BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238522.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 = 3,723,832 number of mapped reads = 3,421,983 (91.89%) number of supplementary alignments = 25,270 (0.68%) number of secondary alignments = 0 number of mapped bases = 210,329,366 bp number of sequenced bases = 210,230,064 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 702,163 duplication rate = 16.57% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 40.8465 >>>>>>> ACTG content number of A's = 51,613,784 bp (24.55%) number of C's = 36,636,190 bp (17.43%) number of T's = 70,823,331 bp (33.69%) number of G's = 51,142,557 bp (24.33%) number of N's = 14,202 bp (0.01%) GC percentage = 41.75% >>>>>>> Mismatches and indels general error rate = 0.0057 number of mismatches = 1,170,335 number of insertions = 12,504 mapped reads with insertion percentage = 0.36% number of deletions = 58,100 mapped reads with deletion percentage = 1.68% homopolymer indels = 42.62% >>>>>>> Coverage mean coverageData = 0.0679X std coverageData = 0.7992X There is a 4.13% of reference with a coverageData >= 1X There is a 1.48% of reference with a coverageData >= 2X There is a 0.59% of reference with a coverageData >= 3X There is a 0.25% of reference with a coverageData >= 4X There is a 0.11% of reference with a coverageData >= 5X There is a 0.05% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% 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% 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 24948792 0.10009520497844618 1.3374138066388 chr2 243199373 20820209 0.0856096327189133 1.673864553161536 chr3 198022430 8079253 0.0407996861769649 0.316322391975663 chr4 191154276 5247041 0.027449247329418884 0.2617200176601804 chr5 180915260 21958017 0.12137183452628596 0.5381804735912876 chr6 171115067 12094284 0.0706792464979136 0.7425073065011292 chr7 159138663 16801950 0.1055805652960651 1.1201986366216654 chr8 146364022 17812007 0.12169662159188274 0.7979471578933482 chr9 141213431 1370950 0.009708354157898762 0.24066512981552973 chr10 135534747 11291064 0.08330752260894396 0.5453139882708987 chr11 135006516 1318710 0.009767750765451944 0.16015709679667786 chr12 133851895 7416975 0.0554118042183863 0.364186176838336 chr13 115169878 7606545 0.06604630596205024 0.5131239664557847 chr14 107349540 2471965 0.02302725284151194 0.23404017718815606 chr15 102531392 6824225 0.06655742077509295 0.5306378046109158 chr16 90354753 3550277 0.03929264241362045 0.34924865999949484 chr17 81195210 4990071 0.06145770175358867 0.3826619753432367 chr18 78077248 7022645 0.08994483258426321 1.1457806504529857 chr19 59128983 3044610 0.051490992158617035 0.8792144130323267 chr20 63025520 6106111 0.09688315145991655 0.4842852459752747 chr21 48129895 3953666 0.0821457433056939 0.45823127014428744 chr22 51304566 422693 0.008238896319676498 0.1269638148607915 chrMT 16571 26069 1.5731699957757528 2.033984800367563 chrX 155270560 14585332 0.09393494813182872 0.4853411334794281 chrY 59373566 565905 0.00953126177396857 0.30164260986310143