BamQC report ----------------------------------- >>>>>>> Input bam file = SRR2046542.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP058890/SRP058890.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 = 7,738,976 number of mapped reads = 7,622,439 (98.49%) number of supplementary alignments = 42,890 (0.55%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 3,857,548 number of mapped paired reads (second in pair) = 3,764,891 number of mapped paired reads (both in pair) = 7,518,894 number of mapped paired reads (singletons) = 103,545 number of mapped bases = 729,449,314 bp number of sequenced bases = 729,253,059 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 5,033,493 duplication rate = 36.41% >>>>>>> Insert size mean insert size = 32,911.7578 std insert size = 1,917,240.0726 median insert size = 134 >>>>>>> Mapping quality mean mapping quality = 53.1385 >>>>>>> ACTG content number of A's = 214,827,795 bp (29.46%) number of C's = 151,007,448 bp (20.71%) number of T's = 213,095,969 bp (29.22%) number of G's = 150,259,284 bp (20.6%) number of N's = 62,563 bp (0.01%) GC percentage = 41.31% >>>>>>> Mismatches and indels general error rate = 0.0045 number of mismatches = 3,124,187 number of insertions = 66,136 mapped reads with insertion percentage = 0.85% number of deletions = 72,135 mapped reads with deletion percentage = 0.92% homopolymer indels = 47.94% >>>>>>> Coverage mean coverageData = 0.2356X std coverageData = 16.3502X There is a 3.38% of reference with a coverageData >= 1X There is a 1.81% of reference with a coverageData >= 2X There is a 0.41% of reference with a coverageData >= 3X There is a 0.29% of reference with a coverageData >= 4X There is a 0.14% of reference with a coverageData >= 5X There is a 0.12% of reference with a coverageData >= 6X There is a 0.1% of reference with a coverageData >= 7X There is a 0.09% of reference with a coverageData >= 8X There is a 0.09% of reference with a coverageData >= 9X There is a 0.08% of reference with a coverageData >= 10X There is a 0.08% of reference with a coverageData >= 11X There is a 0.08% of reference with a coverageData >= 12X There is a 0.07% of reference with a coverageData >= 13X There is a 0.07% of reference with a coverageData >= 14X There is a 0.07% of reference with a coverageData >= 15X There is a 0.07% of reference with a coverageData >= 16X There is a 0.07% of reference with a coverageData >= 17X There is a 0.06% of reference with a coverageData >= 18X There is a 0.06% of reference with a coverageData >= 19X There is a 0.06% of reference with a coverageData >= 20X There is a 0.06% of reference with a coverageData >= 21X There is a 0.06% of reference with a coverageData >= 22X There is a 0.06% of reference with a coverageData >= 23X There is a 0.06% of reference with a coverageData >= 24X There is a 0.06% of reference with a coverageData >= 25X There is a 0.05% of reference with a coverageData >= 26X There is a 0.05% of reference with a coverageData >= 27X There is a 0.05% of reference with a coverageData >= 28X There is a 0.05% of reference with a coverageData >= 29X There is a 0.05% of reference with a coverageData >= 30X There is a 0.05% of reference with a coverageData >= 31X There is a 0.05% of reference with a coverageData >= 32X There is a 0.05% of reference with a coverageData >= 33X There is a 0.05% of reference with a coverageData >= 34X There is a 0.05% of reference with a coverageData >= 35X There is a 0.05% of reference with a coverageData >= 36X There is a 0.05% of reference with a coverageData >= 37X There is a 0.05% of reference with a coverageData >= 38X There is a 0.05% 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 0.04% 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 0.04% of reference with a coverageData >= 47X There is a 0.04% of reference with a coverageData >= 48X There is a 0.04% of reference with a coverageData >= 49X There is a 0.04% of reference with a coverageData >= 50X There is a 0.04% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 123895737 0.49707293206703784 27.43575221031723 chr2 243199373 63895496 0.26272886813733687 14.933019202907637 chr3 198022430 43829045 0.22133373981927199 11.678938357019446 chr4 191154276 22948274 0.12005106283889773 8.510543473907559 chr5 180915260 43962186 0.24299877191122518 17.599776374669243 chr6 171115067 46571713 0.27216605654018766 14.78720733440289 chr7 159138663 44913132 0.2822264002557317 22.312085812150958 chr8 146364022 58767214 0.4015140688057889 21.4662632067331 chr9 141213431 14267678 0.10103626757712586 6.228728578938817 chr10 135534747 32535889 0.24005570320649952 17.810069934870313 chr11 135006516 26889511 0.1991719495968624 11.519251585395793 chr12 133851895 13083681 0.09774744690764371 6.419701350200843 chr13 115169878 17162272 0.14901701988431384 7.005453872980809 chr14 107349540 31070898 0.2894367130031484 17.862421647986835 chr15 102531392 17768942 0.17330245550552947 8.977285649348469 chr16 90354753 23912803 0.2646546219876225 15.722799136024655 chr17 81195210 47473985 0.5846894786034792 36.58094076499313 chr18 78077248 4463256 0.05716461727749421 1.7733495151231295 chr19 59128983 6864922 0.11610079611888471 5.681871378668742 chr20 63025520 16102823 0.25549686857006493 18.504367319310404 chr21 48129895 3510200 0.07293180257301621 6.366145229138719 chr22 51304566 4354894 0.08488316614938328 5.13751972546488 chrMT 16571 37234 2.246937420795365 2.3092555945341813 chrX 155270560 21001878 0.13525988442367953 13.085802676184638 chrY 59373566 165651 0.0027899789613445147 0.13650502102858836