BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237849.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,525,116 number of mapped reads = 1,857,662 (73.57%) number of supplementary alignments = 9,172 (0.36%) number of secondary alignments = 0 number of mapped bases = 113,814,763 bp number of sequenced bases = 113,749,976 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 193,957 duplication rate = 8.45% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.5252 >>>>>>> ACTG content number of A's = 29,793,683 bp (26.19%) number of C's = 20,129,130 bp (17.7%) number of T's = 36,492,031 bp (32.08%) number of G's = 27,250,330 bp (23.96%) number of N's = 84,802 bp (0.07%) GC percentage = 41.65% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 968,025 number of insertions = 9,323 mapped reads with insertion percentage = 0.5% number of deletions = 39,905 mapped reads with deletion percentage = 2.12% homopolymer indels = 47.95% >>>>>>> Coverage mean coverageData = 0.0368X std coverageData = 0.345X There is a 2.57% of reference with a coverageData >= 1X There is a 0.68% of reference with a coverageData >= 2X There is a 0.22% of reference with a coverageData >= 3X There is a 0.08% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 9756491 0.03914329665802518 0.5094123518800774 chr2 243199373 9719408 0.03996477408681477 0.4058062544092069 chr3 198022430 8050053 0.04065222813395432 0.28486099724742736 chr4 191154276 7060018 0.03693361272232278 0.28558509097861773 chr5 180915260 6424876 0.035513178932501326 0.2567323483897474 chr6 171115067 6465314 0.03778342908868452 0.3000418625254085 chr7 159138663 6859648 0.04310484875696109 0.43369995432398384 chr8 146364022 6022045 0.0411442984260162 0.34412857711704836 chr9 141213431 4768355 0.0337670076155858 0.3150461879140702 chr10 135534747 5506573 0.04062849654339931 0.4645515832675595 chr11 135006516 5195889 0.03848620906564243 0.3489205405674212 chr12 133851895 5716393 0.04270685147939071 0.29093138837352783 chr13 115169878 3542277 0.030756974492931216 0.24417187809010096 chr14 107349540 3409338 0.031759223188101225 0.2570554211262161 chr15 102531392 3046777 0.029715552871846313 0.23564243254185932 chr16 90354753 2981281 0.03299528692198406 0.2834062320931846 chr17 81195210 2721953 0.03352356623007687 0.26996263316932917 chr18 78077248 2812664 0.03602411806317764 0.48038293007172933 chr19 59128983 2045253 0.03458968675311057 0.399396627027404 chr20 63025520 2231677 0.03540910094831427 0.26722993476563356 chr21 48129895 1433951 0.029793354005862676 0.2562235649623096 chr22 51304566 1147704 0.022370406563813443 0.20272162592032428 chrMT 16571 56746 3.4244161486935005 3.184105183678553 chrX 155270560 6459903 0.041604171454009055 0.30370085158475163 chrY 59373566 380176 0.006403118855956875 0.1619157260091723