BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716598.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 = 948,509 number of mapped reads = 840,965 (88.66%) number of supplementary alignments = 5,650 (0.6%) number of secondary alignments = 0 number of mapped bases = 48,956,259 bp number of sequenced bases = 48,942,055 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 20,498 duplication rate = 1.9% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.9205 >>>>>>> ACTG content number of A's = 12,292,464 bp (25.12%) number of C's = 9,499,769 bp (19.41%) number of T's = 15,307,494 bp (31.28%) number of G's = 11,841,733 bp (24.2%) number of N's = 595 bp (0%) GC percentage = 43.61% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 247,345 number of insertions = 3,407 mapped reads with insertion percentage = 0.4% number of deletions = 8,891 mapped reads with deletion percentage = 1.05% homopolymer indels = 40.62% >>>>>>> Coverage mean coverageData = 0.0158X std coverageData = 0.1584X There is a 1.47% of reference with a coverageData >= 1X There is a 0.08% 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 3836812 0.01539338993261726 0.21652577902083728 chr2 243199373 4116303 0.0169256316298151 0.18846605814061584 chr3 198022430 3198142 0.016150402759929773 0.13375473837985788 chr4 191154276 3183028 0.016651618088836265 0.1458141604779471 chr5 180915260 2926768 0.01617756290983967 0.1344072577579495 chr6 171115067 2837901 0.01658475229419745 0.14376750789723064 chr7 159138663 2655501 0.01668671176406704 0.19939316435229246 chr8 146364022 2508032 0.01713557721172762 0.1664073171092583 chr9 141213431 2095549 0.014839587036165136 0.1426459372701836 chr10 135534747 2365167 0.017450632050834906 0.16508819968228317 chr11 135006516 2178305 0.016134813818912266 0.15400122710334602 chr12 133851895 2184863 0.016322988927426094 0.13601829300626478 chr13 115169878 1528135 0.013268530162027262 0.12211168939122308 chr14 107349540 1488490 0.013865825601115756 0.12867169728133906 chr15 102531392 1445864 0.014101671417861956 0.12699309393492195 chr16 90354753 1419069 0.015705526858116693 0.1370482499144245 chr17 81195210 1379990 0.016995953332715072 0.143346996568792 chr18 78077248 1287250 0.016486877201409556 0.20131438582874087 chr19 59128983 1066174 0.018031326532370766 0.1912154855571136 chr20 63025520 1064038 0.01688265324903309 0.13966127112253013 chr21 48129895 645297 0.013407405106535137 0.12928213790228402 chr22 51304566 603582 0.01176468386848843 0.11421914076928505 chrMT 16571 15529 0.937119063424054 1.104112073583034 chrX 155270560 2786953 0.017949011068163854 0.14796227492186537 chrY 59373566 139517 0.0023498167517847926 0.07424153575030537