BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238600.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 = 5,251,607 number of mapped reads = 4,847,516 (92.31%) number of supplementary alignments = 21,315 (0.41%) number of secondary alignments = 0 number of mapped bases = 306,873,134 bp number of sequenced bases = 306,728,956 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 568,566 duplication rate = 9.7% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.876 >>>>>>> ACTG content number of A's = 76,338,899 bp (24.89%) number of C's = 55,450,674 bp (18.08%) number of T's = 100,747,041 bp (32.85%) number of G's = 74,175,958 bp (24.18%) number of N's = 16,384 bp (0.01%) GC percentage = 42.26% >>>>>>> Mismatches and indels general error rate = 0.0057 number of mismatches = 1,706,706 number of insertions = 20,267 mapped reads with insertion percentage = 0.41% number of deletions = 83,680 mapped reads with deletion percentage = 1.71% homopolymer indels = 42.71% >>>>>>> Coverage mean coverageData = 0.0991X std coverageData = 0.947X There is a 7.21% of reference with a coverageData >= 1X There is a 1.75% of reference with a coverageData >= 2X There is a 0.49% of reference with a coverageData >= 3X There is a 0.16% 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% 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 24063917 0.09654506337217912 1.0641115560168266 chr2 243199373 24069267 0.09896928064859772 2.11357171347433 chr3 198022430 20429835 0.10316929753866771 0.4368179662147728 chr4 191154276 14435766 0.07551892796789961 0.3825421232560163 chr5 180915260 17849182 0.09866045572938402 0.43072137034979685 chr6 171115067 22948305 0.13411037030421172 0.9026366876574109 chr7 159138663 22439479 0.1410058283573741 1.458068427612024 chr8 146364022 18548264 0.12672693566729124 0.9074387180175735 chr9 141213431 11631280 0.08236666949902237 0.8153906965297126 chr10 135534747 15332020 0.1131224305159178 0.5961007961209444 chr11 135006516 10560945 0.0782254465406692 0.5252704458614477 chr12 133851895 10992042 0.08212092925542817 0.440441621095769 chr13 115169878 8410635 0.07302807944278625 0.5028511380126441 chr14 107349540 8236681 0.0767276785722603 0.5008638485294795 chr15 102531392 6754571 0.06587807761353713 0.48977121191682904 chr16 90354753 10163329 0.112482505485904 0.5885591330576537 chr17 81195210 6020523 0.07414874596666478 0.38004797030840165 chr18 78077248 13435668 0.17208173115937692 1.809798592438644 chr19 59128983 5991163 0.10132362668913146 0.7899491318928167 chr20 63025520 8852841 0.14046438648979018 0.5471649334065015 chr21 48129895 6327176 0.13146041561071348 0.5529021236598249 chr22 51304566 2891711 0.05636361878589909 0.30723811181157024 chrMT 16571 47347 2.8572204453563455 2.94879927624842 chrX 155270560 15762611 0.10151706157303741 0.5228892555599117 chrY 59373566 678576 0.011428924447623712 0.2946722578249078