BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818833.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 2,357,106 number of mapped reads = 2,249,986 (95.46%) number of supplementary alignments = 36,068 (1.53%) number of secondary alignments = 0 number of mapped bases = 208,377,618 bp number of sequenced bases = 208,247,454 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 641,931 duplication rate = 24.62% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.3434 >>>>>>> ACTG content number of A's = 59,284,242 bp (28.47%) number of C's = 43,624,095 bp (20.95%) number of T's = 60,111,055 bp (28.87%) number of G's = 45,225,324 bp (21.72%) number of N's = 2,738 bp (0%) GC percentage = 42.67% >>>>>>> Mismatches and indels general error rate = 0.0063 number of mismatches = 1,245,066 number of insertions = 28,194 mapped reads with insertion percentage = 1.21% number of deletions = 66,599 mapped reads with deletion percentage = 2.89% homopolymer indels = 41.49% >>>>>>> Coverage mean coverageData = 0.0673X std coverageData = 0.7844X There is a 4.21% of reference with a coverageData >= 1X There is a 1.4% of reference with a coverageData >= 2X There is a 0.52% of reference with a coverageData >= 3X There is a 0.21% of reference with a coverageData >= 4X There is a 0.09% of reference with a coverageData >= 5X There is a 0.05% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% 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 19749311 0.07923475143518298 1.1959966309174102 chr2 243199373 15703901 0.06457212782370125 1.1250050038510921 chr3 198022430 13374710 0.06754138912445423 0.3801277638098381 chr4 191154276 10657006 0.05575081145451332 0.4834629297833437 chr5 180915260 9294570 0.051375268178040924 0.3466469503117162 chr6 171115067 10341386 0.06043527423566973 0.40181033061579824 chr7 159138663 18810885 0.11820436747039907 1.6624848371192236 chr8 146364022 18205758 0.1243868387273479 0.6652097622190838 chr9 141213431 7708461 0.05458730763364853 0.6139737313364887 chr10 135534747 9640266 0.07112763489350815 1.0733241409384526 chr11 135006516 9156271 0.06782095613814669 0.4713426686100372 chr12 133851895 8123321 0.06068887556653568 0.3620239761159819 chr13 115169878 6408281 0.05564198826363261 0.34027230960389127 chr14 107349540 6127100 0.057076164462372174 0.39342595097302674 chr15 102531392 5807196 0.056638224515668335 0.34181686631331226 chr16 90354753 5232232 0.05790765650147923 0.8059356434789168 chr17 81195210 5139179 0.06329411550262633 0.4926887858313219 chr18 78077248 3219238 0.041231448116613945 0.7494954444582261 chr19 59128983 3605939 0.060984289210588995 0.9848023840973569 chr20 63025520 8567755 0.13594104419923866 0.591289767765549 chr21 48129895 2022272 0.04201696263829373 0.40717599129789156 chr22 51304566 1901140 0.03705596106202321 0.3536224145594789 chrMT 16571 314868 19.001146581377103 12.134637240710594 chrX 155270560 8464172 0.05451240724577795 0.4069646433817877 chrY 59373566 802400 0.013514431658021013 1.02423809824304