BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231724.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 = 2,429,704 number of mapped reads = 1,794,096 (73.84%) number of supplementary alignments = 8,896 (0.37%) number of secondary alignments = 0 number of mapped bases = 112,155,871 bp number of sequenced bases = 112,086,026 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 86,551 duplication rate = 3.7% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.1382 >>>>>>> ACTG content number of A's = 29,003,016 bp (25.88%) number of C's = 20,615,783 bp (18.39%) number of T's = 35,007,555 bp (31.23%) number of G's = 27,440,765 bp (24.48%) number of N's = 18,907 bp (0.02%) GC percentage = 42.87% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 970,710 number of insertions = 9,095 mapped reads with insertion percentage = 0.5% number of deletions = 39,205 mapped reads with deletion percentage = 2.16% homopolymer indels = 45.93% >>>>>>> Coverage mean coverageData = 0.0362X std coverageData = 0.3392X There is a 3.03% of reference with a coverageData >= 1X There is a 0.42% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.02% 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 10158227 0.04075507198034223 0.5233427488519931 chr2 243199373 7697428 0.031650690152067125 0.41651538867787263 chr3 198022430 10476035 0.05290327464419056 0.27056641994480646 chr4 191154276 4737626 0.024784305635935658 0.21050074371701305 chr5 180915260 6601964 0.03649202394535431 0.22704880463784766 chr6 171115067 7320599 0.042781732364923775 0.30443407673639405 chr7 159138663 6878158 0.043221162414818076 0.5556610504769826 chr8 146364022 4682226 0.03199027968772271 0.36122394052026613 chr9 141213431 4418370 0.03128859605429458 0.2911133957304103 chr10 135534747 5334089 0.039355878238367906 0.30371039937839117 chr11 135006516 5400242 0.03999986193258998 0.403443264709822 chr12 133851895 4225622 0.03156938495342184 0.20924767909132536 chr13 115169878 4274970 0.03711882025263585 0.23677799369170355 chr14 107349540 5454062 0.050806570759408934 0.28144417920153586 chr15 102531392 2647119 0.02581764421963568 0.20670179935155694 chr16 90354753 3246245 0.03592777238846528 0.24685950648347732 chr17 81195210 3152483 0.03882597261587229 0.27248271031787313 chr18 78077248 2121092 0.02716658251069505 0.4792375270644231 chr19 59128983 3094732 0.05233866444142968 0.42022257642931954 chr20 63025520 2767363 0.04390861035339336 0.2668956957832819 chr21 48129895 1789192 0.037174234433713184 0.23634949954076856 chr22 51304566 1139145 0.022203579307151725 0.17138132170574447 chrMT 16571 73479 4.434192263593024 4.117485059663591 chrX 155270560 4087619 0.026325782556590252 0.21686700432899256 chrY 59373566 377784 0.006362831567165765 0.12268655183070439