BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716886.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 = 1,766,050 number of mapped reads = 1,244,456 (70.47%) number of supplementary alignments = 5,544 (0.31%) number of secondary alignments = 0 number of mapped bases = 71,651,176 bp number of sequenced bases = 71,630,632 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 41,213 duplication rate = 2.5% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6007 >>>>>>> ACTG content number of A's = 18,271,683 bp (25.51%) number of C's = 13,252,628 bp (18.5%) number of T's = 23,217,057 bp (32.41%) number of G's = 16,887,234 bp (23.58%) number of N's = 2,030 bp (0%) GC percentage = 42.08% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 353,827 number of insertions = 4,575 mapped reads with insertion percentage = 0.37% number of deletions = 13,090 mapped reads with deletion percentage = 1.04% homopolymer indels = 43.28% >>>>>>> Coverage mean coverageData = 0.0231X std coverageData = 0.2267X There is a 2.11% of reference with a coverageData >= 1X There is a 0.15% of reference with a coverageData >= 2X There is a 0.02% 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 8170127 0.032778762866151494 0.38810151641820406 chr2 243199373 6155070 0.025308741235940603 0.30148468646770177 chr3 198022430 6427754 0.0324597269107343 0.19486564513255616 chr4 191154276 3400362 0.01778857408348009 0.14964153365891766 chr5 180915260 3209180 0.017738581035121083 0.14552705648807074 chr6 171115067 5163192 0.030173801118284927 0.2411958883030083 chr7 159138663 4096762 0.02574334811396524 0.27284601003932 chr8 146364022 4760765 0.03252688013725122 0.21510858127601207 chr9 141213431 2672408 0.018924602150626878 0.19310138044121206 chr10 135534747 3684258 0.027183125224707137 0.2458859539677829 chr11 135006516 2365904 0.017524368971939104 0.18772441579556703 chr12 133851895 3180267 0.02375959638076099 0.1685847761618702 chr13 115169878 1663877 0.014447154315818585 0.1295608338568133 chr14 107349540 1608494 0.01498370649748476 0.14234498531124803 chr15 102531392 2135691 0.020829630402364966 0.15596446672564881 chr16 90354753 1535589 0.016995110373441008 0.1566454580746369 chr17 81195210 1583113 0.019497615684472027 0.15406688191698945 chr18 78077248 1428316 0.0182936263327314 0.3195650244283863 chr19 59128983 1517793 0.025669188323431843 0.28521169171503613 chr20 63025520 1097296 0.01741034425420052 0.14269958842235056 chr21 48129895 673321 0.013989662765730115 0.13822943343096097 chr22 51304566 1114317 0.02171964577187925 0.15985842081709944 chrMT 16571 4527 0.2731880996922334 0.5405428585355129 chrX 155270560 3827728 0.0246519881167428 0.19252990544330864 chrY 59373566 175065 0.0029485343696553446 0.07484985843940853