BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975213.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP029757/SRP029757.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 = 3,065,678 number of mapped reads = 3,033,203 (98.94%) number of supplementary alignments = 178,074 (5.81%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,518,406 number of mapped paired reads (second in pair) = 1,514,797 number of mapped paired reads (both in pair) = 3,024,450 number of mapped paired reads (singletons) = 8,753 number of mapped bases = 412,956,644 bp number of sequenced bases = 412,714,920 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 701,448 duplication rate = 23.14% >>>>>>> Insert size mean insert size = 248,694.0678 std insert size = 4,888,941.4243 median insert size = 151 >>>>>>> Mapping quality mean mapping quality = 52.6623 >>>>>>> ACTG content number of A's = 115,845,356 bp (28.07%) number of C's = 90,026,633 bp (21.81%) number of T's = 114,215,513 bp (27.67%) number of G's = 92,603,020 bp (22.44%) number of N's = 24,398 bp (0.01%) GC percentage = 44.25% >>>>>>> Mismatches and indels general error rate = 0.0108 number of mismatches = 4,211,482 number of insertions = 90,783 mapped reads with insertion percentage = 2.82% number of deletions = 93,169 mapped reads with deletion percentage = 2.93% homopolymer indels = 40.27% >>>>>>> Coverage mean coverageData = 0.1334X std coverageData = 2.6211X There is a 7.1% of reference with a coverageData >= 1X There is a 4.84% of reference with a coverageData >= 2X There is a 0.37% of reference with a coverageData >= 3X There is a 0.21% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% 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 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% 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 35989884 0.1443923543925694 6.632532031745279 chr2 243199373 33655962 0.1383883584272234 1.667044520730991 chr3 198022430 23021816 0.11625862787362018 0.6013983824156365 chr4 191154276 24221197 0.12671020239170586 1.5516756434018995 chr5 180915260 25344206 0.14008882390573354 0.5346576896927 chr6 171115067 20732347 0.12116026579938749 0.7421357371455076 chr7 159138663 24825379 0.15599841378584411 1.878080264449154 chr8 146364022 19923736 0.13612454568924048 2.155765759874384 chr9 141213431 16184253 0.11460845392248843 2.732189291699267 chr10 135534747 22891136 0.16889496241137336 5.677149470930999 chr11 135006516 18292844 0.13549600820748534 0.9352990414431831 chr12 133851895 17469815 0.13051600801019664 0.5060560057823258 chr13 115169878 11212311 0.09735454438876805 0.43011310815956993 chr14 107349540 12354855 0.115089966850347 0.4969118387772989 chr15 102531392 10726224 0.10461404834921191 0.4453492105469961 chr16 90354753 14810562 0.16391569351088814 1.5914843803041459 chr17 81195210 14390441 0.1772326347822735 1.1105450968358865 chr18 78077248 9547548 0.12228335711832466 2.905848508099814 chr19 59128983 11241701 0.19012167011226966 3.3617320005448623 chr20 63025520 9002152 0.14283344270701773 0.8035178646684012 chr21 48129895 5475033 0.11375534893645622 0.9708906898140205 chr22 51304566 6143102 0.11973791962298248 0.48289961295219336 chrMT 16571 713158 43.03650956490254 13.431609073231282 chrX 155270560 23023195 0.14827791565896328 0.7500887096152973 chrY 59373566 1763787 0.029706603777175856 1.7767521253733438