BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013250.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 = 1,972,919 number of mapped reads = 1,689,948 (85.66%) number of supplementary alignments = 10,420 (0.53%) number of secondary alignments = 0 number of mapped bases = 112,950,174 bp number of sequenced bases = 112,889,136 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 87,676 duplication rate = 4.1% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.2517 >>>>>>> ACTG content number of A's = 30,999,502 bp (27.46%) number of C's = 21,237,915 bp (18.81%) number of T's = 35,431,125 bp (31.39%) number of G's = 25,219,022 bp (22.34%) number of N's = 1,572 bp (0%) GC percentage = 41.15% >>>>>>> Mismatches and indels general error rate = 0.0079 number of mismatches = 874,472 number of insertions = 8,113 mapped reads with insertion percentage = 0.48% number of deletions = 34,616 mapped reads with deletion percentage = 2.02% homopolymer indels = 48.3% >>>>>>> Coverage mean coverageData = 0.0365X std coverageData = 0.3538X There is a 2.9% of reference with a coverageData >= 1X There is a 0.54% 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% 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 10057598 0.040351345804671035 0.6644225268895978 chr2 243199373 12522726 0.051491604791267284 0.420252024611346 chr3 198022430 6015380 0.030377265848116296 0.21020272242055157 chr4 191154276 6196432 0.032415869159003276 0.23257145951275618 chr5 180915260 7288479 0.040286701077620536 0.24203161182958338 chr6 171115067 7128680 0.04166015374905589 0.31377980562795843 chr7 159138663 5716295 0.03592021506426757 0.49884531835895385 chr8 146364022 6423415 0.04388657070383048 0.3971217959152225 chr9 141213431 4359067 0.03086864308254078 0.3113613225831309 chr10 135534747 6008571 0.04433232903736486 0.35528253415528527 chr11 135006516 5097978 0.03776097740349066 0.3119107221851357 chr12 133851895 5093445 0.03805284191157697 0.24111267336153186 chr13 115169878 2511686 0.021808532262229192 0.17655322506060853 chr14 107349540 3840013 0.03577111741699126 0.23801439398117297 chr15 102531392 2416790 0.023571220022059195 0.18876217557623415 chr16 90354753 4655647 0.051526309855553475 0.28603984173999814 chr17 81195210 2390784 0.029444889667752567 0.23291324126161578 chr18 78077248 2221475 0.02845227075626436 0.5048274336274193 chr19 59128983 2291618 0.03875625596334035 0.41543265729675877 chr20 63025520 2679677 0.042517332661436195 0.25708544770877384 chr21 48129895 2063727 0.042878277627657405 0.2652856609463571 chr22 51304566 1094454 0.021332487248795752 0.17497678614646636 chrMT 16571 16912 1.0205781183996139 1.3294997233743906 chrX 155270560 4634131 0.0298455225510876 0.2313896377392448 chrY 59373566 225194 0.003792832655528893 0.10273227080872911