BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617416.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP017032/SRP017032.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 = 32,000,000 number of mapped reads = 29,550,050 (92.34%) number of supplementary alignments = 467,402 (1.46%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 14,985,327 number of mapped paired reads (second in pair) = 14,564,723 number of mapped paired reads (both in pair) = 28,869,148 number of mapped paired reads (singletons) = 680,902 number of mapped bases = 2,903,969,000 bp number of sequenced bases = 2,903,308,519 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,364,152 duplication rate = 4.14% >>>>>>> Insert size mean insert size = 60,127.0554 std insert size = 2,359,178.2661 median insert size = 213 >>>>>>> Mapping quality mean mapping quality = 53.8389 >>>>>>> ACTG content number of A's = 865,173,619 bp (29.8%) number of C's = 584,107,199 bp (20.12%) number of T's = 858,563,626 bp (29.57%) number of G's = 594,844,626 bp (20.49%) number of N's = 619,449 bp (0.02%) GC percentage = 40.61% >>>>>>> Mismatches and indels general error rate = 0.0108 number of mismatches = 30,941,021 number of insertions = 248,922 mapped reads with insertion percentage = 0.83% number of deletions = 293,324 mapped reads with deletion percentage = 0.97% homopolymer indels = 44.37% >>>>>>> Coverage mean coverageData = 0.9381X std coverageData = 2.8841X There is a 29.4% of reference with a coverageData >= 1X There is a 16.77% of reference with a coverageData >= 2X There is a 10.7% of reference with a coverageData >= 3X There is a 7.38% of reference with a coverageData >= 4X There is a 5.35% of reference with a coverageData >= 5X There is a 4.02% of reference with a coverageData >= 6X There is a 3.1% of reference with a coverageData >= 7X There is a 2.45% of reference with a coverageData >= 8X There is a 1.97% of reference with a coverageData >= 9X There is a 1.61% of reference with a coverageData >= 10X There is a 1.33% of reference with a coverageData >= 11X There is a 1.11% of reference with a coverageData >= 12X There is a 0.94% of reference with a coverageData >= 13X There is a 0.8% of reference with a coverageData >= 14X There is a 0.69% of reference with a coverageData >= 15X There is a 0.6% of reference with a coverageData >= 16X There is a 0.52% of reference with a coverageData >= 17X There is a 0.46% of reference with a coverageData >= 18X There is a 0.4% of reference with a coverageData >= 19X There is a 0.35% of reference with a coverageData >= 20X There is a 0.31% of reference with a coverageData >= 21X There is a 0.28% of reference with a coverageData >= 22X There is a 0.25% of reference with a coverageData >= 23X There is a 0.22% of reference with a coverageData >= 24X There is a 0.2% of reference with a coverageData >= 25X There is a 0.18% of reference with a coverageData >= 26X There is a 0.16% of reference with a coverageData >= 27X There is a 0.15% of reference with a coverageData >= 28X There is a 0.14% 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 0.1% of reference with a coverageData >= 32X There is a 0.09% of reference with a coverageData >= 33X There is a 0.09% of reference with a coverageData >= 34X There is a 0.08% of reference with a coverageData >= 35X There is a 0.07% of reference with a coverageData >= 36X There is a 0.07% of reference with a coverageData >= 37X There is a 0.06% of reference with a coverageData >= 38X There is a 0.06% of reference with a coverageData >= 39X There is a 0.05% of reference with a coverageData >= 40X There is a 0.05% of reference with a coverageData >= 41X There is a 0.05% of reference with a coverageData >= 42X There is a 0.04% of reference with a coverageData >= 43X There is a 0.04% of reference with a coverageData >= 44X There is a 0.04% of reference with a coverageData >= 45X There is a 0.04% of reference with a coverageData >= 46X There is a 0.03% of reference with a coverageData >= 47X There is a 0.03% of reference with a coverageData >= 48X There is a 0.03% of reference with a coverageData >= 49X There is a 0.03% of reference with a coverageData >= 50X There is a 0.03% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 186843954 0.7496228224041215 2.691025761580749 chr2 243199373 289315147 1.189621270117337 3.0574923642944527 chr3 198022430 245047104 1.2374714520976235 3.37286652563735 chr4 191154276 139284886 0.7286516886496434 2.238724168176609 chr5 180915260 185383987 1.0247006637251053 2.8164104918718817 chr6 171115067 132991641 0.7772059078818583 2.562963735962103 chr7 159138663 217218843 1.3649658662772604 3.1888633392112755 chr8 146364022 128574351 0.8784559842172143 3.214050932558385 chr9 141213431 115773474 0.8198474690413832 2.5625767642966806 chr10 135534747 93132442 0.6871480860919008 2.383020097497157 chr11 135006516 215925884 1.5993737961506984 3.7842942253859193 chr12 133851895 138293215 1.0331808526132558 2.7516551307336226 chr13 115169878 125913975 1.0932891237411921 2.7268104366004176 chr14 107349540 84253363 0.7848507129140936 2.8554088741172805 chr15 102531392 66762125 0.6511383850128554 2.34259528593267 chr16 90354753 73330877 0.8115884838952523 3.267651208130928 chr17 81195210 90032772 1.1088433911310778 3.6218054613446395 chr18 78077248 41414686 0.5304321945363648 1.9490344379608817 chr19 59128983 41880713 0.7082941541544863 2.3249658397685775 chr20 63025520 99518713 1.5790224816867833 4.684313822904477 chr21 48129895 39643147 0.8236699248980286 2.477849655251101 chr22 51304566 23733091 0.46259217941732517 2.0741347886839354 chrMT 16571 183330 11.063303361293826 5.2537655293618055 chrX 155270560 127180418 0.8190890662080436 2.5205387761257825 chrY 59373566 2336862 0.03935862636244554 0.6014003522886827