BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472630.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 17,145,816 number of mapped reads = 17,037,177 (99.37%) number of supplementary alignments = 86,315 (0.5%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,541,473 number of mapped paired reads (second in pair) = 8,495,704 number of mapped paired reads (both in pair) = 16,960,140 number of mapped paired reads (singletons) = 77,037 number of mapped bases = 1,679,666,082 bp number of sequenced bases = 1,679,432,883 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,622,506 duplication rate = 49.64% >>>>>>> Insert size mean insert size = 22,190.1845 std insert size = 1,503,689.4427 median insert size = 224 >>>>>>> Mapping quality mean mapping quality = 54.9763 >>>>>>> ACTG content number of A's = 448,026,693 bp (26.68%) number of C's = 393,721,975 bp (23.44%) number of T's = 447,616,013 bp (26.65%) number of G's = 389,757,028 bp (23.21%) number of N's = 311,174 bp (0.02%) GC percentage = 46.65% >>>>>>> Mismatches and indels general error rate = 0.0062 number of mismatches = 10,165,426 number of insertions = 99,944 mapped reads with insertion percentage = 0.58% number of deletions = 93,650 mapped reads with deletion percentage = 0.54% homopolymer indels = 45.48% >>>>>>> Coverage mean coverageData = 0.5426X std coverageData = 22.2383X There is a 3.42% of reference with a coverageData >= 1X There is a 1.53% of reference with a coverageData >= 2X There is a 0.75% of reference with a coverageData >= 3X There is a 0.57% of reference with a coverageData >= 4X There is a 0.45% of reference with a coverageData >= 5X There is a 0.41% of reference with a coverageData >= 6X There is a 0.37% of reference with a coverageData >= 7X There is a 0.35% of reference with a coverageData >= 8X There is a 0.33% of reference with a coverageData >= 9X There is a 0.32% of reference with a coverageData >= 10X There is a 0.31% of reference with a coverageData >= 11X There is a 0.3% of reference with a coverageData >= 12X There is a 0.29% of reference with a coverageData >= 13X There is a 0.28% of reference with a coverageData >= 14X There is a 0.27% of reference with a coverageData >= 15X There is a 0.27% of reference with a coverageData >= 16X There is a 0.26% of reference with a coverageData >= 17X There is a 0.25% of reference with a coverageData >= 18X There is a 0.25% of reference with a coverageData >= 19X There is a 0.24% of reference with a coverageData >= 20X There is a 0.24% of reference with a coverageData >= 21X There is a 0.23% of reference with a coverageData >= 22X There is a 0.23% of reference with a coverageData >= 23X There is a 0.22% of reference with a coverageData >= 24X There is a 0.22% of reference with a coverageData >= 25X There is a 0.22% of reference with a coverageData >= 26X There is a 0.21% of reference with a coverageData >= 27X There is a 0.21% of reference with a coverageData >= 28X There is a 0.21% of reference with a coverageData >= 29X There is a 0.2% of reference with a coverageData >= 30X There is a 0.2% of reference with a coverageData >= 31X There is a 0.2% of reference with a coverageData >= 32X There is a 0.19% of reference with a coverageData >= 33X There is a 0.19% of reference with a coverageData >= 34X There is a 0.19% of reference with a coverageData >= 35X There is a 0.19% of reference with a coverageData >= 36X There is a 0.18% of reference with a coverageData >= 37X There is a 0.18% of reference with a coverageData >= 38X There is a 0.18% of reference with a coverageData >= 39X There is a 0.18% of reference with a coverageData >= 40X There is a 0.17% of reference with a coverageData >= 41X There is a 0.17% of reference with a coverageData >= 42X There is a 0.17% of reference with a coverageData >= 43X There is a 0.17% of reference with a coverageData >= 44X There is a 0.16% of reference with a coverageData >= 45X There is a 0.16% of reference with a coverageData >= 46X There is a 0.16% of reference with a coverageData >= 47X There is a 0.16% of reference with a coverageData >= 48X There is a 0.16% of reference with a coverageData >= 49X There is a 0.16% of reference with a coverageData >= 50X There is a 0.15% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 252506076 1.0130609704679532 30.77949350857312 chr2 243199373 88227663 0.36277915486237705 15.887665867399667 chr3 198022430 157727914 0.7965153947459386 24.2897200267812 chr4 191154276 26652973 0.13943173837241288 5.661717082881121 chr5 180915260 82277637 0.45478550012862373 21.25421010722935 chr6 171115067 151730106 0.8867138859256619 31.71967803525156 chr7 159138663 75439867 0.47405115499807865 16.874906971165046 chr8 146364022 84551819 0.577681713337995 19.534657669181577 chr9 141213431 94642735 0.6702105764996249 35.450605278933544 chr10 135534747 33806356 0.24942943966981396 20.340454031434913 chr11 135006516 59608072 0.4415199633771751 17.530118793292285 chr12 133851895 52175909 0.3898032896732616 15.746446347156757 chr13 115169878 39595543 0.3438012064230892 13.38443321911016 chr14 107349540 35642529 0.33202311812421365 16.117794610094666 chr15 102531392 25526439 0.24896218126054506 9.889108032156198 chr16 90354753 63969971 0.7079867840488702 23.76880215198501 chr17 81195210 88844802 1.0942123556303383 41.30186491827252 chr18 78077248 16531210 0.21172890212523884 8.617241031468986 chr19 59128983 43353175 0.7331966964491846 24.041921844246357 chr20 63025520 72600565 1.1519233002758247 31.374432238655494 chr21 48129895 10284959 0.2136916982677814 12.284144978306408 chr22 51304566 15000253 0.29237656936811435 9.605170311807676 chrMT 16571 5987 0.3612938265644801 0.9417804853845255 chrX 155270560 108106189 0.6962439563559247 23.366902553594063 chrY 59373566 857333 0.014439641371717509 0.7807143997721757