BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549117.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 = 11,940,785 number of mapped reads = 7,083,123 (59.32%) number of secondary alignments = 0 number of mapped bases = 279,583,695 bp number of sequenced bases = 279,549,628 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 343,617 duplication rate = 3.76% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 40.3286 >>>>>>> ACTG content number of A's = 80,877,398 bp (28.93%) number of C's = 58,866,813 bp (21.06%) number of T's = 80,960,339 bp (28.96%) number of G's = 58,834,059 bp (21.05%) number of N's = 11,019 bp (0%) GC percentage = 42.1% >>>>>>> Mismatches and indels general error rate = 0.0037 number of mismatches = 1,016,351 number of insertions = 10,383 mapped reads with insertion percentage = 0.15% number of deletions = 27,226 mapped reads with deletion percentage = 0.38% homopolymer indels = 45.08% >>>>>>> Coverage mean coverageData = 0.0903X std coverageData = 0.6329X There is a 6.79% of reference with a coverageData >= 1X There is a 1.47% of reference with a coverageData >= 2X There is a 0.42% of reference with a coverageData >= 3X There is a 0.14% 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% 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 23067519 0.09254748857777169 0.9506401255494138 chr2 243199373 23745077 0.09763625911979633 0.5688516105240994 chr3 198022430 18844747 0.09516470937155957 0.4038686160840043 chr4 191154276 17215739 0.09006201357483627 0.39676313392792784 chr5 180915260 17264232 0.09542717402611588 0.4120169757579966 chr6 171115067 16278382 0.09513120197650392 0.43203056506200177 chr7 159138663 15842611 0.0995522439446409 0.7371978830238853 chr8 146364022 14417972 0.09850762368363995 1.3863907513904918 chr9 141213431 12109670 0.0857543784202793 0.5488379974673594 chr10 135534747 13437428 0.09914378635317776 0.5253186316026602 chr11 135006516 12652805 0.09371995793151199 0.47700956812261774 chr12 133851895 13035022 0.09738391824785148 0.42812941644160757 chr13 115169878 8767525 0.07612689317948222 0.3573004905697269 chr14 107349540 8637223 0.08045887294905968 0.614107365374358 chr15 102531392 8442251 0.08233820720974899 0.3679694153108294 chr16 90354753 8640274 0.09562611498700019 0.42457216134978093 chr17 81195210 8513122 0.10484758891565155 0.4258374322559901 chr18 78077248 7330436 0.09388696691768644 1.0576232104504932 chr19 59128983 6673797 0.11286845572838619 1.0284207650627513 chr20 63025520 6148163 0.09755037324563129 0.42766861500346864 chr21 48129895 3666628 0.0761819239372951 0.40534516840648893 chr22 51304566 3673729 0.07160627769465977 0.37130702058784026 chrMT 16571 119659 7.22098847383984 10.41406618950371 chrX 155270560 9095650 0.05857935979621636 0.39449365471444897 chrY 59373566 1964034 0.033079266284932254 0.26443264159302743