BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084275.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 = 2,815,066 number of mapped reads = 2,553,144 (90.7%) number of supplementary alignments = 18,111 (0.64%) number of secondary alignments = 0 number of mapped bases = 168,265,872 bp number of sequenced bases = 168,209,027 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 87,666 duplication rate = 2.75% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.1742 >>>>>>> ACTG content number of A's = 45,683,586 bp (27.16%) number of C's = 32,521,956 bp (19.33%) number of T's = 51,277,094 bp (30.48%) number of G's = 38,500,041 bp (22.89%) number of N's = 226,350 bp (0.13%) GC percentage = 42.22% >>>>>>> Mismatches and indels general error rate = 0.0102 number of mismatches = 1,698,915 number of insertions = 12,617 mapped reads with insertion percentage = 0.49% number of deletions = 35,189 mapped reads with deletion percentage = 1.37% homopolymer indels = 45.52% >>>>>>> Coverage mean coverageData = 0.0544X std coverageData = 0.3711X There is a 4.61% of reference with a coverageData >= 1X There is a 0.61% of reference with a coverageData >= 2X There is a 0.11% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% 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 16512207 0.0662474056584196 0.5611911472452606 chr2 243199373 16129876 0.06632367428019643 0.45014926419943235 chr3 198022430 10964045 0.05536769243766981 0.2736165312866409 chr4 191154276 7928526 0.04147710512110124 0.2430615082675354 chr5 180915260 8366631 0.04624613202888468 0.24486936915280236 chr6 171115067 8190321 0.04786440576854638 0.29024366895438686 chr7 159138663 9711373 0.0610245984032177 0.5982712338698539 chr8 146364022 8051289 0.05500866189643244 0.33067064163268106 chr9 141213431 6248174 0.04424631535225569 0.304299346412227 chr10 135534747 12106887 0.08932681299799822 0.5611435789007481 chr11 135006516 8183985 0.06061918522510425 0.3530124826176719 chr12 133851895 8760005 0.06544550601991851 0.2946843276307051 chr13 115169878 3979017 0.03454911187802075 0.21398442624205993 chr14 107349540 4640098 0.04322420012232935 0.24602891005161062 chr15 102531392 3824337 0.0372991815033585 0.23103131714930925 chr16 90354753 3714527 0.041110477054815256 0.25848009604324274 chr17 81195210 4874156 0.06003009290819003 0.3003839437242779 chr18 78077248 4348348 0.055692895323359755 0.49129669220258354 chr19 59128983 3392914 0.05738157207946567 0.4439612130987917 chr20 63025520 3526565 0.055954556186129045 0.2757571966027662 chr21 48129895 1736049 0.03607007661246716 0.22619265972022992 chr22 51304566 1887036 0.036781053756501904 0.21812399488960382 chrMT 16571 47853 2.8877557178202884 2.243357392937498 chrX 155270560 10767012 0.0693435510247403 0.33494895845988315 chrY 59373566 374641 0.006309895551835307 0.12247983355248199