BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525140.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 = 671,801 number of mapped reads = 607,813 (90.48%) number of supplementary alignments = 17,048 (2.54%) number of secondary alignments = 0 number of mapped bases = 46,824,187 bp number of sequenced bases = 46,804,845 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 13,226 duplication rate = 1.29% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.9477 >>>>>>> ACTG content number of A's = 12,393,068 bp (26.48%) number of C's = 9,023,050 bp (19.28%) number of T's = 14,540,513 bp (31.07%) number of G's = 10,846,392 bp (23.17%) number of N's = 1,822 bp (0%) GC percentage = 42.45% >>>>>>> Mismatches and indels general error rate = 0.0075 number of mismatches = 341,050 number of insertions = 4,279 mapped reads with insertion percentage = 0.69% number of deletions = 11,278 mapped reads with deletion percentage = 1.83% homopolymer indels = 43.08% >>>>>>> Coverage mean coverageData = 0.0151X std coverageData = 0.1906X There is a 1.4% of reference with a coverageData >= 1X There is a 0.07% of reference with a coverageData >= 2X There is a 0.01% 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 4496192 0.01803883971065412 0.30552496469852763 chr2 243199373 3853127 0.01584349068202573 0.24671303105132772 chr3 198022430 2994454 0.015121792011137324 0.12868861756427047 chr4 191154276 3014238 0.01576861403822324 0.1340560476189002 chr5 180915260 2790008 0.015421628888574684 0.13088159033804433 chr6 171115067 2626413 0.015348812036522769 0.13949464454385008 chr7 159138663 2556502 0.016064619067460685 0.2663331928842236 chr8 146364022 2336867 0.015966129982407835 0.22840721117389282 chr9 141213431 1882448 0.013330516698514322 0.17529016053483643 chr10 135534747 2117837 0.015625786352779336 0.1987256704135325 chr11 135006516 2563656 0.01898912790253768 0.21254449488960675 chr12 133851895 2034490 0.015199560678614225 0.12944118277232794 chr13 115169878 1727753 0.015001778503229812 0.12836644503894645 chr14 107349540 1373086 0.012790795377418477 0.12799574303402766 chr15 102531392 1256231 0.012252159806822871 0.11532124664807497 chr16 90354753 1000829 0.01107666134619393 0.11788128639901013 chr17 81195210 1321419 0.016274593045574978 0.14435100225964986 chr18 78077248 1268267 0.01624374619351338 0.2919410378382226 chr19 59128983 845536 0.014299856975385489 0.22566628656958845 chr20 63025520 883505 0.014018210401120054 0.12664318148081644 chr21 48129895 613144 0.012739358770676728 0.12328195162612866 chr22 51304566 466908 0.009100710451385555 0.09887827939377188 chrMT 16571 2751 0.1660129141270895 0.45497925616814805 chrX 155270560 2691413 0.017333698030070864 0.1653683399511704 chrY 59373566 107113 0.0018040519917567356 0.05464500289146191