BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1777286.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP052908/SRP052908.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 = 257,508,860 number of mapped reads = 254,295,719 (98.75%) number of supplementary alignments = 938,063 (0.36%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 127,413,293 number of mapped paired reads (second in pair) = 126,882,426 number of mapped paired reads (both in pair) = 253,214,136 number of mapped paired reads (singletons) = 1,081,583 number of mapped bases = 24,594,588,682 bp number of sequenced bases = 24,587,628,149 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 33,372,451 duplication rate = 8.48% >>>>>>> Insert size mean insert size = 108,298.2179 std insert size = 3,225,564.0875 median insert size = 166 >>>>>>> Mapping quality mean mapping quality = 53.5664 >>>>>>> ACTG content number of A's = 7,132,987,598 bp (29.01%) number of C's = 5,136,556,023 bp (20.89%) number of T's = 7,018,516,322 bp (28.54%) number of G's = 5,264,299,787 bp (21.41%) number of N's = 35,268,419 bp (0.14%) GC percentage = 42.3% >>>>>>> Mismatches and indels general error rate = 0.0092 number of mismatches = 220,655,799 number of insertions = 2,453,223 mapped reads with insertion percentage = 0.94% number of deletions = 2,944,700 mapped reads with deletion percentage = 1.13% homopolymer indels = 43.09% >>>>>>> Coverage mean coverageData = 7.9448X std coverageData = 98.0632X There is a 91.7% of reference with a coverageData >= 1X There is a 90.08% of reference with a coverageData >= 2X There is a 87.03% of reference with a coverageData >= 3X There is a 82.28% of reference with a coverageData >= 4X There is a 75.77% of reference with a coverageData >= 5X There is a 67.71% of reference with a coverageData >= 6X There is a 58.57% of reference with a coverageData >= 7X There is a 48.98% of reference with a coverageData >= 8X There is a 39.57% of reference with a coverageData >= 9X There is a 30.91% of reference with a coverageData >= 10X There is a 23.36% of reference with a coverageData >= 11X There is a 17.12% of reference with a coverageData >= 12X There is a 12.19% of reference with a coverageData >= 13X There is a 8.47% of reference with a coverageData >= 14X There is a 5.76% of reference with a coverageData >= 15X There is a 3.86% of reference with a coverageData >= 16X There is a 2.57% of reference with a coverageData >= 17X There is a 1.72% of reference with a coverageData >= 18X There is a 1.17% of reference with a coverageData >= 19X There is a 0.82% of reference with a coverageData >= 20X There is a 0.6% of reference with a coverageData >= 21X There is a 0.46% of reference with a coverageData >= 22X There is a 0.38% of reference with a coverageData >= 23X There is a 0.32% of reference with a coverageData >= 24X There is a 0.28% of reference with a coverageData >= 25X There is a 0.25% of reference with a coverageData >= 26X There is a 0.23% of reference with a coverageData >= 27X There is a 0.22% of reference with a coverageData >= 28X There is a 0.2% of reference with a coverageData >= 29X There is a 0.19% of reference with a coverageData >= 30X There is a 0.18% of reference with a coverageData >= 31X There is a 0.17% of reference with a coverageData >= 32X There is a 0.16% of reference with a coverageData >= 33X There is a 0.16% of reference with a coverageData >= 34X There is a 0.15% of reference with a coverageData >= 35X There is a 0.14% of reference with a coverageData >= 36X There is a 0.14% of reference with a coverageData >= 37X There is a 0.13% of reference with a coverageData >= 38X There is a 0.13% of reference with a coverageData >= 39X There is a 0.12% of reference with a coverageData >= 40X There is a 0.12% of reference with a coverageData >= 41X There is a 0.11% of reference with a coverageData >= 42X There is a 0.11% of reference with a coverageData >= 43X There is a 0.1% of reference with a coverageData >= 44X There is a 0.1% of reference with a coverageData >= 45X There is a 0.1% of reference with a coverageData >= 46X There is a 0.1% of reference with a coverageData >= 47X There is a 0.09% of reference with a coverageData >= 48X There is a 0.09% of reference with a coverageData >= 49X There is a 0.09% of reference with a coverageData >= 50X There is a 0.08% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 2061939216 8.272553976906641 232.73373112735166 chr2 243199373 2108145032 8.668381854750917 59.029853549041825 chr3 198022430 1612582140 8.143431731445776 21.729018146860366 chr4 191154276 1593010453 8.333637553574789 62.09886321038207 chr5 180915260 1467053265 8.109063132651166 8.654126813135589 chr6 171115067 1413436384 8.260151538847248 50.7962122131492 chr7 159138663 1331472724 8.366745697744111 80.62530536654937 chr8 146364022 1220317103 8.337548301316836 29.75331294928116 chr9 141213431 1060471668 7.5097082514764475 87.32282207889502 chr10 135534747 1364931892 10.070715607710545 256.6785745375576 chr11 135006516 1158172693 8.578642922686784 52.78872481536827 chr12 133851895 1099083119 8.211188336183062 7.884326026553279 chr13 115169878 759909556 6.598162377145177 4.916363065453172 chr14 107349540 747379793 6.962114537239749 8.785443335817176 chr15 102531392 712522257 6.949308334758588 5.339116193500362 chr16 90354753 783671250 8.673270901421201 39.77199762437436 chr17 81195210 735449654 9.057796069497202 52.352682093202354 chr18 78077248 680244881 8.712459755241373 112.29088638067873 chr19 59128983 542618125 9.176855367189386 109.14871891370213 chr20 63025520 542404542 8.60610974728967 16.879613810318272 chr21 48129895 345218646 7.172644901884785 29.652941636566293 chr22 51304566 325598173 6.346378078707459 12.440628716525607 chrMT 16571 27275171 1645.9580592601533 176.7619065150903 chrX 155270560 661092328 4.257679807427757 23.56042195842324 chrY 59373566 240588617 4.052116677647423 72.03488076249981