BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1153307.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 = 75,821,710 number of mapped reads = 74,839,841 (98.71%) number of supplementary alignments = 486,723 (0.64%) number of secondary alignments = 0 number of mapped bases = 7,439,451,167 bp number of sequenced bases = 7,438,472,965 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 34,687,120 duplication rate = 36.71% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.8837 >>>>>>> ACTG content number of A's = 1,916,582,584 bp (25.77%) number of C's = 1,798,863,723 bp (24.18%) number of T's = 1,916,367,145 bp (25.76%) number of G's = 1,806,322,747 bp (24.28%) number of N's = 336,766 bp (0%) GC percentage = 48.47% >>>>>>> Mismatches and indels general error rate = 0.0032 number of mismatches = 23,101,882 number of insertions = 638,217 mapped reads with insertion percentage = 0.84% number of deletions = 432,959 mapped reads with deletion percentage = 0.57% homopolymer indels = 47.45% >>>>>>> Coverage mean coverageData = 2.4032X std coverageData = 26.4316X There is a 13.06% of reference with a coverageData >= 1X There is a 7.33% of reference with a coverageData >= 2X There is a 5.67% of reference with a coverageData >= 3X There is a 5% of reference with a coverageData >= 4X There is a 4.57% of reference with a coverageData >= 5X There is a 4.26% of reference with a coverageData >= 6X There is a 4% of reference with a coverageData >= 7X There is a 3.79% of reference with a coverageData >= 8X There is a 3.6% of reference with a coverageData >= 9X There is a 3.44% of reference with a coverageData >= 10X There is a 3.29% of reference with a coverageData >= 11X There is a 3.16% of reference with a coverageData >= 12X There is a 3.04% of reference with a coverageData >= 13X There is a 2.92% of reference with a coverageData >= 14X There is a 2.82% of reference with a coverageData >= 15X There is a 2.72% of reference with a coverageData >= 16X There is a 2.63% of reference with a coverageData >= 17X There is a 2.55% of reference with a coverageData >= 18X There is a 2.47% of reference with a coverageData >= 19X There is a 2.39% of reference with a coverageData >= 20X There is a 2.32% of reference with a coverageData >= 21X There is a 2.25% of reference with a coverageData >= 22X There is a 2.19% of reference with a coverageData >= 23X There is a 2.13% of reference with a coverageData >= 24X There is a 2.07% of reference with a coverageData >= 25X There is a 2.01% of reference with a coverageData >= 26X There is a 1.96% of reference with a coverageData >= 27X There is a 1.91% of reference with a coverageData >= 28X There is a 1.86% of reference with a coverageData >= 29X There is a 1.81% of reference with a coverageData >= 30X There is a 1.77% of reference with a coverageData >= 31X There is a 1.73% of reference with a coverageData >= 32X There is a 1.68% of reference with a coverageData >= 33X There is a 1.64% of reference with a coverageData >= 34X There is a 1.61% of reference with a coverageData >= 35X There is a 1.57% of reference with a coverageData >= 36X There is a 1.53% of reference with a coverageData >= 37X There is a 1.5% of reference with a coverageData >= 38X There is a 1.47% of reference with a coverageData >= 39X There is a 1.44% of reference with a coverageData >= 40X There is a 1.4% of reference with a coverageData >= 41X There is a 1.37% of reference with a coverageData >= 42X There is a 1.35% of reference with a coverageData >= 43X There is a 1.32% of reference with a coverageData >= 44X There is a 1.29% of reference with a coverageData >= 45X There is a 1.26% of reference with a coverageData >= 46X There is a 1.24% of reference with a coverageData >= 47X There is a 1.21% of reference with a coverageData >= 48X There is a 1.19% of reference with a coverageData >= 49X There is a 1.17% of reference with a coverageData >= 50X There is a 1.15% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 740748631 2.9719028503443528 26.262975217840427 chr2 243199373 554040524 2.278133027916976 22.1061635130229 chr3 198022430 371149459 1.874279893444394 16.739353104077658 chr4 191154276 222613863 1.1645769462148992 12.84980318911903 chr5 180915260 375898849 2.07776198094069 25.229116431445693 chr6 171115067 193726048 1.1321390418530473 11.970830668251587 chr7 159138663 324836442 2.0412163573348607 28.090953613183093 chr8 146364022 488709839 3.3390025248144655 61.65778793698445 chr9 141213431 139673693 0.9890963771002774 11.416136413989266 chr10 135534747 417954317 3.0837429238717657 27.891077006780126 chr11 135006516 392764711 2.9092278109006235 21.159923215039875 chr12 133851895 402052095 3.0037086512671336 24.825291151864963 chr13 115169878 103671771 0.9001639386993185 9.90998128631068 chr14 107349540 187737008 1.7488384952557785 15.728684210624069 chr15 102531392 341767420 3.333295426243701 26.161859217193754 chr16 90354753 296749970 3.2842762571660176 26.289606564063238 chr17 81195210 359014512 4.4216218173461215 28.354900465923514 chr18 78077248 91233191 1.168499061339867 11.827110590144805 chr19 59128983 582969683 9.859288176831994 58.54807492409803 chr20 63025520 193012801 3.0624547167560063 23.48955899565769 chr21 48129895 135788664 2.8212956624983287 43.957889621631 chr22 51304566 131953915 2.5719721515624943 20.038437196109527 chrMT 16571 1385 0.08357974775209703 0.30378320307028994 chrX 155270560 383244330 2.468235639776143 24.122365725584146 chrY 59373566 8138046 0.13706513770791534 6.502629225066775