BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1163163.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 107,344,996 number of mapped reads = 103,759,043 (96.66%) number of supplementary alignments = 1,028,509 (0.96%) number of secondary alignments = 0 number of mapped bases = 10,325,925,723 bp number of sequenced bases = 10,324,309,908 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 60,594,940 duplication rate = 51.61% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.335 >>>>>>> ACTG content number of A's = 2,724,828,298 bp (26.39%) number of C's = 2,432,479,190 bp (23.56%) number of T's = 2,756,770,400 bp (26.7%) number of G's = 2,405,674,088 bp (23.3%) number of N's = 4,557,932 bp (0.04%) GC percentage = 46.86% >>>>>>> Mismatches and indels general error rate = 0.0073 number of mismatches = 74,205,017 number of insertions = 744,148 mapped reads with insertion percentage = 0.71% number of deletions = 778,551 mapped reads with deletion percentage = 0.74% homopolymer indels = 46.63% >>>>>>> Coverage mean coverageData = 3.3356X std coverageData = 32.3494X There is a 10.02% of reference with a coverageData >= 1X There is a 7.01% of reference with a coverageData >= 2X There is a 5.72% of reference with a coverageData >= 3X There is a 5.13% of reference with a coverageData >= 4X There is a 4.74% of reference with a coverageData >= 5X There is a 4.47% of reference with a coverageData >= 6X There is a 4.25% of reference with a coverageData >= 7X There is a 4.07% of reference with a coverageData >= 8X There is a 3.91% of reference with a coverageData >= 9X There is a 3.77% of reference with a coverageData >= 10X There is a 3.65% of reference with a coverageData >= 11X There is a 3.54% of reference with a coverageData >= 12X There is a 3.44% of reference with a coverageData >= 13X There is a 3.34% of reference with a coverageData >= 14X There is a 3.25% of reference with a coverageData >= 15X There is a 3.17% of reference with a coverageData >= 16X There is a 3.09% of reference with a coverageData >= 17X There is a 3.02% of reference with a coverageData >= 18X There is a 2.95% of reference with a coverageData >= 19X There is a 2.88% of reference with a coverageData >= 20X There is a 2.82% of reference with a coverageData >= 21X There is a 2.76% of reference with a coverageData >= 22X There is a 2.7% of reference with a coverageData >= 23X There is a 2.64% of reference with a coverageData >= 24X There is a 2.59% of reference with a coverageData >= 25X There is a 2.54% of reference with a coverageData >= 26X There is a 2.49% of reference with a coverageData >= 27X There is a 2.44% of reference with a coverageData >= 28X There is a 2.4% of reference with a coverageData >= 29X There is a 2.35% of reference with a coverageData >= 30X There is a 2.31% of reference with a coverageData >= 31X There is a 2.27% of reference with a coverageData >= 32X There is a 2.23% of reference with a coverageData >= 33X There is a 2.19% of reference with a coverageData >= 34X There is a 2.15% of reference with a coverageData >= 35X There is a 2.12% of reference with a coverageData >= 36X There is a 2.08% of reference with a coverageData >= 37X There is a 2.05% of reference with a coverageData >= 38X There is a 2.01% of reference with a coverageData >= 39X There is a 1.98% of reference with a coverageData >= 40X There is a 1.95% of reference with a coverageData >= 41X There is a 1.92% of reference with a coverageData >= 42X There is a 1.89% of reference with a coverageData >= 43X There is a 1.86% of reference with a coverageData >= 44X There is a 1.83% of reference with a coverageData >= 45X There is a 1.8% of reference with a coverageData >= 46X There is a 1.77% of reference with a coverageData >= 47X There is a 1.75% of reference with a coverageData >= 48X There is a 1.72% of reference with a coverageData >= 49X There is a 1.69% of reference with a coverageData >= 50X There is a 1.67% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1150377355 4.615343987447879 38.087314745266205 chr2 243199373 709607095 2.917799853867222 26.776076374187795 chr3 198022430 504451320 2.547445357578937 22.133391858620502 chr4 191154276 406549419 2.1268131035687636 23.762569673205725 chr5 180915260 511065445 2.824888541740481 36.65812989063151 chr6 171115067 521079847 3.0452014316191103 27.644442345630406 chr7 159138663 590746041 3.7121465636543647 37.635593036912816 chr8 146364022 488754015 3.3393043476217126 56.521197336769625 chr9 141213431 462568598 3.275669989209454 28.88267609008506 chr10 135534747 431368507 3.182715256036889 29.144747763325707 chr11 135006516 472797401 3.502033938865588 25.668191670750886 chr12 133851895 503931972 3.76484749804999 28.922840310676534 chr13 115169878 201797823 1.7521753648119693 19.68049059585556 chr14 107349540 301785352 2.8112402903636102 24.496305144978333 chr15 102531392 420059946 4.096891086780524 31.81166940218926 chr16 90354753 345177960 3.820252377868821 28.144983659010315 chr17 81195210 480872829 5.922428539811647 39.462232244603975 chr18 78077248 160847779 2.060110763637571 20.258776846152216 chr19 59128983 595229088 10.066621440115078 58.34629748025448 chr20 63025520 204264078 3.2409741006500226 26.271107553663718 chr21 48129895 132803823 2.75927930031844 41.9152328394152 chr22 51304566 175279429 3.4164489180163806 26.510311232903558 chrMT 16571 4911 0.2963611127873997 0.6346068712702129 chrX 155270560 540623911 3.4818185173029583 32.600711775650765 chrY 59373566 13881779 0.23380402989438095 18.081792976011943