BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124861.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 1,173,904 number of mapped reads = 1,152,181 (98.15%) number of supplementary alignments = 8,947 (0.76%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 576,447 number of mapped paired reads (second in pair) = 575,734 number of mapped paired reads (both in pair) = 1,148,096 number of mapped paired reads (singletons) = 4,085 number of mapped bases = 156,499,413 bp number of sequenced bases = 156,409,304 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 163,825 duplication rate = 14.63% >>>>>>> Insert size mean insert size = 46,311.402 std insert size = 1,936,986.7627 median insert size = 176 >>>>>>> Mapping quality mean mapping quality = 53.5481 >>>>>>> ACTG content number of A's = 45,980,962 bp (29.4%) number of C's = 31,485,556 bp (20.13%) number of T's = 45,869,461 bp (29.33%) number of G's = 33,059,358 bp (21.14%) number of N's = 13,967 bp (0.01%) GC percentage = 41.27% >>>>>>> Mismatches and indels general error rate = 0.0117 number of mismatches = 1,778,632 number of insertions = 25,464 mapped reads with insertion percentage = 2.14% number of deletions = 50,700 mapped reads with deletion percentage = 4.28% homopolymer indels = 47.9% >>>>>>> Coverage mean coverageData = 0.0506X std coverageData = 0.5805X There is a 3.02% of reference with a coverageData >= 1X There is a 1.57% of reference with a coverageData >= 2X There is a 0.17% of reference with a coverageData >= 3X There is a 0.09% of reference with a coverageData >= 4X There is a 0.02% 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 0.01% 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 7836387 0.03143978927137758 0.7146623329970463 chr2 243199373 12652907 0.05202688988840444 0.5743596178730591 chr3 198022430 7170962 0.03621287750079625 0.2585358930654742 chr4 191154276 6360452 0.03327391954339541 0.3133120487229298 chr5 180915260 9261176 0.05119068452268758 0.3062984776440663 chr6 171115067 18178497 0.10623551343962014 0.718066011420395 chr7 159138663 12895845 0.08103527299333915 1.1046697442720168 chr8 146364022 10177880 0.06953812734115765 0.3883638415604377 chr9 141213431 7285852 0.051594610713764186 0.7713003264830993 chr10 135534747 6775009 0.04998724791953166 0.9337737853683572 chr11 135006516 8454151 0.0626203182667124 0.49676008841057046 chr12 133851895 6673156 0.04985477418903931 0.30071970786211993 chr13 115169878 7056253 0.0612682163299678 0.3848056801113468 chr14 107349540 2672268 0.02489314812154761 0.21867039833608895 chr15 102531392 2517174 0.0245502762705104 0.2097141169598163 chr16 90354753 4902298 0.05425611644359207 0.8146866336199057 chr17 81195210 3498618 0.04308897039616007 0.6919241435343131 chr18 78077248 4240567 0.05431245476274983 0.8559954655634526 chr19 59128983 2488411 0.042084454589722944 0.45868017835510466 chr20 63025520 3113934 0.04940750984680491 0.3121952821511767 chr21 48129895 442996 0.009204175492175913 0.1720730879801282 chr22 51304566 1297702 0.0252940839612599 0.21348436538356816 chrMT 16571 58479 3.528996439563092 2.7586444047781757 chrX 155270560 10246403 0.06599063595829113 0.3952985564642679 chrY 59373566 242036 0.004076494243246229 0.23729584467070639