BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716975.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 = 6,847,297 number of mapped reads = 5,942,322 (86.78%) number of supplementary alignments = 23,495 (0.34%) number of secondary alignments = 0 number of mapped bases = 335,144,618 bp number of sequenced bases = 335,047,418 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 339,639 duplication rate = 4.09% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.9946 >>>>>>> ACTG content number of A's = 81,752,476 bp (24.4%) number of C's = 64,595,551 bp (19.28%) number of T's = 105,777,543 bp (31.57%) number of G's = 82,916,839 bp (24.75%) number of N's = 5,009 bp (0%) GC percentage = 44.03% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 1,731,272 number of insertions = 22,918 mapped reads with insertion percentage = 0.38% number of deletions = 60,369 mapped reads with deletion percentage = 1.01% homopolymer indels = 40.09% >>>>>>> Coverage mean coverageData = 0.1083X std coverageData = 0.733X There is a 8.26% of reference with a coverageData >= 1X There is a 1.66% of reference with a coverageData >= 2X There is a 0.44% of reference with a coverageData >= 3X There is a 0.15% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% 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 27701352 0.11113854757457153 1.0615965594471273 chr2 243199373 32439389 0.13338598944496458 1.2315305178342202 chr3 198022430 21656156 0.10936213640040676 0.45012306689750076 chr4 191154276 18492728 0.09674242390476266 0.46004463383972327 chr5 180915260 17660838 0.09761939374268373 0.4006361785881657 chr6 171115067 18389899 0.10747095111151142 0.5330469733128439 chr7 159138663 16112566 0.10124859475538009 1.2015977869462546 chr8 146364022 29488331 0.20147253810775984 0.7994855837888544 chr9 141213431 13898878 0.09842461798127404 0.5397184282481622 chr10 135534747 15833354 0.11682136389718571 0.9150926668015376 chr11 135006516 11403046 0.08446293066328739 0.5733539579189724 chr12 133851895 15500713 0.115804957412071 0.4590241751102871 chr13 115169878 8714957 0.07567045438738765 0.34725671583032625 chr14 107349540 10779281 0.1004129221233738 0.44151964593320975 chr15 102531392 8026569 0.07828401471424479 0.3870942967408997 chr16 90354753 10337997 0.11441564120041366 0.48534127462753796 chr17 81195210 14496216 0.17853535941344323 0.6202410102031914 chr18 78077248 7136106 0.09139802161059775 0.9369950500056989 chr19 59128983 7342222 0.12417297960291318 0.9833393843883921 chr20 63025520 7526718 0.11942333835563752 0.45599195304404905 chr21 48129895 4171000 0.08666131517635764 0.41905621963261125 chr22 51304566 5147685 0.10033580636857936 0.42072917979673263 chrMT 16571 210866 12.725001508659707 8.673449533710512 chrX 155270560 11905324 0.07667470253214775 0.4671233738537063 chrY 59373566 772427 0.013009611044753485 0.2901628404600911