BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006379.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP030642/SRP030642.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 = 8,845,598 number of mapped reads = 4,007,222 (45.3%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,033,063 number of mapped paired reads (second in pair) = 1,974,159 number of mapped paired reads (both in pair) = 3,586,656 number of mapped paired reads (singletons) = 420,566 number of mapped bases = 155,052,857 bp number of sequenced bases = 155,033,108 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 191,485 duplication rate = 4.18% >>>>>>> Insert size mean insert size = 89,079.0526 std insert size = 2,900,663.1073 median insert size = 161 >>>>>>> Mapping quality mean mapping quality = 47.9278 >>>>>>> ACTG content number of A's = 43,564,462 bp (28.1%) number of C's = 33,317,145 bp (21.49%) number of T's = 44,040,066 bp (28.41%) number of G's = 34,105,008 bp (22%) number of N's = 6,427 bp (0%) GC percentage = 43.49% >>>>>>> Mismatches and indels general error rate = 0.0038 number of mismatches = 580,399 number of insertions = 4,431 mapped reads with insertion percentage = 0.11% number of deletions = 14,841 mapped reads with deletion percentage = 0.37% homopolymer indels = 42.37% >>>>>>> Coverage mean coverageData = 0.0501X std coverageData = 0.4155X There is a 4.35% of reference with a coverageData >= 1X There is a 0.51% of reference with a coverageData >= 2X There is a 0.07% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 12562279 0.0504001913800648 0.41318677378131996 chr2 243199373 13110129 0.053906919406408176 0.6361202970957922 chr3 198022430 10347562 0.05225449460447486 0.25361889692673756 chr4 191154276 10105133 0.05286375597478133 0.28259771887473634 chr5 180915260 9707279 0.05365649641716238 0.8418563918662239 chr6 171115067 8787373 0.051353590037749274 0.37821052455340665 chr7 159138663 8448858 0.05309117118823601 0.3309139197508553 chr8 146364022 7697628 0.052592350871582365 0.7104648211389009 chr9 141213431 6386965 0.04522916095707639 0.2578917919239472 chr10 135534747 7550271 0.05570727187766839 0.347266592156489 chr11 135006516 7084075 0.05247209697641557 0.3004962820156946 chr12 133851895 6762449 0.050521877183733556 0.25031099734293843 chr13 115169878 4777351 0.04148090701285626 0.22649330183172345 chr14 107349540 4834815 0.04503805978115975 0.2616281851325677 chr15 102531392 4552168 0.04439779770082513 0.23502917807859455 chr16 90354753 4470697 0.04947937824587933 0.28078681153315815 chr17 81195210 4253087 0.05238100868265505 0.28354677833078673 chr18 78077248 3933867 0.05038429377019026 0.3775172639999607 chr19 59128983 3143114 0.05315690953115158 0.3299443313787973 chr20 63025520 3538347 0.056141496333548695 0.27364692890956643 chr21 48129895 2017657 0.04192107628740931 0.2967198391398796 chr22 51304566 1938793 0.03778987234781403 0.22273207855866278 chrMT 16571 2473 0.14923661818840142 0.6955958526335235 chrX 155270560 8639891 0.05564410278419811 0.2740567752594574 chrY 59373566 400596 0.00674704295174051 0.17180425533483984