BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716818.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 = 686,394 number of mapped reads = 544,515 (79.33%) number of supplementary alignments = 2,611 (0.38%) number of secondary alignments = 0 number of mapped bases = 31,599,115 bp number of sequenced bases = 31,590,765 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 13,317 duplication rate = 1.95% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.693 >>>>>>> ACTG content number of A's = 8,114,634 bp (25.69%) number of C's = 5,506,223 bp (17.43%) number of T's = 10,004,315 bp (31.67%) number of G's = 7,965,398 bp (25.21%) number of N's = 195 bp (0%) GC percentage = 42.64% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 153,118 number of insertions = 2,230 mapped reads with insertion percentage = 0.41% number of deletions = 5,396 mapped reads with deletion percentage = 0.98% homopolymer indels = 43.4% >>>>>>> Coverage mean coverageData = 0.0102X std coverageData = 0.1265X There is a 0.96% of reference with a coverageData >= 1X There is a 0.05% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% 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 4130916 0.01657334286039753 0.19267892172560766 chr2 243199373 3065420 0.012604555522435496 0.16332216269976993 chr3 198022430 2989309 0.015095810105956179 0.12842264412897564 chr4 191154276 1261712 0.006600490590124178 0.09033816788385647 chr5 180915260 2176506 0.012030527441410968 0.11504467354382077 chr6 171115067 1160697 0.006783137337637252 0.09168456544290016 chr7 159138663 2019462 0.012689952032586826 0.18585031478563285 chr8 146364022 1321099 0.009026118454164917 0.1126300742800684 chr9 141213431 830850 0.005883647144017059 0.09087749527339842 chr10 135534747 1357146 0.010013269881265208 0.11669546463585236 chr11 135006516 1313820 0.009731530291471264 0.11607220509085833 chr12 133851895 1105430 0.00825860552814736 0.09595079313733562 chr13 115169878 872629 0.007576885685335188 0.09111813135310975 chr14 107349540 641839 0.005978963673249089 0.0822130085089223 chr15 102531392 1312310 0.01279910449279768 0.11876966319090168 chr16 90354753 869571 0.009623965216306884 0.10508820573597083 chr17 81195210 1155184 0.014227243208066091 0.12891653591853083 chr18 78077248 780353 0.009994627372112297 0.1571871117956999 chr19 59128983 477298 0.008072149659668593 0.13776056517936872 chr20 63025520 798525 0.012669867698037239 0.1182324315707779 chr21 48129895 380907 0.007914145667677022 0.09541844061587303 chr22 51304566 354521 0.006910125699143425 0.08717235894142528 chrMT 16571 2906 0.17536660430873213 0.42565604623071657 chrX 155270560 1146650 0.007384851320172994 0.09384246407856875 chrY 59373566 74055 0.001247272228856862 0.04354472151003023