BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716615.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 = 2,388,261 number of mapped reads = 2,185,475 (91.51%) number of supplementary alignments = 6,093 (0.26%) number of secondary alignments = 0 number of mapped bases = 125,186,332 bp number of sequenced bases = 125,148,183 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 148,243 duplication rate = 5.46% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4981 >>>>>>> ACTG content number of A's = 31,705,644 bp (25.33%) number of C's = 23,931,151 bp (19.12%) number of T's = 39,977,446 bp (31.94%) number of G's = 29,532,669 bp (23.6%) number of N's = 1,273 bp (0%) GC percentage = 42.72% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 597,021 number of insertions = 7,529 mapped reads with insertion percentage = 0.34% number of deletions = 24,012 mapped reads with deletion percentage = 1.09% homopolymer indels = 44.18% >>>>>>> Coverage mean coverageData = 0.0404X std coverageData = 0.3326X There is a 3.32% of reference with a coverageData >= 1X There is a 0.52% of reference with a coverageData >= 2X There is a 0.1% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 9901979 0.03972699831307542 0.45670827374765965 chr2 243199373 10745160 0.04418251522383654 0.4811612547995209 chr3 198022430 8233074 0.04157647191785294 0.2444334024646899 chr4 191154276 8084033 0.042290620796785104 0.26489493581122475 chr5 180915260 7673882 0.0424169967751753 0.2440068163718792 chr6 171115067 7318664 0.04277042418479724 0.300900948578939 chr7 159138663 6860091 0.04310763249280283 0.46090685680357674 chr8 146364022 6296387 0.04301867982283242 0.33713592732751985 chr9 141213431 5111136 0.03619440419941358 0.28426596318838976 chr10 135534747 6058730 0.04470241125694505 0.38128897363045705 chr11 135006516 5641936 0.041790101449621884 0.3096600873252737 chr12 133851895 5693547 0.04253617029478739 0.24650382186099679 chr13 115169878 3932062 0.03414140978772245 0.21849020357611654 chr14 107349540 3775998 0.035174794414582496 0.22910652582108207 chr15 102531392 3574886 0.034866258326035404 0.2238260793483566 chr16 90354753 3785966 0.041901127215742594 0.2755580357973136 chr17 81195210 3436281 0.04232122806259138 0.2642566720811044 chr18 78077248 3394627 0.04347780034460231 0.5162904900864536 chr19 59128983 2510675 0.042460987363844904 0.3655454941744417 chr20 63025520 2640922 0.04190242301848521 0.24981648071936416 chr21 48129895 1611981 0.03349230244528894 0.24009691815967577 chr22 51304566 1457845 0.028415502043229447 0.20136978328138835 chrMT 16571 7840 0.47311568402631105 0.8161022616391448 chrX 155270560 7073036 0.04555297539984399 0.2788955199604413 chrY 59373566 365594 0.006157521345441842 0.15977447605473444