BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716303.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 = 4,796,268 number of mapped reads = 4,328,674 (90.25%) number of supplementary alignments = 22,414 (0.47%) number of secondary alignments = 0 number of mapped bases = 248,347,667 bp number of sequenced bases = 248,278,652 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 243,426 duplication rate = 3.98% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.9162 >>>>>>> ACTG content number of A's = 62,965,665 bp (25.36%) number of C's = 46,795,994 bp (18.85%) number of T's = 78,669,238 bp (31.69%) number of G's = 59,843,884 bp (24.1%) number of N's = 3,871 bp (0%) GC percentage = 42.95% >>>>>>> Mismatches and indels general error rate = 0.0056 number of mismatches = 1,342,438 number of insertions = 19,350 mapped reads with insertion percentage = 0.45% number of deletions = 41,547 mapped reads with deletion percentage = 0.95% homopolymer indels = 39.59% >>>>>>> Coverage mean coverageData = 0.0802X std coverageData = 0.6995X There is a 6.47% of reference with a coverageData >= 1X There is a 1.04% of reference with a coverageData >= 2X There is a 0.22% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% 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 18059644 0.07245576330981338 1.3200313841144555 chr2 243199373 19505720 0.08020464756708069 0.771729087761851 chr3 198022430 15890281 0.08024485408041908 0.3358904512397455 chr4 191154276 14251330 0.07455407379953143 0.39065019974737947 chr5 180915260 14192925 0.07845067906377826 0.3437988413611715 chr6 171115067 13516906 0.07899307896714905 0.4219875068965003 chr7 159138663 17579664 0.11046758637151552 1.0982316481121297 chr8 146364022 10948611 0.07480397744194267 0.6183408450327805 chr9 141213431 10752749 0.07614537033662187 0.7736553310231808 chr10 135534747 10379868 0.07658455288959959 0.6460629451810765 chr11 135006516 9305518 0.06892643611364654 0.5701665968245799 chr12 133851895 17927197 0.1339330832783503 0.5383466586228244 chr13 115169878 8621118 0.0748556666874302 0.3209795907368581 chr14 107349540 8628564 0.08037821121543698 0.4729852795879469 chr15 102531392 6759189 0.06592311747801102 0.3070967105501169 chr16 90354753 7032620 0.07783342620614546 0.415346257297052 chr17 81195210 7439406 0.09162370538853215 0.3935159933658114 chr18 78077248 7491573 0.0959507819742827 1.4274073204056792 chr19 59128983 4332776 0.07327668733960806 1.0150597938119266 chr20 63025520 7826702 0.12418306108382764 0.45065941269784415 chr21 48129895 2631759 0.05468033952702369 0.39645515597869857 chr22 51304566 2505279 0.04883150166400394 0.25658669828880526 chrMT 16571 113289 6.836581980568463 4.7913402984936315 chrX 155270560 11966581 0.07706922033384822 0.48851572448367236 chrY 59373566 688398 0.0115943516008454 0.24866805606058937