BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975252.sorted.bam outfile = /mainsd/zhouyj/SRP029757/SRP029757.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 = 132,652,904 number of mapped reads = 131,486,058 (99.12%) number of supplementary alignments = 309,658 (0.23%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 65,739,490 number of mapped paired reads (second in pair) = 65,746,568 number of mapped paired reads (both in pair) = 130,963,562 number of mapped paired reads (singletons) = 522,496 number of mapped bases = 11,987,880,234 bp number of sequenced bases = 11,983,660,335 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 88,606,916 duplication rate = 47.89% >>>>>>> Insert size mean insert size = 61,761.6072 std insert size = 2,413,518.585 median insert size = 182 >>>>>>> Mapping quality mean mapping quality = 55.7516 >>>>>>> ACTG content number of A's = 3,300,015,626 bp (27.54%) number of C's = 2,545,173,114 bp (21.24%) number of T's = 3,345,666,244 bp (27.92%) number of G's = 2,792,473,664 bp (23.3%) number of N's = 331,687 bp (0%) GC percentage = 44.54% >>>>>>> Mismatches and indels general error rate = 0.006 number of mismatches = 69,092,919 number of insertions = 1,304,173 mapped reads with insertion percentage = 0.98% number of deletions = 2,785,528 mapped reads with deletion percentage = 2.09% homopolymer indels = 47.03% >>>>>>> Coverage mean coverageData = 3.8724X std coverageData = 62.5066X There is a 25.56% of reference with a coverageData >= 1X There is a 15.29% of reference with a coverageData >= 2X There is a 9.55% of reference with a coverageData >= 3X There is a 6.87% of reference with a coverageData >= 4X There is a 5.13% of reference with a coverageData >= 5X There is a 4.16% of reference with a coverageData >= 6X There is a 3.49% of reference with a coverageData >= 7X There is a 3.06% of reference with a coverageData >= 8X There is a 2.74% of reference with a coverageData >= 9X There is a 2.52% of reference with a coverageData >= 10X There is a 2.35% of reference with a coverageData >= 11X There is a 2.22% of reference with a coverageData >= 12X There is a 2.11% of reference with a coverageData >= 13X There is a 2.03% of reference with a coverageData >= 14X There is a 1.95% of reference with a coverageData >= 15X There is a 1.89% of reference with a coverageData >= 16X There is a 1.84% of reference with a coverageData >= 17X There is a 1.79% of reference with a coverageData >= 18X There is a 1.75% of reference with a coverageData >= 19X There is a 1.71% of reference with a coverageData >= 20X There is a 1.67% of reference with a coverageData >= 21X There is a 1.64% of reference with a coverageData >= 22X There is a 1.6% of reference with a coverageData >= 23X There is a 1.57% of reference with a coverageData >= 24X There is a 1.55% of reference with a coverageData >= 25X There is a 1.52% of reference with a coverageData >= 26X There is a 1.49% of reference with a coverageData >= 27X There is a 1.47% of reference with a coverageData >= 28X There is a 1.45% of reference with a coverageData >= 29X There is a 1.43% of reference with a coverageData >= 30X There is a 1.41% of reference with a coverageData >= 31X There is a 1.39% of reference with a coverageData >= 32X There is a 1.37% of reference with a coverageData >= 33X There is a 1.35% of reference with a coverageData >= 34X There is a 1.33% of reference with a coverageData >= 35X There is a 1.31% of reference with a coverageData >= 36X There is a 1.3% of reference with a coverageData >= 37X There is a 1.28% of reference with a coverageData >= 38X There is a 1.26% of reference with a coverageData >= 39X There is a 1.25% of reference with a coverageData >= 40X There is a 1.23% of reference with a coverageData >= 41X There is a 1.22% of reference with a coverageData >= 42X There is a 1.2% of reference with a coverageData >= 43X There is a 1.19% of reference with a coverageData >= 44X There is a 1.18% of reference with a coverageData >= 45X There is a 1.16% of reference with a coverageData >= 46X There is a 1.15% of reference with a coverageData >= 47X There is a 1.14% of reference with a coverageData >= 48X There is a 1.13% of reference with a coverageData >= 49X There is a 1.12% of reference with a coverageData >= 50X There is a 1.1% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1213092762 4.8669598379857195 56.45860003165478 chr2 243199373 941116141 3.8697309511566873 47.674495497270144 chr3 198022430 686904224 3.4688202947514584 44.64589696063678 chr4 191154276 532648320 2.78648393928682 146.88342310466209 chr5 180915260 640167893 3.5384958294839253 47.47883714038786 chr6 171115067 1042653415 6.093288179000625 76.73110066491995 chr7 159138663 600300302 3.772183897259461 51.526673503089235 chr8 146364022 519150483 3.5469815321144975 46.57135291942245 chr9 141213431 465204881 3.294338772917429 45.47511318653306 chr10 135534747 475326852 3.507047915911925 49.33725975291974 chr11 135006516 615376806 4.558126705528791 54.21750783787083 chr12 133851895 658139937 4.916926555279624 56.94915261835227 chr13 115169878 333986788 2.899949134269292 45.079472529522214 chr14 107349540 387517595 3.6098673082343904 48.571417474292886 chr15 102531392 347287911 3.3871373852019877 44.72202664596116 chr16 90354753 369433684 4.088702273360207 49.51601969644026 chr17 81195210 469067575 5.777035061551045 59.96330274629552 chr18 78077248 270860914 3.469140126455277 51.5997493584444 chr19 59128983 387428996 6.552268893243099 95.1728179865641 chr20 63025520 293787962 4.661412742013076 58.72131202170996 chr21 48129895 121692982 2.5284281629951613 38.4716428684928 chr22 51304566 147392632 2.872895016790513 47.810510156432166 chrMT 16571 462689 27.921610041639006 31.093362803420124 chrX 155270560 449378543 2.894164502272678 40.7418137823377 chrY 59373566 19499947 0.32842809205699386 8.550026226349262