BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716613.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 = 583,138 number of mapped reads = 525,047 (90.04%) number of supplementary alignments = 1,816 (0.31%) number of secondary alignments = 0 number of mapped bases = 30,504,950 bp number of sequenced bases = 30,494,825 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,391 duplication rate = 1.75% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.7602 >>>>>>> ACTG content number of A's = 7,874,346 bp (25.82%) number of C's = 5,639,565 bp (18.49%) number of T's = 9,428,951 bp (30.92%) number of G's = 7,551,653 bp (24.76%) number of N's = 310 bp (0%) GC percentage = 43.26% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 150,495 number of insertions = 2,230 mapped reads with insertion percentage = 0.42% number of deletions = 6,294 mapped reads with deletion percentage = 1.19% homopolymer indels = 41.93% >>>>>>> Coverage mean coverageData = 0.0099X std coverageData = 0.1172X There is a 0.93% of reference with a coverageData >= 1X There is a 0.04% 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 2410277 0.009670094262272671 0.14193881706292333 chr2 243199373 2543594 0.01045888387220472 0.14113181307128164 chr3 198022430 2014189 0.010171519458679504 0.1050947894920992 chr4 191154276 2017895 0.010556368616101479 0.1119673437596019 chr5 180915260 1825532 0.01009053630965127 0.10454266171660753 chr6 171115067 1786333 0.010439367095593049 0.11454694011442708 chr7 159138663 1677795 0.010542975342202039 0.13680668955001973 chr8 146364022 1594497 0.01089405017853363 0.12482252931855126 chr9 141213431 1259377 0.008918252258880389 0.10431413677537359 chr10 135534747 1477549 0.010901625101347626 0.1315565046683032 chr11 135006516 1367471 0.010128925925323487 0.11414897907315276 chr12 133851895 1392664 0.0104045146316382 0.10652491651199222 chr13 115169878 988609 0.008583919833621775 0.09649504243550497 chr14 107349540 930609 0.0086689612270346 0.09769059976653975 chr15 102531392 851238 0.008302218309881133 0.09467311847285338 chr16 90354753 904256 0.010007840982089785 0.10984068707371202 chr17 81195210 804697 0.009910646206839048 0.10541336885495772 chr18 78077248 809931 0.010373457322676126 0.1483065965368054 chr19 59128983 589433 0.009968596956927197 0.1265887555782223 chr20 63025520 634142 0.01006167025674679 0.10548157849182027 chr21 48129895 403520 0.008383978398456926 0.09890114873217118 chr22 51304566 347142 0.0067662983446736494 0.08556003676189333 chrMT 16571 13478 0.813348621085028 1.0323633001201353 chrX 155270560 1764744 0.011365605946162621 0.11422383828920381 chrY 59373566 95978 0.0016165106202312323 0.054667649922294635