BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080983.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 = 3,917,180 number of mapped reads = 3,228,494 (82.42%) number of supplementary alignments = 22,592 (0.58%) number of secondary alignments = 0 number of mapped bases = 218,117,095 bp number of sequenced bases = 218,040,786 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 242,851 duplication rate = 6.17% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.4414 >>>>>>> ACTG content number of A's = 61,808,927 bp (28.35%) number of C's = 38,193,667 bp (17.52%) number of T's = 71,501,623 bp (32.79%) number of G's = 46,098,453 bp (21.14%) number of N's = 438,116 bp (0.2%) GC percentage = 38.66% >>>>>>> Mismatches and indels general error rate = 0.0098 number of mismatches = 2,102,859 number of insertions = 16,245 mapped reads with insertion percentage = 0.5% number of deletions = 43,758 mapped reads with deletion percentage = 1.34% homopolymer indels = 49.32% >>>>>>> Coverage mean coverageData = 0.0705X std coverageData = 0.5038X There is a 4.87% of reference with a coverageData >= 1X There is a 1.4% of reference with a coverageData >= 2X There is a 0.45% of reference with a coverageData >= 3X There is a 0.15% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 17771662 0.07130037200589362 0.679861775995414 chr2 243199373 14318697 0.058876373007754425 0.43890526685056513 chr3 198022430 19546585 0.0987089442342466 0.42851566992113205 chr4 191154276 14690936 0.0768538183263031 0.3874718888135348 chr5 180915260 12449154 0.06881207256922385 0.3551429030875944 chr6 171115067 19105772 0.11165452776873237 0.5668414715730026 chr7 159138663 10524511 0.0661342178047581 0.4558851817572502 chr8 146364022 16902697 0.11548396094225943 1.051468381765983 chr9 141213431 10416112 0.07376148236211327 0.5757109565270139 chr10 135534747 9290125 0.0685442309491307 0.4154751200116081 chr11 135006516 9891357 0.07326577481637997 0.41488586469590655 chr12 133851895 11737711 0.08769178053101154 0.4114543870841473 chr13 115169878 5874302 0.05100554157051378 0.3042408717450209 chr14 107349540 6140944 0.05720512635638681 0.3761691013480377 chr15 102531392 5631196 0.05492167706062159 0.3160636323703165 chr16 90354753 3967053 0.04390530512545367 0.32225259236734966 chr17 81195210 4398112 0.054167136214069773 0.3159069098299987 chr18 78077248 5270858 0.06750824516765755 0.9036459101807331 chr19 59128983 3678628 0.06221361865804457 0.5124187554913568 chr20 63025520 3326281 0.052776732345881476 0.32240298723051986 chr21 48129895 4236388 0.08801988867833599 0.4530110669266877 chr22 51304566 1795801 0.035002751996771594 0.24900531275673585 chrMT 16571 13350 0.8056242833866393 1.1492065206510516 chrX 155270560 6694069 0.043112287351832826 0.3063156892640306 chrY 59373566 444794 0.007491448298726069 0.15630544733402285