BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173970.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 6,854,794 number of mapped reads = 6,706,813 (97.84%) number of supplementary alignments = 921,922 (13.45%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 3,353,302 number of mapped paired reads (second in pair) = 3,353,511 number of mapped paired reads (both in pair) = 6,611,050 number of mapped paired reads (singletons) = 95,763 number of mapped bases = 761,596,176 bp number of sequenced bases = 761,055,108 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 5,296,983 duplication rate = 64.43% >>>>>>> Insert size mean insert size = 1,202,373.2579 std insert size = 9,776,572.8926 median insert size = 157 >>>>>>> Mapping quality mean mapping quality = 52.5365 >>>>>>> ACTG content number of A's = 226,728,508 bp (29.79%) number of C's = 151,541,384 bp (19.91%) number of T's = 225,095,712 bp (29.58%) number of G's = 157,683,973 bp (20.72%) number of N's = 5,531 bp (0%) GC percentage = 40.63% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 6,514,294 number of insertions = 84,456 mapped reads with insertion percentage = 1.21% number of deletions = 228,065 mapped reads with deletion percentage = 3.32% homopolymer indels = 40.68% >>>>>>> Coverage mean coverageData = 0.246X std coverageData = 4.0939X There is a 5.55% of reference with a coverageData >= 1X There is a 4.13% of reference with a coverageData >= 2X There is a 3.03% of reference with a coverageData >= 3X There is a 2.4% of reference with a coverageData >= 4X There is a 1.76% of reference with a coverageData >= 5X There is a 1.45% of reference with a coverageData >= 6X There is a 1.06% of reference with a coverageData >= 7X There is a 0.92% of reference with a coverageData >= 8X There is a 0.67% of reference with a coverageData >= 9X There is a 0.6% of reference with a coverageData >= 10X There is a 0.44% of reference with a coverageData >= 11X There is a 0.4% of reference with a coverageData >= 12X There is a 0.29% of reference with a coverageData >= 13X There is a 0.27% of reference with a coverageData >= 14X There is a 0.19% of reference with a coverageData >= 15X There is a 0.18% of reference with a coverageData >= 16X There is a 0.13% of reference with a coverageData >= 17X There is a 0.12% of reference with a coverageData >= 18X There is a 0.09% of reference with a coverageData >= 19X There is a 0.08% of reference with a coverageData >= 20X There is a 0.06% of reference with a coverageData >= 21X There is a 0.06% of reference with a coverageData >= 22X There is a 0.04% of reference with a coverageData >= 23X There is a 0.04% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.03% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% 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 60708241 0.24356304813378982 2.2932488226446557 chr2 243199373 69800252 0.2870083550749944 13.116068908380193 chr3 198022430 50701970 0.2560415504445633 1.4778503914662215 chr4 191154276 53687709 0.2808606227568773 2.1474924434880074 chr5 180915260 46328627 0.25607915551181254 1.4736551431387448 chr6 171115067 46498209 0.27173649763991853 1.8279468682602558 chr7 159138663 40506362 0.25453501516473087 2.0121002460791493 chr8 146364022 37071995 0.25328625500602875 2.482174132569635 chr9 141213431 31078668 0.22008294664266037 1.8951654991658118 chr10 135534747 39313879 0.2900649454858982 2.632470356289966 chr11 135006516 35234763 0.26098564753719 1.536134182134954 chr12 133851895 33755468 0.2521852081362016 1.5045808237953857 chr13 115169878 25256726 0.21929975475010924 1.3636231028370553 chr14 107349540 23762915 0.2213601939980367 1.3758017231268402 chr15 102531392 21876890 0.21336772644225876 1.3753584416295281 chr16 90354753 24161614 0.267408334346285 1.9219104837858738 chr17 81195210 21736661 0.2677086616316406 1.7041136127498722 chr18 78077248 20719292 0.265369138010602 2.7459410154017454 chr19 59128983 14630695 0.24743694644638145 1.8047706613920187 chr20 63025520 16769138 0.26606901458329896 1.5847269636155326 chr21 48129895 10683473 0.22197166646634073 1.843608573375686 chr22 51304566 9872168 0.19242279527323164 1.566659846655535 chrMT 16571 876300 52.881540039828614 47.74417854632505 chrX 155270560 20492671 0.1319804024665075 1.0761854287071673 chrY 59373566 6071490 0.10225914340398554 1.6621432770001874