BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716797.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 = 1,434,915 number of mapped reads = 1,042,168 (72.63%) number of supplementary alignments = 1,063 (0.07%) number of secondary alignments = 0 number of mapped bases = 54,428,410 bp number of sequenced bases = 54,413,601 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 77,722 duplication rate = 6.4% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.2011 >>>>>>> ACTG content number of A's = 11,116,977 bp (20.43%) number of C's = 9,514,349 bp (17.49%) number of T's = 18,142,733 bp (33.34%) number of G's = 15,638,700 bp (28.74%) number of N's = 842 bp (0%) GC percentage = 46.23% >>>>>>> Mismatches and indels general error rate = 0.0073 number of mismatches = 389,087 number of insertions = 3,102 mapped reads with insertion percentage = 0.3% number of deletions = 8,711 mapped reads with deletion percentage = 0.83% homopolymer indels = 40.02% >>>>>>> Coverage mean coverageData = 0.0176X std coverageData = 0.1807X There is a 1.51% of reference with a coverageData >= 1X There is a 0.18% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% 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 5114423 0.02051919862618918 0.19810333098654448 chr2 243199373 4569329 0.018788407813863896 0.2963088821167397 chr3 198022430 3845554 0.01941978997025741 0.16048634043320806 chr4 191154276 3558208 0.018614325948952352 0.16881109733070032 chr5 180915260 3346357 0.01849682000291186 0.1552460923273862 chr6 171115067 2222814 0.01299017111099866 0.1621491266995727 chr7 159138663 3181402 0.019991383237899892 0.187093554093134 chr8 146364022 3110001 0.02124839805235743 0.17488061133701502 chr9 141213431 2442182 0.01729426147856998 0.16622261999351243 chr10 135534747 2809163 0.0207265152455702 0.2028390127873798 chr11 135006516 2297737 0.017019452601828494 0.16543399134725048 chr12 133851895 2696608 0.020146207119443472 0.16412507503641502 chr13 115169878 858263 0.007452148208405673 0.10166332132900781 chr14 107349540 1791374 0.016687300197094464 0.15301759086655992 chr15 102531392 1057431 0.010313241431463253 0.11702452368044382 chr16 90354753 1519744 0.01681974605143351 0.16562089736371763 chr17 81195210 2335403 0.028762817412505 0.203187115564524 chr18 78077248 1455169 0.018637554950707277 0.17969573291827734 chr19 59128983 1590126 0.026892497034829772 0.23082722524327362 chr20 63025520 1517739 0.02408134038402222 0.18766843258503413 chr21 48129895 793423 0.01648503492475934 0.1604975754646865 chr22 51304566 639497 0.012464719027152476 0.1331896678595454 chrMT 16571 1705 0.10289059199806891 0.37449163764245685 chrX 155270560 1507605 0.009709535407098423 0.11813816073006937 chrY 59373566 167153 0.002815276414423213 0.0882657168828578