BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716747.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 = 413,424 number of mapped reads = 326,765 (79.04%) number of supplementary alignments = 342 (0.08%) number of secondary alignments = 0 number of mapped bases = 17,161,543 bp number of sequenced bases = 17,157,190 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 14,358 duplication rate = 3.97% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.3911 >>>>>>> ACTG content number of A's = 3,680,884 bp (21.45%) number of C's = 3,150,781 bp (18.36%) number of T's = 5,584,466 bp (32.55%) number of G's = 4,740,729 bp (27.63%) number of N's = 330 bp (0%) GC percentage = 46% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 109,735 number of insertions = 1,110 mapped reads with insertion percentage = 0.34% number of deletions = 2,592 mapped reads with deletion percentage = 0.79% homopolymer indels = 39.36% >>>>>>> Coverage mean coverageData = 0.0055X std coverageData = 0.0835X There is a 0.51% of reference with a coverageData >= 1X There is a 0.03% of reference with a coverageData >= 2X There is a 0% 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 1397410 0.00560644540981906 0.08379447533268906 chr2 243199373 1418554 0.005832885103696382 0.10409701375887362 chr3 198022430 1079266 0.005450220967392431 0.07850833969441955 chr4 191154276 1035357 0.005416342347476444 0.08015392031470969 chr5 180915260 978225 0.005407089484878169 0.07833908593293482 chr6 171115067 960490 0.005613123477899232 0.08299328179393733 chr7 159138663 954218 0.005996141867799907 0.08802502769909241 chr8 146364022 844538 0.005770120200714353 0.08220480924422018 chr9 141213431 727890 0.005154538026910485 0.07872482761511292 chr10 135534747 835329 0.006163209202729393 0.08899203834947579 chr11 135006516 799260 0.005920158698117949 0.08501875607718101 chr12 133851895 765976 0.005722563733595255 0.08097322307230068 chr13 115169878 511155 0.004438269874697618 0.0712609972353878 chr14 107349540 523718 0.0048786236065846205 0.07521407779650172 chr15 102531392 496784 0.004845189266522393 0.07448039651819231 chr16 90354753 567304 0.006278629304647648 0.08735467230512807 chr17 81195210 535958 0.006600857365847074 0.08832507673290242 chr18 78077248 426071 0.005457044285167428 0.08470175097641064 chr19 59128983 444175 0.0075119675236085155 0.10001404240345088 chr20 63025520 406331 0.006447086830858357 0.0866148116989121 chr21 48129895 234792 0.0048782986125359305 0.07667513109057295 chr22 51304566 251642 0.004904865582529243 0.0759030464594484 chrMT 16571 2554 0.15412467563816307 0.43809083080067934 chrX 155270560 903528 0.005819055460352562 0.08190916786899904 chrY 59373566 61018 0.0010276963994380933 0.0389520677817351