BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716865.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 = 1,139,272 number of mapped reads = 694,952 (61%) number of supplementary alignments = 2,349 (0.21%) number of secondary alignments = 0 number of mapped bases = 39,343,324 bp number of sequenced bases = 39,331,649 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 13,353 duplication rate = 1.45% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.2867 >>>>>>> ACTG content number of A's = 10,254,301 bp (26.07%) number of C's = 7,210,482 bp (18.33%) number of T's = 12,182,936 bp (30.97%) number of G's = 9,683,313 bp (24.62%) number of N's = 617 bp (0%) GC percentage = 42.95% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 206,276 number of insertions = 2,770 mapped reads with insertion percentage = 0.4% number of deletions = 7,309 mapped reads with deletion percentage = 1.04% homopolymer indels = 40.47% >>>>>>> Coverage mean coverageData = 0.0127X std coverageData = 0.1367X There is a 1.2% of reference with a coverageData >= 1X There is a 0.05% 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 3136799 0.012584919497552626 0.16044967186338543 chr2 243199373 3320186 0.013652115788966282 0.18972421849038792 chr3 198022430 2594484 0.013101970317200935 0.11939818713902933 chr4 191154276 2506319 0.013111498484083087 0.1261384049663895 chr5 180915260 2364937 0.013072070316235347 0.1192300695175914 chr6 171115067 2250434 0.013151582963760872 0.1276163742350879 chr7 159138663 2172925 0.013654287142025316 0.1635104483171179 chr8 146364022 1948024 0.01330944567784561 0.1339715066087248 chr9 141213431 1627706 0.01152656647794359 0.12253843077775918 chr10 135534747 1884207 0.013902021745021592 0.1478230781028428 chr11 135006516 1785108 0.013222384021820103 0.13275312763579653 chr12 133851895 1789713 0.013370845440776165 0.12128394598726934 chr13 115169878 1213115 0.010533266345910343 0.10712480649712564 chr14 107349540 1203443 0.011210509146103467 0.11194265065915517 chr15 102531392 1161695 0.011330139748809809 0.11236824074978632 chr16 90354753 1211514 0.013408414718371262 0.12469437182742213 chr17 81195210 1149907 0.014162251689477741 0.12806897109683113 chr18 78077248 1020361 0.01306860866817437 0.16364004363609883 chr19 59128983 885166 0.014970086666296966 0.15467489478390622 chr20 63025520 840837 0.013341214796799773 0.12249008852613581 chr21 48129895 513620 0.01067153792876548 0.11256695574083345 chr22 51304566 478429 0.009325271360837552 0.10054769269021122 chrMT 16571 2608 0.1573833806046708 0.40381483612652697 chrX 155270560 2160355 0.013913487527835283 0.12960172081136448 chrY 59373566 121432 0.0020452199216061907 0.06137543654467613