BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524866.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 917,376 number of mapped reads = 824,363 (89.86%) number of supplementary alignments = 4,036 (0.44%) number of secondary alignments = 0 number of mapped bases = 46,958,285 bp number of sequenced bases = 46,942,357 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 22,026 duplication rate = 1.87% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.2258 >>>>>>> ACTG content number of A's = 12,080,931 bp (25.74%) number of C's = 8,314,520 bp (17.71%) number of T's = 15,581,534 bp (33.19%) number of G's = 10,964,357 bp (23.36%) number of N's = 1,015 bp (0%) GC percentage = 41.07% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 250,116 number of insertions = 3,258 mapped reads with insertion percentage = 0.39% number of deletions = 10,155 mapped reads with deletion percentage = 1.22% homopolymer indels = 41.64% >>>>>>> Coverage mean coverageData = 0.0152X std coverageData = 0.1849X There is a 1.42% of reference with a coverageData >= 1X There is a 0.06% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% 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 4443835 0.017828782059483815 0.3101174314162188 chr2 243199373 3921350 0.01612401360919627 0.2401316554320938 chr3 198022430 3730326 0.018837896292859348 0.14429983894263948 chr4 191154276 2734797 0.014306752939180916 0.12777498151996622 chr5 180915260 2174313 0.012018405744214169 0.11567117538470752 chr6 171115067 3033345 0.017726931083164057 0.15032216471904555 chr7 159138663 3492487 0.021946187897783204 0.3250189352195383 chr8 146364022 2715555 0.01855343248219839 0.17928683428212192 chr9 141213431 1569120 0.011111690926906238 0.13954622580623763 chr10 135534747 2459798 0.018148836770249033 0.1967135158931369 chr11 135006516 2129881 0.015776134834854932 0.15311069190141738 chr12 133851895 2109439 0.015759500453841165 0.133789648853779 chr13 115169878 1503230 0.013052284382900884 0.11981478634966088 chr14 107349540 1731296 0.016127651781274517 0.13426762849155788 chr15 102531392 1254103 0.012231405187593669 0.11787577287942526 chr16 90354753 1264433 0.013994095031171189 0.13263744376936903 chr17 81195210 804339 0.009906237079748916 0.10666070208608266 chr18 78077248 1002089 0.012834584026322239 0.21905753556870444 chr19 59128983 758337 0.012825131797041055 0.2099339889050218 chr20 63025520 1022818 0.01622863246507129 0.13413995270150694 chr21 48129895 645576 0.013413201919513848 0.12233268488210544 chr22 51304566 341562 0.006657536095325317 0.08487204451328334 chrMT 16571 65167 3.9325930843039045 3.0134413609559765 chrX 155270560 1927601 0.012414465433756405 0.12606960581343254 chrY 59373566 123488 0.0020798481263530643 0.06836509612240439