BamQC report ----------------------------------- >>>>>>> Input bam file = SRR961014.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 = 392,604,452 number of mapped reads = 379,708,747 (96.72%) number of supplementary alignments = 6,441,337 (1.64%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 193,874,601 number of mapped paired reads (second in pair) = 185,834,146 number of mapped paired reads (both in pair) = 370,736,568 number of mapped paired reads (singletons) = 8,972,179 number of mapped bases = 37,206,862,612 bp number of sequenced bases = 37,196,069,049 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 61,908,043 duplication rate = 11.31% >>>>>>> Insert size mean insert size = 85,806.0454 std insert size = 2,817,499.5658 median insert size = 142 >>>>>>> Mapping quality mean mapping quality = 53.1541 >>>>>>> ACTG content number of A's = 10,867,428,938 bp (29.22%) number of C's = 7,685,762,191 bp (20.66%) number of T's = 10,804,561,837 bp (29.05%) number of G's = 7,749,483,380 bp (20.83%) number of N's = 88,832,703 bp (0.24%) GC percentage = 41.5% >>>>>>> Mismatches and indels general error rate = 0.0119 number of mismatches = 430,395,749 number of insertions = 3,761,225 mapped reads with insertion percentage = 0.96% number of deletions = 4,421,602 mapped reads with deletion percentage = 1.13% homopolymer indels = 40.63% >>>>>>> Coverage mean coverageData = 12.0189X std coverageData = 149.5041X There is a 91.31% of reference with a coverageData >= 1X There is a 90.51% of reference with a coverageData >= 2X There is a 89.05% of reference with a coverageData >= 3X There is a 86.85% of reference with a coverageData >= 4X There is a 83.78% of reference with a coverageData >= 5X There is a 79.86% of reference with a coverageData >= 6X There is a 75.15% of reference with a coverageData >= 7X There is a 69.81% of reference with a coverageData >= 8X There is a 64.02% of reference with a coverageData >= 9X There is a 57.97% of reference with a coverageData >= 10X There is a 51.85% of reference with a coverageData >= 11X There is a 45.85% of reference with a coverageData >= 12X There is a 40.1% of reference with a coverageData >= 13X There is a 34.71% of reference with a coverageData >= 14X There is a 29.76% of reference with a coverageData >= 15X There is a 25.29% of reference with a coverageData >= 16X There is a 21.31% of reference with a coverageData >= 17X There is a 17.84% of reference with a coverageData >= 18X There is a 14.83% of reference with a coverageData >= 19X There is a 12.26% of reference with a coverageData >= 20X There is a 10.09% of reference with a coverageData >= 21X There is a 8.28% of reference with a coverageData >= 22X There is a 6.77% of reference with a coverageData >= 23X There is a 5.53% of reference with a coverageData >= 24X There is a 4.51% of reference with a coverageData >= 25X There is a 3.68% of reference with a coverageData >= 26X There is a 3% of reference with a coverageData >= 27X There is a 2.46% of reference with a coverageData >= 28X There is a 2.02% of reference with a coverageData >= 29X There is a 1.66% of reference with a coverageData >= 30X There is a 1.38% of reference with a coverageData >= 31X There is a 1.15% of reference with a coverageData >= 32X There is a 0.96% of reference with a coverageData >= 33X There is a 0.81% of reference with a coverageData >= 34X There is a 0.69% of reference with a coverageData >= 35X There is a 0.59% of reference with a coverageData >= 36X There is a 0.52% of reference with a coverageData >= 37X There is a 0.45% of reference with a coverageData >= 38X There is a 0.4% of reference with a coverageData >= 39X There is a 0.36% of reference with a coverageData >= 40X There is a 0.32% of reference with a coverageData >= 41X There is a 0.3% of reference with a coverageData >= 42X There is a 0.27% of reference with a coverageData >= 43X There is a 0.25% of reference with a coverageData >= 44X There is a 0.24% of reference with a coverageData >= 45X There is a 0.22% of reference with a coverageData >= 46X There is a 0.21% of reference with a coverageData >= 47X There is a 0.2% of reference with a coverageData >= 48X There is a 0.19% of reference with a coverageData >= 49X There is a 0.18% of reference with a coverageData >= 50X There is a 0.17% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 3440501137 13.803380401607907 380.0876130887279 chr2 243199373 3146377419 12.937440504832223 88.90959389637905 chr3 198022430 2521963938 12.735748864408945 32.86357540736585 chr4 191154276 2228525896 11.658258149558737 101.9113757966826 chr5 180915260 1789351058 9.890547972570142 14.816542863925871 chr6 171115067 1827909490 10.682340965334163 46.152715059412074 chr7 159138663 2100303053 13.197943311865075 94.21998251896495 chr8 146364022 1914435937 13.079962622235128 132.44855231147503 chr9 141213431 1770710791 12.539251956848211 116.43553832623219 chr10 135534747 1847045575 13.627837996406928 330.23254992038943 chr11 135006516 1686001789 12.48829937215771 63.59787902353396 chr12 133851895 1395235100 10.423723175529192 12.677593873964971 chr13 115169878 1139212384 9.891582797369987 7.3458774433743335 chr14 107349540 818113643 7.621026070535561 12.018547649895002 chr15 102531392 981662691 9.574264738354474 7.411228671085499 chr16 90354753 1383328641 15.309970920954209 155.18256858652094 chr17 81195210 791878161 9.752769418294504 37.74610803030294 chr18 78077248 1416743603 18.14540905693807 145.35562811843798 chr19 59128983 819647202 13.862020965251508 185.44027786734628 chr20 63025520 724408429 11.493890554175515 36.74401588536071 chr21 48129895 521170395 10.82841329697478 55.077231703881935 chr22 51304566 426969900 8.322259270256763 9.805284854164091 chrMT 16571 8326759 502.4898316335767 88.31871512725553 chrX 155270560 2378479144 15.318287922707306 48.89425065389229 chrY 59373566 128560477 2.1652813812800127 114.87957021114849