BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716310.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 = 1,464,916 number of mapped reads = 1,350,252 (92.17%) number of supplementary alignments = 25,988 (1.77%) number of secondary alignments = 0 number of mapped bases = 106,812,697 bp number of sequenced bases = 106,765,204 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 46,988 duplication rate = 2.48% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.4614 >>>>>>> ACTG content number of A's = 28,016,197 bp (26.24%) number of C's = 20,799,258 bp (19.48%) number of T's = 32,974,069 bp (30.88%) number of G's = 24,968,373 bp (23.39%) number of N's = 7,307 bp (0.01%) GC percentage = 42.87% >>>>>>> Mismatches and indels general error rate = 0.0068 number of mismatches = 703,770 number of insertions = 8,334 mapped reads with insertion percentage = 0.61% number of deletions = 24,768 mapped reads with deletion percentage = 1.81% homopolymer indels = 42.81% >>>>>>> Coverage mean coverageData = 0.0345X std coverageData = 0.3396X There is a 3.03% of reference with a coverageData >= 1X There is a 0.3% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 10624581 0.04262609640599451 0.7187635753268284 chr2 243199373 9012422 0.037057751789516334 0.352364063495395 chr3 198022430 6992285 0.03531057062576194 0.20458192387576113 chr4 191154276 6748493 0.03530390813752971 0.24363469353230532 chr5 180915260 6532724 0.036109303327977973 0.20928400721919316 chr6 171115067 5881011 0.034368750239860524 0.22161096884561218 chr7 159138663 5739417 0.036065509737253476 0.40354014489668666 chr8 146364022 3026699 0.02067925545254557 0.3415584994382107 chr9 141213431 4411976 0.031243317075130055 0.27817348154016497 chr10 135534747 5025768 0.0370810298557609 0.31802740596284423 chr11 135006516 6118010 0.04531640532076244 0.35961360666263203 chr12 133851895 4776220 0.03568287172923476 0.20797691010937625 chr13 115169878 3835164 0.033300061323326226 0.20144807126343398 chr14 107349540 3115776 0.02902458641182813 0.20071220818688568 chr15 102531392 3062044 0.029864453610461077 0.19000593925995737 chr16 90354753 2461571 0.027243403565056504 0.1965831160321553 chr17 81195210 3368378 0.04148493488716884 0.2648508620051628 chr18 78077248 2793087 0.03577337920516871 0.4583651287064318 chr19 59128983 2101085 0.03553392758336466 0.4992901980387261 chr20 63025520 2209046 0.035050024180681094 0.2132799848879993 chr21 48129895 1427049 0.029649950410238792 0.21212025159574732 chr22 51304566 1237174 0.02411430592746852 0.17107899812161886 chrMT 16571 8170 0.4930299921549695 0.8376059866030732 chrX 155270560 5991771 0.03858922773254634 0.24862661281062026 chrY 59373566 312776 0.005267933544702368 0.17680981420329164