percentage = 0.32% homopolymer indels = 45.35% >>>>>>> Coverage mean coverageData = 0.1166X std coverageData = 0.8434X There is a 8.48% of reference with a coverageData >= 1X There is a 2.15% of reference with a coverageData >= 2X There is a 0.58% of reference with a coverageData >= 3X There is a 0.17% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% 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% 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 29561968 0.11860338755184084 1.8306440341634485 chr2 243199373 30920560 0.12714078831116066 0.7083550901961618 chr3 198022430 24713215 0.12480007946574537 0.4591790602232595 chr4 191154276 23754666 0.12426960305088859 0.5336597587983025 chr5 180915260 22627342 0.12507149479817237 0.4734930482283205 chr6 171115067 21339350 0.12470760391894654 0.5048032111047892 chr7 159138663 20316404 0.12766479004539583 1.175384260441045 chr8 146364022 18666889 0.1275374148983143 0.9937330981769519 chr9 141213431 15299285 0.10834157127731002 0.6595560375723548 chr10 135534747 17256099 0.12731863512461494 0.7871916935948279 chr11 135006516 16684769 0.12358491644951418 0.6541698130308161 chr12 133851895 16518963 0.12341224605000922 0.48611995817573866 chr13 115169878 11599599 0.10071729866727826 0.4055743010012427 chr14 107349540 11142011 0.10379188397081161 0.5414768660052642 chr15 102531392 12655478 0.123430275871023 0.44967232330050877 chr16 90354753 10129410 0.11210710741470346 0.49908383596055955 chr17 81195210 9368416 0.11538138764589685 0.48959017189827597 chr18 78077248 9671889 0.12387589531844155 1.363409852919909 chr19 59128983 6802574 0.11504635552415979 1.3350927769925023 chr20 63025520 7546339 0.11973465669144816 0.5046392278549277 chr21 48129895 4875945 0.10130803318810482 0.5255498775435689 chr22 51304566 4106846 0.08004835281132677 0.3846886470553126 chrMT 16571 124311 7.501719872065657 10.257062670981773 chrX 155270560 11856736 0.07636177778968531 0.48482513779220465 chrY 59373566 3373632 0.0568204375664416 0.6439286184733715