BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716703.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 = 3,255,396 number of mapped reads = 2,879,299 (88.45%) number of supplementary alignments = 10,462 (0.32%) number of secondary alignments = 0 number of mapped bases = 163,450,553 bp number of sequenced bases = 163,403,906 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 100,232 duplication rate = 2.47% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.3181 >>>>>>> ACTG content number of A's = 41,341,110 bp (25.3%) number of C's = 30,873,483 bp (18.89%) number of T's = 49,942,515 bp (30.56%) number of G's = 41,245,627 bp (25.24%) number of N's = 1,171 bp (0%) GC percentage = 44.14% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 851,381 number of insertions = 11,584 mapped reads with insertion percentage = 0.4% number of deletions = 29,847 mapped reads with deletion percentage = 1.03% homopolymer indels = 40.2% >>>>>>> Coverage mean coverageData = 0.0528X std coverageData = 0.3803X There is a 4.51% of reference with a coverageData >= 1X There is a 0.55% of reference with a coverageData >= 2X There is a 0.1% 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 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 13759726 0.05520438001235712 0.48409317892146514 chr2 243199373 12827914 0.052746492894946734 0.5754448248176957 chr3 198022430 9418664 0.047563621959391164 0.2546339963114903 chr4 191154276 9969906 0.0521563326158605 0.2918150219905311 chr5 180915260 9280674 0.051298458736979954 0.2571002143962659 chr6 171115067 8767264 0.051236072624744375 0.32767239269431514 chr7 159138663 9334638 0.058657260429541246 0.5933323639857208 chr8 146364022 8452592 0.05775047641147768 0.3565719648160834 chr9 141213431 5449717 0.03859205856983958 0.2843163254067483 chr10 135534747 7192470 0.05306735106090544 0.4830187355496496 chr11 135006516 5725135 0.042406360593736085 0.32195094520791123 chr12 133851895 8191352 0.06119713135178251 0.287376506809216 chr13 115169878 4919831 0.04271803604758529 0.23699171806683667 chr14 107349540 5485681 0.051101113241845283 0.27309052767389647 chr15 102531392 6006780 0.05858478932969134 0.29323117217896055 chr16 90354753 5655098 0.06258772020548825 0.31434584065715276 chr17 81195210 7313762 0.09007627420386005 0.37359136762117945 chr18 78077248 3038548 0.038917201589892106 0.483134517957879 chr19 59128983 4375947 0.07400680305967718 0.48659085177772143 chr20 63025520 5255676 0.0833896491452986 0.3578347132516014 chr21 48129895 2043592 0.042459930569140034 0.26274070799880156 chr22 51304566 1513200 0.02949445084478446 0.19849596704716502 chrMT 16571 63525 3.833504314766761 3.269541026962214 chrX 155270560 8935011 0.057544785051332335 0.30161710457923835 chrY 59373566 473850 0.007980824328456202 0.2050145667182012