BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008686.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 = 2,045,106 number of mapped reads = 1,760,750 (86.1%) number of supplementary alignments = 6,795 (0.33%) number of secondary alignments = 0 number of mapped bases = 111,041,866 bp number of sequenced bases = 110,969,452 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 64,208 duplication rate = 2.54% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.3087 >>>>>>> ACTG content number of A's = 28,779,397 bp (25.93%) number of C's = 20,751,369 bp (18.7%) number of T's = 34,238,831 bp (30.85%) number of G's = 27,153,551 bp (24.47%) number of N's = 46,304 bp (0.04%) GC percentage = 43.17% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 955,612 number of insertions = 7,741 mapped reads with insertion percentage = 0.44% number of deletions = 41,422 mapped reads with deletion percentage = 2.32% homopolymer indels = 42.96% >>>>>>> Coverage mean coverageData = 0.0359X std coverageData = 0.3723X There is a 3.17% of reference with a coverageData >= 1X There is a 0.28% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% 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 8884612 0.03564529534311572 0.764583135353449 chr2 243199373 9491092 0.03902597232436122 0.4717282786653731 chr3 198022430 7378463 0.03726074364404073 0.21380505804232347 chr4 191154276 6910456 0.03615119758032512 0.2181499779804713 chr5 180915260 6109942 0.03377239708800684 0.20286703184180374 chr6 171115067 6275610 0.03667479497874959 0.24699665953064076 chr7 159138663 6462740 0.04061074711932197 0.39584727692411087 chr8 146364022 6621556 0.045240325522074 0.3100012386521466 chr9 141213431 3947478 0.027953984065439214 0.34343892153369904 chr10 135534747 5774109 0.042602425782371514 0.4074954399121195 chr11 135006516 4812785 0.03564853862312838 0.32240703300862184 chr12 133851895 4802325 0.03587790072004584 0.21400309137177068 chr13 115169878 3296658 0.028624307477342296 0.18330195165235516 chr14 107349540 3731784 0.034762924927298246 0.22987191346488053 chr15 102531392 3153621 0.030757614214386164 0.19227385488336418 chr16 90354753 3249713 0.035966154431300364 0.25575401737411263 chr17 81195210 3406987 0.04196044323304293 0.26604781672085454 chr18 78077248 2600350 0.033304836768836936 0.5884793813265827 chr19 59128983 2519271 0.042606364462585124 0.5175580831340852 chr20 63025520 2395173 0.038003224725476285 0.22168418821441424 chr21 48129895 1228042 0.02551516058782177 0.190005271067981 chr22 51304566 1444470 0.028154803999316552 0.18257520449776912 chrMT 16571 332189 20.046406372578602 10.585799478222661 chrX 155270560 5874284 0.037832567873781094 0.258847481307878 chrY 59373566 338156 0.005695396500186632 0.15951875340076704