BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238298.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 = 3,724,085 number of mapped reads = 3,323,002 (89.23%) number of supplementary alignments = 30,535 (0.82%) number of secondary alignments = 0 number of mapped bases = 217,390,252 bp number of sequenced bases = 217,296,045 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 168,430 duplication rate = 3.87% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.118 >>>>>>> ACTG content number of A's = 59,044,618 bp (27.17%) number of C's = 41,682,568 bp (19.18%) number of T's = 66,504,540 bp (30.61%) number of G's = 50,006,042 bp (23.01%) number of N's = 58,277 bp (0.03%) GC percentage = 42.2% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 1,793,033 number of insertions = 16,626 mapped reads with insertion percentage = 0.5% number of deletions = 56,833 mapped reads with deletion percentage = 1.69% homopolymer indels = 46.06% >>>>>>> Coverage mean coverageData = 0.0702X std coverageData = 0.5526X There is a 5.55% of reference with a coverageData >= 1X There is a 1.03% of reference with a coverageData >= 2X There is a 0.23% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 13365004 0.053620745041192894 0.9197059441193276 chr2 243199373 13380125 0.055017103189653374 0.6383078865753963 chr3 198022430 13720511 0.06928766099880705 0.3179388311923106 chr4 191154276 16653020 0.08711821858486703 0.3879747622245958 chr5 180915260 14617499 0.08079749049361563 0.3480434330142746 chr6 171115067 10959537 0.06404776149840738 0.36808170484932795 chr7 159138663 15025310 0.09441646496678183 0.9910375693264348 chr8 146364022 12643071 0.08638100283961861 0.7276271313173256 chr9 141213431 10411377 0.07372795155724246 0.4804540143841263 chr10 135534747 12491679 0.09216587831901144 0.5536025119827891 chr11 135006516 11797282 0.08738305638521922 0.5461313361988185 chr12 133851895 11831730 0.08839419120663178 0.3678494073404506 chr13 115169878 6143626 0.05334403497414489 0.2794332937016813 chr14 107349540 4106029 0.038249153186869736 0.2719915128258476 chr15 102531392 6886551 0.06716529314261138 0.32835670224713126 chr16 90354753 6916858 0.07655223184551233 0.3731644170027787 chr17 81195210 6173894 0.0760376628128679 0.4314717589703665 chr18 78077248 3473098 0.04448284345267907 0.7897531756898486 chr19 59128983 5159599 0.0872600666918286 0.6473446617648072 chr20 63025520 5443666 0.08637240914474009 0.3672216103032272 chr21 48129895 3286808 0.06829036298541687 0.3484775164047423 chr22 51304566 2852450 0.05559836526051112 0.2904395947676245 chrMT 16571 16244 0.9802667310361475 1.2602937893177855 chrX 155270560 9470377 0.06099274067150914 0.36041157375851063 chrY 59373566 564907 0.009514452946956227 0.32384043244856386