BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6236087.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,632,969 number of mapped reads = 1,419,582 (86.93%) number of supplementary alignments = 9,359 (0.57%) number of secondary alignments = 0 number of mapped bases = 94,176,561 bp number of sequenced bases = 94,128,033 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 68,940 duplication rate = 3.78% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4298 >>>>>>> ACTG content number of A's = 26,165,004 bp (27.8%) number of C's = 16,839,214 bp (17.89%) number of T's = 30,409,925 bp (32.31%) number of G's = 20,674,952 bp (21.96%) number of N's = 38,938 bp (0.04%) GC percentage = 39.85% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 769,644 number of insertions = 7,045 mapped reads with insertion percentage = 0.49% number of deletions = 27,913 mapped reads with deletion percentage = 1.94% homopolymer indels = 46.26% >>>>>>> Coverage mean coverageData = 0.0304X std coverageData = 0.327X There is a 2.59% of reference with a coverageData >= 1X There is a 0.33% 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 8506191 0.03412706040961078 0.5760607814011648 chr2 243199373 7685820 0.03160295976585433 0.3713059473738659 chr3 198022430 10545108 0.05325208866490529 0.261468420028455 chr4 191154276 3882600 0.020311342656023034 0.18219168326363153 chr5 180915260 5628013 0.031108558780503094 0.2021840532806597 chr6 171115067 7760514 0.04535260474754102 0.36411169933686355 chr7 159138663 5823130 0.036591547837749525 0.3704878070086615 chr8 146364022 6416740 0.043840965233928865 0.5521253343857946 chr9 141213431 3930146 0.02783124786480119 0.3253735812144935 chr10 135534747 3497808 0.02580746323302614 0.284058803842777 chr11 135006516 4232857 0.0313529829923172 0.2587979520815656 chr12 133851895 2409116 0.01799837051242345 0.16427627980970408 chr13 115169878 2331224 0.020241612134033866 0.16007131454020776 chr14 107349540 2488571 0.023181943769856862 0.18780939027022536 chr15 102531392 3318276 0.032363512630356174 0.2053935048727901 chr16 90354753 2348097 0.025987531613306497 0.20006798689873823 chr17 81195210 2633330 0.03243208558731482 0.24336898513704475 chr18 78077248 3333640 0.042696689309541236 0.5159811833573852 chr19 59128983 1114269 0.018844717826450693 0.37904587360025926 chr20 63025520 1980102 0.03141746390985747 0.20392754240533553 chr21 48129895 1789831 0.0371875110053741 0.2415180677226054 chr22 51304566 753239 0.014681714684030267 0.13441831654572958 chrMT 16571 89365 5.392854987628991 3.930983749187315 chrX 155270560 1481424 0.009540920055933334 0.1353975394320991 chrY 59373566 197150 0.0033205012479796143 0.11130738347688689