BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124918.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 5,254,468 number of mapped reads = 5,192,656 (98.82%) number of supplementary alignments = 18,526 (0.35%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,600,308 number of mapped paired reads (second in pair) = 2,592,348 number of mapped paired reads (both in pair) = 5,172,762 number of mapped paired reads (singletons) = 19,894 number of mapped bases = 450,170,915 bp number of sequenced bases = 449,928,408 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 460,737 duplication rate = 6.27% >>>>>>> Insert size mean insert size = 30,662.8085 std insert size = 1,634,976.6012 median insert size = 193 >>>>>>> Mapping quality mean mapping quality = 52.7748 >>>>>>> ACTG content number of A's = 125,835,640 bp (27.97%) number of C's = 84,312,323 bp (18.74%) number of T's = 133,418,909 bp (29.65%) number of G's = 105,915,535 bp (23.54%) number of N's = 446,001 bp (0.1%) GC percentage = 42.28% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 3,832,555 number of insertions = 61,044 mapped reads with insertion percentage = 1.15% number of deletions = 144,685 mapped reads with deletion percentage = 2.73% homopolymer indels = 47.84% >>>>>>> Coverage mean coverageData = 0.1454X std coverageData = 1.3167X There is a 9.73% of reference with a coverageData >= 1X There is a 2.8% of reference with a coverageData >= 2X There is a 0.85% of reference with a coverageData >= 3X There is a 0.34% of reference with a coverageData >= 4X There is a 0.15% of reference with a coverageData >= 5X There is a 0.08% of reference with a coverageData >= 6X There is a 0.04% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.02% 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% 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 39910564 0.16012222493118683 1.7569905043780962 chr2 243199373 38941007 0.16011968501251028 1.458404566352351 chr3 198022430 28801018 0.14544321065042987 0.5155049011284444 chr4 191154276 23918398 0.12512614679882966 0.9995524948795306 chr5 180915260 28037303 0.15497478211622392 0.5470547654564174 chr6 171115067 20226685 0.11820516658535977 0.764057475061255 chr7 159138663 33173500 0.2084565709842617 1.906137338140257 chr8 146364022 34772019 0.23757217467008387 0.9808731007885596 chr9 141213431 21768452 0.15415284400249435 1.5368677878412522 chr10 135534747 21446662 0.15823737067218638 3.150774989548623 chr11 135006516 20004397 0.14817356667436704 0.8678970230866329 chr12 133851895 25838987 0.19304162260833138 0.603775849332854 chr13 115169878 13703722 0.118987032355804 0.45426166085285563 chr14 107349540 10756855 0.10020401577873553 0.4919613415253296 chr15 102531392 8944982 0.08724139822465299 0.40755078301210446 chr16 90354753 14109080 0.15615205101606552 1.3645388862577588 chr17 81195210 10684723 0.13159302131246411 2.0069342452054837 chr18 78077248 8359358 0.1070652234054151 1.634726816993129 chr19 59128983 5265224 0.089046415697696 1.0861388117972979 chr20 63025520 8139117 0.12914002137546823 0.5519346854100822 chr21 48129895 4769865 0.09910399762974759 0.6278092085094683 chr22 51304566 3090601 0.060240271791793344 0.3436545139506432 chrMT 16571 278160 16.785951360811055 53.04788538991133 chrX 155270560 21541188 0.13873324086678118 0.6736090919788449 chrY 59373566 3689048 0.06213283534292011 1.4390860225139774