BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238653.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 = 4,476,150 number of mapped reads = 3,800,564 (84.91%) number of supplementary alignments = 31,048 (0.69%) number of secondary alignments = 0 number of mapped bases = 234,393,374 bp number of sequenced bases = 234,290,299 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,163,287 duplication rate = 21.17% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.8005 >>>>>>> ACTG content number of A's = 58,680,851 bp (25.05%) number of C's = 41,430,865 bp (17.68%) number of T's = 78,338,743 bp (33.44%) number of G's = 55,834,568 bp (23.83%) number of N's = 5,272 bp (0%) GC percentage = 41.51% >>>>>>> Mismatches and indels general error rate = 0.0059 number of mismatches = 1,350,843 number of insertions = 15,896 mapped reads with insertion percentage = 0.41% number of deletions = 59,906 mapped reads with deletion percentage = 1.56% homopolymer indels = 41.56% >>>>>>> Coverage mean coverageData = 0.0757X std coverageData = 1.118X There is a 3.07% of reference with a coverageData >= 1X There is a 1.59% of reference with a coverageData >= 2X There is a 0.96% of reference with a coverageData >= 3X There is a 0.6% of reference with a coverageData >= 4X There is a 0.38% of reference with a coverageData >= 5X There is a 0.25% of reference with a coverageData >= 6X There is a 0.17% of reference with a coverageData >= 7X There is a 0.11% of reference with a coverageData >= 8X There is a 0.08% of reference with a coverageData >= 9X There is a 0.05% of reference with a coverageData >= 10X There is a 0.04% of reference with a coverageData >= 11X There is a 0.03% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.02% 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% 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 19152558 0.07684056281649145 1.4370564209173813 chr2 243199373 10582676 0.043514404948733154 2.340803158994706 chr3 198022430 13292337 0.06712541099510798 0.5781489801419972 chr4 191154276 19540784 0.1022251995032536 0.7025252430660137 chr5 180915260 16426000 0.09079388880738971 0.6539383882237204 chr6 171115067 10585626 0.06186261786053007 0.9637183243594303 chr7 159138663 11831749 0.07434867666319403 0.764357210254265 chr8 146364022 3864307 0.026402027951923868 0.775348911361774 chr9 141213431 12241601 0.08668864507654375 0.864724415640735 chr10 135534747 10535916 0.0777359033990007 0.7888894581154839 chr11 135006516 8537383 0.0632368218434731 0.689871148913877 chr12 133851895 13324268 0.09954485889049236 0.6813700114326124 chr13 115169878 12923512 0.11221260475764332 0.8642437594606263 chr14 107349540 8991156 0.08375588754269464 0.6621749244876751 chr15 102531392 11782916 0.11492008223198608 0.8171840574633595 chr16 90354753 4856062 0.053744400142403136 0.6003222715734751 chr17 81195210 7221791 0.08894355960160705 0.6583462426102654 chr18 78077248 3869705 0.04956251787972855 2.846048649669166 chr19 59128983 3847108 0.06506298273386504 1.0313540550181295 chr20 63025520 4204909 0.0667175613941781 0.5478239566447147 chr21 48129895 3074263 0.06387429268233392 0.5690219470999524 chr22 51304566 4414425 0.08604351121496671 0.6122506819288464 chrMT 16571 30176 1.8210126123951482 2.726736423541508 chrX 155270560 18443001 0.1187797673944114 0.7757846356804001 chrY 59373566 819145 0.013796459522070816 0.4835904225017915