BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081105.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,288,202 number of mapped reads = 2,108,158 (92.13%) number of supplementary alignments = 17,718 (0.77%) number of secondary alignments = 0 number of mapped bases = 145,051,380 bp number of sequenced bases = 144,994,278 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 90,582 duplication rate = 3.01% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.9461 >>>>>>> ACTG content number of A's = 41,589,438 bp (28.68%) number of C's = 27,127,136 bp (18.71%) number of T's = 45,482,526 bp (31.37%) number of G's = 30,793,499 bp (21.24%) number of N's = 1,679 bp (0%) GC percentage = 39.95% >>>>>>> Mismatches and indels general error rate = 0.0093 number of mismatches = 1,317,070 number of insertions = 12,601 mapped reads with insertion percentage = 0.59% number of deletions = 34,299 mapped reads with deletion percentage = 1.61% homopolymer indels = 47.26% >>>>>>> Coverage mean coverageData = 0.0469X std coverageData = 0.4731X There is a 4% of reference with a coverageData >= 1X There is a 0.47% 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 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 12981032 0.05208023935073767 0.8120355350136018 chr2 243199373 9827617 0.04040971355629276 0.4947550396787589 chr3 198022430 11295250 0.05704025549024926 0.27495337200248565 chr4 191154276 9349579 0.04891116848466419 0.29124605050925606 chr5 180915260 7034574 0.03888325396099809 0.22975797280432597 chr6 171115067 12453142 0.07277642009163343 0.5229118684629307 chr7 159138663 7694039 0.048348018356796175 0.4346919110330409 chr8 146364022 10928901 0.07466931320048037 0.5825186221998745 chr9 141213431 6737590 0.04771210466517169 0.5938595153525719 chr10 135534747 5598299 0.04130526764476124 0.4718355657077522 chr11 135006516 6946098 0.05145009445321883 0.36834504026244114 chr12 133851895 7209516 0.053861889665439554 0.2895460627406292 chr13 115169878 3646457 0.03166155129555664 0.19811984528164403 chr14 107349540 4205429 0.03917510033112392 0.340722479145226 chr15 102531392 3683417 0.0359247731660563 0.2125183403218175 chr16 90354753 3689696 0.040835660300017645 0.35337723711057106 chr17 81195210 3197757 0.03938356708480709 0.23977667315589446 chr18 78077248 3705821 0.04746351971831794 1.1595314000328918 chr19 59128983 2934616 0.04963075383860399 0.5883680500141385 chr20 63025520 2161543 0.03429631362026049 0.2491361267512903 chr21 48129895 3428337 0.07123092622578961 0.37956718924445265 chr22 51304566 1321248 0.02575302946720181 0.17722124136035744 chrMT 16571 227738 13.743165771528574 7.991178610052893 chrX 155270560 4388555 0.028263922021019308 0.24847848722981747 chrY 59373566 405129 0.006823390058801589 0.20198060235472037