BamQC report ----------------------------------- >>>>>>> Input bam file = SRR960913.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 = 198,413,316 number of mapped reads = 188,621,312 (95.06%) number of supplementary alignments = 2,973,626 (1.5%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 94,980,140 number of mapped paired reads (second in pair) = 93,641,172 number of mapped paired reads (both in pair) = 183,319,382 number of mapped paired reads (singletons) = 5,301,930 number of mapped bases = 16,020,358,643 bp number of sequenced bases = 16,016,116,758 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 24,634,726 duplication rate = 7.32% >>>>>>> Insert size mean insert size = 159,624.2666 std insert size = 4,092,123.0813 median insert size = 149 >>>>>>> Mapping quality mean mapping quality = 52.2149 >>>>>>> ACTG content number of A's = 4,678,289,681 bp (29.21%) number of C's = 3,269,974,082 bp (20.42%) number of T's = 4,805,444,380 bp (30%) number of G's = 3,261,240,708 bp (20.36%) number of N's = 1,167,907 bp (0.01%) GC percentage = 40.78% >>>>>>> Mismatches and indels general error rate = 0.0172 number of mismatches = 271,508,254 number of insertions = 2,339,909 mapped reads with insertion percentage = 1.22% number of deletions = 2,009,390 mapped reads with deletion percentage = 1.04% homopolymer indels = 36.78% >>>>>>> Coverage mean coverageData = 5.175X std coverageData = 68.8936X There is a 87.94% of reference with a coverageData >= 1X There is a 80.81% of reference with a coverageData >= 2X There is a 70.9% of reference with a coverageData >= 3X There is a 59.68% of reference with a coverageData >= 4X There is a 48.37% of reference with a coverageData >= 5X There is a 37.95% of reference with a coverageData >= 6X There is a 28.94% of reference with a coverageData >= 7X There is a 21.55% of reference with a coverageData >= 8X There is a 15.72% of reference with a coverageData >= 9X There is a 11.29% of reference with a coverageData >= 10X There is a 8.01% of reference with a coverageData >= 11X There is a 5.63% of reference with a coverageData >= 12X There is a 3.94% of reference with a coverageData >= 13X There is a 2.76% of reference with a coverageData >= 14X There is a 1.94% of reference with a coverageData >= 15X There is a 1.38% of reference with a coverageData >= 16X There is a 0.99% of reference with a coverageData >= 17X There is a 0.73% of reference with a coverageData >= 18X There is a 0.55% of reference with a coverageData >= 19X There is a 0.43% of reference with a coverageData >= 20X There is a 0.34% of reference with a coverageData >= 21X There is a 0.28% of reference with a coverageData >= 22X There is a 0.24% of reference with a coverageData >= 23X There is a 0.21% of reference with a coverageData >= 24X There is a 0.18% of reference with a coverageData >= 25X There is a 0.17% of reference with a coverageData >= 26X There is a 0.15% of reference with a coverageData >= 27X There is a 0.14% of reference with a coverageData >= 28X There is a 0.13% of reference with a coverageData >= 29X There is a 0.12% of reference with a coverageData >= 30X There is a 0.11% of reference with a coverageData >= 31X There is a 0.11% of reference with a coverageData >= 32X There is a 0.1% of reference with a coverageData >= 33X There is a 0.1% of reference with a coverageData >= 34X There is a 0.09% of reference with a coverageData >= 35X There is a 0.09% of reference with a coverageData >= 36X There is a 0.08% of reference with a coverageData >= 37X There is a 0.08% of reference with a coverageData >= 38X There is a 0.08% of reference with a coverageData >= 39X There is a 0.07% of reference with a coverageData >= 40X There is a 0.07% of reference with a coverageData >= 41X There is a 0.07% of reference with a coverageData >= 42X There is a 0.07% of reference with a coverageData >= 43X There is a 0.06% of reference with a coverageData >= 44X There is a 0.06% of reference with a coverageData >= 45X There is a 0.06% of reference with a coverageData >= 46X There is a 0.06% of reference with a coverageData >= 47X There is a 0.06% of reference with a coverageData >= 48X There is a 0.06% of reference with a coverageData >= 49X There is a 0.05% of reference with a coverageData >= 50X There is a 0.05% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1475643366 5.920319717077054 177.81964285022983 chr2 243199373 1391203286 5.7204229963208 93.2107392441264 chr3 198022430 1118251674 5.6470960082653265 11.105709500648901 chr4 191154276 980278961 5.128208384938247 29.01260576706745 chr5 180915260 787939954 4.355298464043332 6.751562460919224 chr6 171115067 807342481 4.718126201008354 22.156286846911716 chr7 159138663 910819037 5.72343024523211 46.43552029544858 chr8 146364022 838744696 5.730538724878714 60.52842156744656 chr9 141213431 764758608 5.4156223142825555 52.50179433795596 chr10 135534747 769379311 5.676620409377382 112.07364036894282 chr11 135006516 724019862 5.362851241935611 32.437644696526434 chr12 133851895 598989899 4.475019939015432 6.1869116509851825 chr13 115169878 506754068 4.400057348328527 4.105439149273992 chr14 107349540 353096734 3.2892244717583328 27.125433019412014 chr15 102531392 414133292 4.039087775185965 5.009578248757772 chr16 90354753 551094512 6.099231016657198 58.87184045833585 chr17 81195210 308441701 3.7987672056023993 16.958477777964063 chr18 78077248 623175245 7.981521646357208 64.69765828920303 chr19 59128983 305479000 5.1663158150377795 78.40405434184946 chr20 63025520 293863849 4.662616809825607 13.877952924461049 chr21 48129895 228006226 4.737309857002597 20.842481690476756 chr22 51304566 160805258 3.13432644572025 4.763695938148363 chrMT 16571 3215927 194.06957938567376 40.4009391664606 chrX 155270560 1055512447 6.797891673733901 22.62893958116063 chrY 59373566 49409249 0.8321758709928253 35.473312916227684