BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013289.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 = 1,872,769 number of mapped reads = 1,376,885 (73.52%) number of supplementary alignments = 14,225 (0.76%) number of secondary alignments = 0 number of mapped bases = 88,799,587 bp number of sequenced bases = 88,760,361 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 141,913 duplication rate = 8.37% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8419 >>>>>>> ACTG content number of A's = 23,355,060 bp (26.31%) number of C's = 16,543,614 bp (18.64%) number of T's = 28,001,297 bp (31.55%) number of G's = 20,859,392 bp (23.5%) number of N's = 998 bp (0%) GC percentage = 42.14% >>>>>>> Mismatches and indels general error rate = 0.0077 number of mismatches = 668,613 number of insertions = 5,864 mapped reads with insertion percentage = 0.42% number of deletions = 23,042 mapped reads with deletion percentage = 1.66% homopolymer indels = 46.6% >>>>>>> Coverage mean coverageData = 0.0287X std coverageData = 0.3245X There is a 1.84% of reference with a coverageData >= 1X There is a 0.62% of reference with a coverageData >= 2X There is a 0.23% of reference with a coverageData >= 3X There is a 0.09% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% 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 6746048 0.02706532073193912 0.43666037000048125 chr2 243199373 5394490 0.02218134830470965 0.3731050830512366 chr3 198022430 5371808 0.027127270380431147 0.23742987349075456 chr4 191154276 5119340 0.026781195310535456 0.23924805758229917 chr5 180915260 7305514 0.040380861183296535 0.2944862076920176 chr6 171115067 3418502 0.019977796578252223 0.22975494460725976 chr7 159138663 6658247 0.041839279496774455 0.6706211275918607 chr8 146364022 5495767 0.037548619701090205 0.345230058754136 chr9 141213431 2230030 0.015791911464852093 0.2138377213525098 chr10 135534747 2442294 0.01801968907648457 0.22127784290910313 chr11 135006516 3944492 0.029217049049691794 0.2695854905028397 chr12 133851895 3808088 0.028450011858255724 0.24549025614771142 chr13 115169878 1558590 0.013532965624918002 0.1700938131759468 chr14 107349540 2668680 0.024859724596863666 0.2326213467559395 chr15 102531392 1696809 0.01654916574233187 0.18922562988615396 chr16 90354753 5641078 0.062432554046160695 0.36767550739728483 chr17 81195210 4925783 0.060665930908978496 0.3698958532567139 chr18 78077248 1583770 0.020284654500117627 0.32273437864551047 chr19 59128983 3063689 0.05181365963963899 0.45011497662531497 chr20 63025520 2768668 0.043929316251575555 0.3082492761765436 chr21 48129895 1104006 0.02293805128808197 0.2203959941757952 chr22 51304566 826002 0.01609997051724402 0.18082788044522133 chrMT 16571 21332 1.2873091545471003 1.7259077964154166 chrX 155270560 4826359 0.0310835421730945 0.2615605469815034 chrY 59373566 180201 0.0030350375114743824 0.07772423496038385