BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124941.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 = 1,877,382 number of mapped reads = 1,846,576 (98.36%) number of supplementary alignments = 12,981 (0.69%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 924,050 number of mapped paired reads (second in pair) = 922,526 number of mapped paired reads (both in pair) = 1,840,820 number of mapped paired reads (singletons) = 5,756 number of mapped bases = 251,155,673 bp number of sequenced bases = 251,005,627 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 260,908 duplication rate = 14.21% >>>>>>> Insert size mean insert size = 59,657.0879 std insert size = 2,349,132.458 median insert size = 176 >>>>>>> Mapping quality mean mapping quality = 53.8037 >>>>>>> ACTG content number of A's = 72,992,195 bp (29.08%) number of C's = 50,795,421 bp (20.24%) number of T's = 73,795,211 bp (29.4%) number of G's = 53,401,280 bp (21.27%) number of N's = 21,520 bp (0.01%) GC percentage = 41.51% >>>>>>> Mismatches and indels general error rate = 0.0116 number of mismatches = 2,816,326 number of insertions = 43,509 mapped reads with insertion percentage = 2.29% number of deletions = 87,274 mapped reads with deletion percentage = 4.59% homopolymer indels = 47.91% >>>>>>> Coverage mean coverageData = 0.0811X std coverageData = 0.8497X There is a 4.69% of reference with a coverageData >= 1X There is a 2.49% of reference with a coverageData >= 2X There is a 0.38% of reference with a coverageData >= 3X There is a 0.19% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.03% 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% 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 21522908 0.08635046891217174 1.064395308023873 chr2 243199373 21476871 0.08830973014062828 0.8676986780317779 chr3 198022430 14852106 0.0750021399091002 0.3779253879760073 chr4 191154276 10665198 0.05579366689134383 0.4438731357498733 chr5 180915260 12409397 0.06859231775141578 0.3621782071947685 chr6 171115067 15328139 0.08957796217909905 0.624571393432217 chr7 159138663 16495584 0.10365541402091584 1.3159097561820121 chr8 146364022 16343819 0.11166554988493005 0.5374569851766869 chr9 141213431 10536980 0.07461740661198155 1.1605853662572596 chr10 135534747 11939503 0.088091823420012 1.8887852602282589 chr11 135006516 17318278 0.128277349220685 0.8148060554469779 chr12 133851895 9265236 0.06922005848329603 0.3626035975403865 chr13 115169878 13485584 0.11709297807886886 0.5893989838961433 chr14 107349540 3943263 0.03673292871119895 0.26824157026048917 chr15 102531392 5265075 0.05135085847659222 0.3130149531688572 chr16 90354753 7314479 0.08095289685535415 1.0893154466131774 chr17 81195210 5698765 0.07018597525642215 1.1967672761130428 chr18 78077248 7152994 0.09161432021784374 1.300755725971703 chr19 59128983 3785620 0.06402308661388612 0.6397470922893396 chr20 63025520 6529717 0.10360433360962353 0.4653867259016144 chr21 48129895 2131473 0.04428584354900421 0.3348301726329318 chr22 51304566 1880822 0.03665993393258604 0.262821294480746 chrMT 16571 175358 10.582221954016052 7.0831614813425885 chrX 155270560 15248851 0.09820825660704773 0.5145780888585242 chrY 59373566 389653 0.006562735342525999 0.3786881844730266