BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716946.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 = 2,490,374 number of mapped reads = 2,260,655 (90.78%) number of supplementary alignments = 12,497 (0.5%) number of secondary alignments = 0 number of mapped bases = 129,895,191 bp number of sequenced bases = 129,861,700 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 123,823 duplication rate = 4.21% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.6529 >>>>>>> ACTG content number of A's = 32,825,449 bp (25.28%) number of C's = 25,815,911 bp (19.88%) number of T's = 40,253,257 bp (31%) number of G's = 30,965,181 bp (23.84%) number of N's = 1,902 bp (0%) GC percentage = 43.72% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 634,492 number of insertions = 8,562 mapped reads with insertion percentage = 0.38% number of deletions = 21,277 mapped reads with deletion percentage = 0.94% homopolymer indels = 42.53% >>>>>>> Coverage mean coverageData = 0.042X std coverageData = 0.354X There is a 3.53% of reference with a coverageData >= 1X There is a 0.48% of reference with a coverageData >= 2X There is a 0.09% of reference with a coverageData >= 3X There is a 0.02% 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 15778145 0.06330232974625166 0.5782102066049605 chr2 243199373 11201437 0.04605865904103297 0.49848839307055764 chr3 198022430 9056067 0.04573253141070938 0.25460907374297276 chr4 191154276 6073387 0.03177217442941219 0.22864990705251384 chr5 180915260 5781725 0.031958194129118794 0.21221346192404572 chr6 171115067 9801421 0.05727970757829291 0.35869230200282143 chr7 159138663 7617096 0.047864521772436906 0.4762747896930413 chr8 146364022 9272225 0.06335043867542804 0.33152695894488915 chr9 141213431 5516314 0.03906366385220114 0.32315711184580215 chr10 135534747 6741671 0.049741274095564586 0.41371000898528115 chr11 135006516 4431959 0.03282774144027241 0.2903901501155425 chr12 133851895 5554039 0.04149391385157453 0.24800548530537903 chr13 115169878 2943364 0.02555671718259526 0.18499497555604316 chr14 107349540 2909677 0.02710469928422609 0.22683527212303087 chr15 102531392 2848830 0.027784953899777348 0.20639185135147672 chr16 90354753 2883494 0.031913030629390354 0.23923120216687457 chr17 81195210 3243057 0.039941481769675824 0.2468000417548957 chr18 78077248 2517096 0.03223853381717552 0.5236570944249519 chr19 59128983 3042647 0.0514577935494003 0.4207704435505291 chr20 63025520 2335035 0.037049039817521535 0.23008072203564756 chr21 48129895 1191532 0.024756588394801195 0.21388174597343462 chr22 51304566 1684061 0.03282477820784996 0.2123319396312371 chrMT 16571 200385 12.092511013215859 7.292150714431844 chrX 155270560 6941969 0.04470885530392883 0.2880607535176317 chrY 59373566 328558 0.005533742069661101 0.13201444873916793