BamQC report ----------------------------------- >>>>>>> Input bam file = SRR630500.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP017516/SRP017516.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 = 102,227,202 number of mapped reads = 101,897,372 (99.68%) number of supplementary alignments = 614,736 (0.6%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 51,053,582 number of mapped paired reads (second in pair) = 50,843,790 number of mapped paired reads (both in pair) = 101,661,542 number of mapped paired reads (singletons) = 235,830 number of mapped bases = 10,167,566,110 bp number of sequenced bases = 10,165,442,000 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 19,784,281 duplication rate = 16.4% >>>>>>> Insert size mean insert size = 47,904.0515 std insert size = 2,050,338.9052 median insert size = 307 >>>>>>> Mapping quality mean mapping quality = 53.7952 >>>>>>> ACTG content number of A's = 3,183,571,835 bp (31.32%) number of C's = 1,897,892,336 bp (18.67%) number of T's = 3,173,517,543 bp (31.22%) number of G's = 1,909,598,919 bp (18.79%) number of N's = 861,367 bp (0.01%) GC percentage = 37.46% >>>>>>> Mismatches and indels general error rate = 0.0079 number of mismatches = 78,839,893 number of insertions = 868,570 mapped reads with insertion percentage = 0.84% number of deletions = 943,394 mapped reads with deletion percentage = 0.9% homopolymer indels = 44.94% >>>>>>> Coverage mean coverageData = 3.2844X std coverageData = 13.0868X There is a 35.54% of reference with a coverageData >= 1X There is a 25.05% of reference with a coverageData >= 2X There is a 19.78% of reference with a coverageData >= 3X There is a 16.44% of reference with a coverageData >= 4X There is a 14.07% of reference with a coverageData >= 5X There is a 12.29% of reference with a coverageData >= 6X There is a 10.89% of reference with a coverageData >= 7X There is a 9.76% of reference with a coverageData >= 8X There is a 8.83% of reference with a coverageData >= 9X There is a 8.05% of reference with a coverageData >= 10X There is a 7.38% of reference with a coverageData >= 11X There is a 6.8% of reference with a coverageData >= 12X There is a 6.3% of reference with a coverageData >= 13X There is a 5.85% of reference with a coverageData >= 14X There is a 5.45% of reference with a coverageData >= 15X There is a 5.1% of reference with a coverageData >= 16X There is a 4.78% of reference with a coverageData >= 17X There is a 4.5% of reference with a coverageData >= 18X There is a 4.23% of reference with a coverageData >= 19X There is a 4% of reference with a coverageData >= 20X There is a 3.78% of reference with a coverageData >= 21X There is a 3.58% of reference with a coverageData >= 22X There is a 3.39% of reference with a coverageData >= 23X There is a 3.22% of reference with a coverageData >= 24X There is a 3.06% of reference with a coverageData >= 25X There is a 2.92% of reference with a coverageData >= 26X There is a 2.78% of reference with a coverageData >= 27X There is a 2.65% of reference with a coverageData >= 28X There is a 2.53% of reference with a coverageData >= 29X There is a 2.42% of reference with a coverageData >= 30X There is a 2.32% of reference with a coverageData >= 31X There is a 2.22% of reference with a coverageData >= 32X There is a 2.13% of reference with a coverageData >= 33X There is a 2.04% of reference with a coverageData >= 34X There is a 1.96% of reference with a coverageData >= 35X There is a 1.88% of reference with a coverageData >= 36X There is a 1.81% of reference with a coverageData >= 37X There is a 1.74% of reference with a coverageData >= 38X There is a 1.67% of reference with a coverageData >= 39X There is a 1.61% of reference with a coverageData >= 40X There is a 1.56% of reference with a coverageData >= 41X There is a 1.5% of reference with a coverageData >= 42X There is a 1.45% of reference with a coverageData >= 43X There is a 1.4% of reference with a coverageData >= 44X There is a 1.35% of reference with a coverageData >= 45X There is a 1.31% of reference with a coverageData >= 46X There is a 1.26% of reference with a coverageData >= 47X There is a 1.22% of reference with a coverageData >= 48X There is a 1.18% of reference with a coverageData >= 49X There is a 1.15% of reference with a coverageData >= 50X There is a 1.11% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 834693214 3.3488109704649442 18.161058020365505 chr2 243199373 936934251 3.8525356354434352 14.146256069156042 chr3 198022430 791341907 3.996223594468566 13.57656555041221 chr4 191154276 824346384 4.312466355709459 14.79752574449428 chr5 180915260 641959979 3.5484014947108387 12.270643356801806 chr6 171115067 642631385 3.755551140332955 13.280458355019622 chr7 159138663 522936616 3.2860437943983483 12.615976377129776 chr8 146364022 552704344 3.776230910079801 13.622774703494246 chr9 141213431 457750158 3.241548305699052 12.941817097070004 chr10 135534747 432900022 3.194015052095829 12.114564735038222 chr11 135006516 424513984 3.144396260103475 12.421136268325387 chr12 133851895 492783332 3.6815566339199006 12.717105412242184 chr13 115169878 351483224 3.0518676419888195 10.651154967650925 chr14 107349540 307729699 2.866614044177553 10.297319018542831 chr15 102531392 305062479 2.9753080793051168 15.200711190881874 chr16 90354753 142549960 1.5776697436160332 6.213866760420918 chr17 81195210 139509959 1.7182043004753607 6.518545087151356 chr18 78077248 258392751 3.309450033382324 11.58175904075794 chr19 59128983 50345160 0.8514464048874306 3.614228243089933 chr20 63025520 159505140 2.530802443200786 10.579568267673178 chr21 48129895 105558057 2.1931910925631564 9.732552971970888 chr22 51304566 56385607 1.0990368186722406 6.707467618685461 chrMT 16571 80 0.00482771106149297 0.06931381007706695 chrX 155270560 727945918 4.688241724638592 16.45240084285768 chrY 59373566 7602500 0.12804519775686035 1.6862012659199375