BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240195.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,886,971 number of mapped reads = 1,538,451 (81.53%) number of supplementary alignments = 8,539 (0.45%) number of secondary alignments = 0 number of mapped bases = 95,761,905 bp number of sequenced bases = 95,713,469 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 123,902 duplication rate = 6.79% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.986 >>>>>>> ACTG content number of A's = 26,553,750 bp (27.74%) number of C's = 16,989,660 bp (17.75%) number of T's = 30,742,234 bp (32.12%) number of G's = 21,402,565 bp (22.36%) number of N's = 25,260 bp (0.03%) GC percentage = 40.11% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 859,553 number of insertions = 6,613 mapped reads with insertion percentage = 0.43% number of deletions = 28,198 mapped reads with deletion percentage = 1.81% homopolymer indels = 49.14% >>>>>>> Coverage mean coverageData = 0.0309X std coverageData = 0.2969X There is a 2.3% of reference with a coverageData >= 1X There is a 0.54% of reference with a coverageData >= 2X There is a 0.14% of reference with a coverageData >= 3X There is a 0.04% 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 7025519 0.028186565681615695 0.43559168872432463 chr2 243199373 10623691 0.043683052587475214 0.3589058692040046 chr3 198022430 6624425 0.03345290227980739 0.23647383406326059 chr4 191154276 6539985 0.034213124272459386 0.24510226433460341 chr5 180915260 5344052 0.029538978635633057 0.22156765407636053 chr6 171115067 5279670 0.03085450096571566 0.2525593592126723 chr7 159138663 5445391 0.03421790090067553 0.4779809615900292 chr8 146364022 5390134 0.036826905453582026 0.371986166313101 chr9 141213431 3646745 0.025824349526639572 0.2590845958997576 chr10 135534747 4247442 0.031338399148669975 0.26334122742292737 chr11 135006516 4319471 0.031994537211818726 0.26768625027261145 chr12 133851895 4494086 0.03357506443969284 0.23537480695531404 chr13 115169878 2578155 0.02238567101720816 0.19229975448753847 chr14 107349540 3215488 0.029953439949533086 0.22781719741296885 chr15 102531392 2517162 0.024550159233183922 0.20992138559825566 chr16 90354753 2555215 0.028279807261495142 0.2207605559964661 chr17 81195210 2330744 0.028705437180345985 0.2244736200896334 chr18 78077248 2215590 0.028376896685702858 0.3994308500898573 chr19 59128983 1593619 0.026951571279350432 0.31491098279899427 chr20 63025520 1909486 0.030297028886076625 0.22777736883445635 chr21 48129895 1368215 0.028427550070491532 0.22099866105749008 chr22 51304566 871658 0.016989871817646794 0.16247612140732284 chrMT 16571 49252 2.972180315008147 3.6486042686659896 chrX 155270560 5367991 0.03457185315748201 0.258154259514813 chrY 59373566 208719 0.0035153522697289226 0.08249021810319358