BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1153309.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 = 153,430,650 number of mapped reads = 148,564,384 (96.83%) number of supplementary alignments = 910,919 (0.59%) number of secondary alignments = 0 number of mapped bases = 14,589,560,230 bp number of sequenced bases = 14,587,156,498 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 78,666,238 duplication rate = 34.1% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.3376 >>>>>>> ACTG content number of A's = 3,672,684,365 bp (25.18%) number of C's = 3,619,302,074 bp (24.81%) number of T's = 3,710,500,245 bp (25.44%) number of G's = 3,581,580,902 bp (24.55%) number of N's = 3,088,912 bp (0.02%) GC percentage = 49.36% >>>>>>> Mismatches and indels general error rate = 0.0041 number of mismatches = 58,113,405 number of insertions = 833,023 mapped reads with insertion percentage = 0.55% number of deletions = 1,082,561 mapped reads with deletion percentage = 0.72% homopolymer indels = 45.31% >>>>>>> Coverage mean coverageData = 4.7129X std coverageData = 36.8994X There is a 54.83% of reference with a coverageData >= 1X There is a 36.94% of reference with a coverageData >= 2X There is a 24.93% of reference with a coverageData >= 3X There is a 17.89% of reference with a coverageData >= 4X There is a 13.42% of reference with a coverageData >= 5X There is a 10.58% of reference with a coverageData >= 6X There is a 8.68% of reference with a coverageData >= 7X There is a 7.38% of reference with a coverageData >= 8X There is a 6.46% of reference with a coverageData >= 9X There is a 5.77% of reference with a coverageData >= 10X There is a 5.25% of reference with a coverageData >= 11X There is a 4.84% of reference with a coverageData >= 12X There is a 4.51% of reference with a coverageData >= 13X There is a 4.24% of reference with a coverageData >= 14X There is a 4.01% of reference with a coverageData >= 15X There is a 3.81% of reference with a coverageData >= 16X There is a 3.64% of reference with a coverageData >= 17X There is a 3.49% of reference with a coverageData >= 18X There is a 3.36% of reference with a coverageData >= 19X There is a 3.23% of reference with a coverageData >= 20X There is a 3.12% of reference with a coverageData >= 21X There is a 3.02% of reference with a coverageData >= 22X There is a 2.93% of reference with a coverageData >= 23X There is a 2.84% of reference with a coverageData >= 24X There is a 2.76% of reference with a coverageData >= 25X There is a 2.68% of reference with a coverageData >= 26X There is a 2.61% of reference with a coverageData >= 27X There is a 2.54% of reference with a coverageData >= 28X There is a 2.48% of reference with a coverageData >= 29X There is a 2.42% of reference with a coverageData >= 30X There is a 2.36% of reference with a coverageData >= 31X There is a 2.3% of reference with a coverageData >= 32X There is a 2.25% of reference with a coverageData >= 33X There is a 2.2% of reference with a coverageData >= 34X There is a 2.15% of reference with a coverageData >= 35X There is a 2.11% of reference with a coverageData >= 36X There is a 2.06% of reference with a coverageData >= 37X There is a 2.02% of reference with a coverageData >= 38X There is a 1.98% of reference with a coverageData >= 39X There is a 1.94% of reference with a coverageData >= 40X There is a 1.9% of reference with a coverageData >= 41X There is a 1.86% of reference with a coverageData >= 42X There is a 1.83% of reference with a coverageData >= 43X There is a 1.79% of reference with a coverageData >= 44X There is a 1.76% of reference with a coverageData >= 45X There is a 1.73% of reference with a coverageData >= 46X There is a 1.7% of reference with a coverageData >= 47X There is a 1.67% of reference with a coverageData >= 48X There is a 1.64% of reference with a coverageData >= 49X There is a 1.61% of reference with a coverageData >= 50X There is a 1.58% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1232758350 4.945858690558689 31.41779092664667 chr2 243199373 748581678 3.0780575984461933 17.287406682890925 chr3 198022430 745741302 3.765943595379574 21.046595768719857 chr4 191154276 463932586 2.4270060587083075 22.9714055915681 chr5 180915260 923237476 5.103148711722826 70.82327519662154 chr6 171115067 324983852 1.899212370351934 13.55190800761963 chr7 159138663 785164858 4.933840986209618 41.40188885157056 chr8 146364022 854329434 5.837018020726433 69.49693318323096 chr9 141213431 392115064 2.7767547408433124 17.010326172187007 chr10 135534747 737771877 5.443415015929458 28.639396696326784 chr11 135006516 731487493 5.418164357341093 27.281799793589844 chr12 133851895 649494284 4.85233536663788 24.204579087536654 chr13 115169878 142332457 1.2358479445467503 8.49236820314942 chr14 107349540 359320783 3.347203751408716 19.584943422424193 chr15 102531392 757757308 7.3904907874458585 42.62371048732647 chr16 90354753 832735473 9.216288522198717 54.57052543920189 chr17 81195210 766880703 9.444900789098273 46.75609166339298 chr18 78077248 152519523 1.953443889313312 11.783880953407985 chr19 59128983 1202292469 20.333386572875774 82.4513576966964 chr20 63025520 437329615 6.938929103639287 32.76661810712893 chr21 48129895 166489977 3.4591801415731322 30.687799962373294 chr22 51304566 382890132 7.463081005304674 41.58991161230516 chrMT 16571 26879 1.6220505702733692 2.146670559684747 chrX 155270560 779897069 5.022826407014955 28.26768023917924 chrY 59373566 19489588 0.3282536204748086 13.118688306318537