BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716988.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 = 1,719,304 number of mapped reads = 1,573,142 (91.5%) number of supplementary alignments = 9,281 (0.54%) number of secondary alignments = 0 number of mapped bases = 91,337,258 bp number of sequenced bases = 91,311,605 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 51,986 duplication rate = 2.34% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.3173 >>>>>>> ACTG content number of A's = 22,623,344 bp (24.78%) number of C's = 16,853,159 bp (18.46%) number of T's = 28,078,496 bp (30.75%) number of G's = 23,755,436 bp (26.02%) number of N's = 1,170 bp (0%) GC percentage = 44.47% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 459,314 number of insertions = 6,153 mapped reads with insertion percentage = 0.39% number of deletions = 16,358 mapped reads with deletion percentage = 1.03% homopolymer indels = 40.38% >>>>>>> Coverage mean coverageData = 0.0295X std coverageData = 0.2744X There is a 2.65% of reference with a coverageData >= 1X There is a 0.21% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% 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 6476634 0.0259844247288756 0.3834039756591861 chr2 243199373 8309797 0.03416866128186934 0.3528540626696832 chr3 198022430 6712668 0.03389852351574516 0.20624888792092197 chr4 191154276 5380406 0.028146929865173406 0.19738510758311684 chr5 180915260 4945249 0.027334615112069596 0.17967019101400322 chr6 171115067 5534660 0.03234466781350119 0.21326725126365845 chr7 159138663 5299569 0.03330158052163603 0.513240517958904 chr8 146364022 6680268 0.04564146235336441 0.3067771306574245 chr9 141213431 3872175 0.027420727423583383 0.2082038501396777 chr10 135534747 4531391 0.03343342648509168 0.3477264648891297 chr11 135006516 2943684 0.021804014259578404 0.2042808362714428 chr12 133851895 4480492 0.0334735044281592 0.21365673612627448 chr13 115169878 2467732 0.02142688733246726 0.15897501043566262 chr14 107349540 2398152 0.022339657906312406 0.1706941511522458 chr15 102531392 2416767 0.023570995700516774 0.17061423119601543 chr16 90354753 2997092 0.03317027494945396 0.2070277575317674 chr17 81195210 3642752 0.04486412437383929 0.23786400621474238 chr18 78077248 2129178 0.02727014661172484 0.32040560350146474 chr19 59128983 1986490 0.033595876323460526 0.33571804892070506 chr20 63025520 2201101 0.034923964133893697 0.21136698047435312 chr21 48129895 866360 0.018000454810882093 0.1543686584097757 chr22 51304566 1225687 0.023890407727062732 0.16685679840135928 chrMT 16571 196879 11.88093657594593 7.402710948443868 chrX 155270560 3437106 0.022136237545610706 0.18331869412679264 chrY 59373566 204969 0.003452192849592359 0.09683979452469714