BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2093978.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP024468/ERP024468.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 = 368,736 number of mapped reads = 353,467 (95.86%) number of supplementary alignments = 21,620 (5.86%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 177,656 number of mapped paired reads (second in pair) = 175,811 number of mapped paired reads (both in pair) = 350,602 number of mapped paired reads (singletons) = 2,865 number of mapped bases = 45,441,767 bp number of sequenced bases = 44,622,275 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 333,362 duplication rate = 50.28% >>>>>>> Insert size mean insert size = 1,017,563.8022 std insert size = 9,174,504.2311 median insert size = 165 >>>>>>> Mapping quality mean mapping quality = 40.4357 >>>>>>> ACTG content number of A's = 11,746,637 bp (26.32%) number of C's = 10,491,799 bp (23.51%) number of T's = 11,108,779 bp (24.9%) number of G's = 11,274,654 bp (25.27%) number of N's = 406 bp (0%) GC percentage = 48.78% >>>>>>> Mismatches and indels general error rate = 0.0354 number of mismatches = 1,532,065 number of insertions = 23,843 mapped reads with insertion percentage = 6.6% number of deletions = 122,677 mapped reads with deletion percentage = 33.36% homopolymer indels = 29.2% >>>>>>> Coverage mean coverageData = 0.0147X std coverageData = 2.8248X There is a 0.02% of reference with a coverageData >= 1X There is a 0.01% of reference with a coverageData >= 2X There is a 0.01% 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 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% 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 885765 0.0035537123095071444 1.1486172196967013 chr2 243199373 2431788 0.009999154068542767 3.03008624612818 chr3 198022430 716252 0.0036170245966580653 1.0805650005621108 chr4 191154276 863282 0.004516153224843372 1.4300348862645753 chr5 180915260 414564 0.0022914816583189277 1.1689627336791906 chr6 171115067 936137 0.005470804040885541 1.5529322310861744 chr7 159138663 766983 0.004819589316268165 1.5316110981242974 chr8 146364022 414569 0.0028324515433171137 1.014184023461737 chr9 141213431 579201 0.004101599939172924 1.179577251580965 chr10 135534747 655899 0.004839342047098815 1.4732793437947813 chr11 135006516 1002094 0.007422560256276816 1.767667643644544 chr12 133851895 1048699 0.007834771409101082 1.9286469076551582 chr13 115169878 819537 0.007115897092467181 1.9109578323107461 chr14 107349540 182564 0.00170065004470443 0.5764081072287958 chr15 102531392 677606 0.006608766220593201 1.741396248466277 chr16 90354753 253743 0.0028082972015871705 0.7905522981045088 chr17 81195210 1246699 0.015354341715478044 3.4136942788141 chr18 78077248 161875 0.0020732672340090675 0.5284901199188135 chr19 59128983 176524 0.002985405651235368 0.7914011910328155 chr20 63025520 388058 0.006157156656541668 2.06042193888037 chr21 48129895 121834 0.0025313581091336267 0.4892954737046844 chr22 51304566 134473 0.0026210727520821443 0.6242601189661361 chrMT 16571 1242523 74.98177539074287 314.5206867575394 chrX 155270560 28680180 0.1847109973712982 9.796823565895476 chrY 59373566 640918 0.01079466912935632 1.6263385004755575