BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472575.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 9,173,020 number of mapped reads = 8,327,893 (90.79%) number of supplementary alignments = 247,268 (2.7%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 4,205,111 number of mapped paired reads (second in pair) = 4,122,782 number of mapped paired reads (both in pair) = 8,115,790 number of mapped paired reads (singletons) = 212,103 number of mapped bases = 678,204,276 bp number of sequenced bases = 677,909,446 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,256,104 duplication rate = 12.6% >>>>>>> Insert size mean insert size = 227,284.0045 std insert size = 4,606,816.2643 median insert size = 131 >>>>>>> Mapping quality mean mapping quality = 50.352 >>>>>>> ACTG content number of A's = 172,895,391 bp (25.5%) number of C's = 135,447,435 bp (19.98%) number of T's = 202,158,277 bp (29.82%) number of G's = 166,951,760 bp (24.63%) number of N's = 456,583 bp (0.07%) GC percentage = 44.61% >>>>>>> Mismatches and indels general error rate = 0.0124 number of mismatches = 8,274,644 number of insertions = 66,444 mapped reads with insertion percentage = 0.78% number of deletions = 155,374 mapped reads with deletion percentage = 1.83% homopolymer indels = 42.17% >>>>>>> Coverage mean coverageData = 0.2191X std coverageData = 2.3865X There is a 12.15% of reference with a coverageData >= 1X There is a 5.35% of reference with a coverageData >= 2X There is a 1.87% of reference with a coverageData >= 3X There is a 0.89% of reference with a coverageData >= 4X There is a 0.41% of reference with a coverageData >= 5X There is a 0.22% of reference with a coverageData >= 6X There is a 0.12% of reference with a coverageData >= 7X There is a 0.07% of reference with a coverageData >= 8X There is a 0.05% of reference with a coverageData >= 9X There is a 0.03% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.02% 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% 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 44347033 0.17792145440632623 3.0121386736585456 chr2 243199373 68232124 0.2805604437146308 3.27015514762082 chr3 198022430 35664239 0.18010201672608503 0.632686024666117 chr4 191154276 34277673 0.1793194152769044 1.3201986369623195 chr5 180915260 32001492 0.17688663742350977 0.6802266861078309 chr6 171115067 44807708 0.2618571747396154 1.270549418773219 chr7 159138663 57808292 0.36325736882683246 4.39064967169146 chr8 146364022 33447444 0.22852230721016945 1.8929058384731412 chr9 141213431 23552238 0.16678468778228325 2.419308037388514 chr10 135534747 26823433 0.19790816446501353 2.1016321649995207 chr11 135006516 24543979 0.18179847704535979 1.7132812827520767 chr12 133851895 34648413 0.25885635014730274 0.7981500124771533 chr13 115169878 31947038 0.2773905690861286 0.8360892289875349 chr14 107349540 17487019 0.16289794068982502 6.021169459560773 chr15 102531392 15820391 0.15429802220962727 0.6010974398060202 chr16 90354753 24803476 0.2745121333019415 1.2200317249108354 chr17 81195210 25724372 0.3168213001727565 1.9684899177475081 chr18 78077248 15127548 0.19375103999567198 4.178143534750656 chr19 59128983 14169876 0.2396434925998981 2.0718263285958836 chr20 63025520 23329024 0.3701520273057644 1.3641059376395355 chr21 48129895 10282376 0.21363803099923653 0.9204213003333911 chr22 51304566 7359854 0.14345417131099014 0.5832236951104144 chrMT 16571 31685 1.9120753122925593 2.4084697399110024 chrX 155270560 30410019 0.19585180217035347 1.0615234806076617 chrY 59373566 1557530 0.026232717772080593 0.9986948881971895