BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716296.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 = 478,826 number of mapped reads = 402,478 (84.06%) number of supplementary alignments = 1,513 (0.32%) number of secondary alignments = 0 number of mapped bases = 23,479,907 bp number of sequenced bases = 23,472,803 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,871 duplication rate = 1.33% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3709 >>>>>>> ACTG content number of A's = 5,947,980 bp (25.34%) number of C's = 4,222,604 bp (17.99%) number of T's = 7,660,815 bp (32.64%) number of G's = 5,640,641 bp (24.03%) number of N's = 763 bp (0%) GC percentage = 42.02% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 118,181 number of insertions = 1,647 mapped reads with insertion percentage = 0.41% number of deletions = 4,460 mapped reads with deletion percentage = 1.1% homopolymer indels = 43.98% >>>>>>> Coverage mean coverageData = 0.0076X std coverageData = 0.1033X There is a 0.73% of reference with a coverageData >= 1X There is a 0.02% 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 1906867 0.007650400196996901 0.1503906612202223 chr2 243199373 2002444 0.008233754780280622 0.11795806950682249 chr3 198022430 1541435 0.0077841434427403 0.09086968402681687 chr4 191154276 1518493 0.007943808696175857 0.09435413631360429 chr5 180915260 1422012 0.007860099805842801 0.09124924425456865 chr6 171115067 1364986 0.007977006490024634 0.09748538924499232 chr7 159138663 1287585 0.008090962785077564 0.11475944386656936 chr8 146364022 1192369 0.00814659903237696 0.10911837220149839 chr9 141213431 969036 0.006862208453812017 0.09247119812836097 chr10 135534747 1117693 0.008246542121040002 0.10616996731981822 chr11 135006516 1070731 0.00793095793983751 0.09835041723581732 chr12 133851895 1041447 0.007780592123854503 0.09121976589911368 chr13 115169878 727935 0.006320532874055836 0.08200467113807666 chr14 107349540 715066 0.006661099805364792 0.08687113930885844 chr15 102531392 680851 0.0066404150642956255 0.08448569922748535 chr16 90354753 684381 0.0075743774098967435 0.09140742030536146 chr17 81195210 635273 0.007824020653435099 0.09198078139486895 chr18 78077248 616667 0.007898165160739271 0.12058854081850302 chr19 59128983 481889 0.008149793477760306 0.12206316036268161 chr20 63025520 494595 0.007847535411052538 0.09157197268738465 chr21 48129895 311357 0.006469097844489376 0.08488008672402952 chr22 51304566 280576 0.0054688309808526596 0.07601929496248411 chrMT 16571 2396 0.14458994629171443 0.3715456016843897 chrX 155270560 1338763 0.008622130299523618 0.09823666703339787 chrY 59373566 75060 0.0012641989534534612 0.04483028121409781