BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1153401.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 = 391,345,290 number of mapped reads = 377,546,960 (96.47%) number of supplementary alignments = 489,079 (0.12%) number of secondary alignments = 0 number of mapped bases = 32,112,482,006 bp number of sequenced bases = 32,104,585,979 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 142,744,235 duplication rate = 36.12% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 50.2247 >>>>>>> ACTG content number of A's = 8,640,315,743 bp (26.91%) number of C's = 7,466,183,812 bp (23.26%) number of T's = 8,862,227,787 bp (27.6%) number of G's = 7,074,807,616 bp (22.04%) number of N's = 61,051,021 bp (0.19%) GC percentage = 45.29% >>>>>>> Mismatches and indels general error rate = 0.008 number of mismatches = 247,966,819 number of insertions = 2,834,739 mapped reads with insertion percentage = 0.73% number of deletions = 3,367,995 mapped reads with deletion percentage = 0.87% homopolymer indels = 39.59% >>>>>>> Coverage mean coverageData = 10.3733X std coverageData = 74.6122X There is a 89.51% of reference with a coverageData >= 1X There is a 87.31% of reference with a coverageData >= 2X There is a 83.73% of reference with a coverageData >= 3X There is a 79.77% of reference with a coverageData >= 4X There is a 74.88% of reference with a coverageData >= 5X There is a 69.6% of reference with a coverageData >= 6X There is a 63.84% of reference with a coverageData >= 7X There is a 57.94% of reference with a coverageData >= 8X There is a 51.96% of reference with a coverageData >= 9X There is a 46.15% of reference with a coverageData >= 10X There is a 40.58% of reference with a coverageData >= 11X There is a 35.38% of reference with a coverageData >= 12X There is a 30.6% of reference with a coverageData >= 13X There is a 26.28% of reference with a coverageData >= 14X There is a 22.43% of reference with a coverageData >= 15X There is a 19.05% of reference with a coverageData >= 16X There is a 16.11% of reference with a coverageData >= 17X There is a 13.59% of reference with a coverageData >= 18X There is a 11.44% of reference with a coverageData >= 19X There is a 9.63% of reference with a coverageData >= 20X There is a 8.11% of reference with a coverageData >= 21X There is a 6.85% of reference with a coverageData >= 22X There is a 5.8% of reference with a coverageData >= 23X There is a 4.94% of reference with a coverageData >= 24X There is a 4.22% of reference with a coverageData >= 25X There is a 3.64% of reference with a coverageData >= 26X There is a 3.15% of reference with a coverageData >= 27X There is a 2.76% of reference with a coverageData >= 28X There is a 2.43% of reference with a coverageData >= 29X There is a 2.15% of reference with a coverageData >= 30X There is a 1.93% of reference with a coverageData >= 31X There is a 1.74% of reference with a coverageData >= 32X There is a 1.58% of reference with a coverageData >= 33X There is a 1.44% of reference with a coverageData >= 34X There is a 1.32% of reference with a coverageData >= 35X There is a 1.22% of reference with a coverageData >= 36X There is a 1.13% of reference with a coverageData >= 37X There is a 1.05% of reference with a coverageData >= 38X There is a 0.98% of reference with a coverageData >= 39X There is a 0.91% of reference with a coverageData >= 40X There is a 0.86% of reference with a coverageData >= 41X There is a 0.8% of reference with a coverageData >= 42X There is a 0.76% of reference with a coverageData >= 43X There is a 0.71% of reference with a coverageData >= 44X There is a 0.67% of reference with a coverageData >= 45X There is a 0.63% of reference with a coverageData >= 46X There is a 0.6% of reference with a coverageData >= 47X There is a 0.57% of reference with a coverageData >= 48X There is a 0.54% of reference with a coverageData >= 49X There is a 0.51% of reference with a coverageData >= 50X There is a 0.48% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 2697073612 10.82072975858303 189.93798322613253 chr2 243199373 2600266233 10.691911746828394 52.59142990843253 chr3 198022430 2001003827 10.104935218702245 19.395927054943055 chr4 191154276 1887162886 9.872459698468896 53.19975174072293 chr5 180915260 1875928259 10.369099096449906 11.384228350195105 chr6 171115067 1660814580 9.705834846209072 23.305983260113294 chr7 159138663 1710788179 10.75029880702215 66.16852117081798 chr8 146364022 1608475849 10.989557590867514 38.618259491108546 chr9 141213431 1321058775 9.355050476749623 46.908412209362254 chr10 135534747 1656046874 12.21861486191434 138.08694928771328 chr11 135006516 1503500526 11.136503411435342 31.60060616627431 chr12 133851895 1410481844 10.53763074478699 10.661259881449267 chr13 115169878 879737159 7.6386045924265025 7.149851223519772 chr14 107349540 956597775 8.911056116309394 11.959585758402765 chr15 102531392 1001491217 9.767654544278498 9.991186863844597 chr16 90354753 1157415031 12.809675114711453 54.06911363436808 chr17 81195210 1050788683 12.941510749217843 35.877216627754045 chr18 78077248 790333462 10.122455417486027 104.288333354703 chr19 59128983 876389974 14.821664935451368 124.56777636967264 chr20 63025520 770896932 12.231504508015165 20.419210586048674 chr21 48129895 454498916 9.443172813902876 44.030643142886035 chr22 51304566 509395682 9.928856663557003 13.68603477158613 chrMT 16571 5408009 326.35381087441914 96.41403407468047 chrX 155270560 1589169856 10.234843334113048 19.328632088352467 chrY 59373566 137757866 2.320188516216122 92.91389647791075