BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238248.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 = 1,995,852 number of mapped reads = 1,827,570 (91.57%) number of supplementary alignments = 14,045 (0.7%) number of secondary alignments = 0 number of mapped bases = 120,797,288 bp number of sequenced bases = 120,742,327 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 59,722 duplication rate = 2.12% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.4901 >>>>>>> ACTG content number of A's = 33,008,969 bp (27.34%) number of C's = 23,938,969 bp (19.83%) number of T's = 35,976,049 bp (29.8%) number of G's = 27,789,356 bp (23.02%) number of N's = 28,984 bp (0.02%) GC percentage = 42.84% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 1,057,961 number of insertions = 10,566 mapped reads with insertion percentage = 0.57% number of deletions = 33,608 mapped reads with deletion percentage = 1.82% homopolymer indels = 44.67% >>>>>>> Coverage mean coverageData = 0.039X std coverageData = 0.3922X There is a 3.41% of reference with a coverageData >= 1X There is a 0.34% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% 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 11860083 0.04758296269199666 0.5200757899998021 chr2 243199373 8380021 0.034457412026304854 0.5743270651691001 chr3 198022430 6265800 0.03164187006492143 0.19545733191371267 chr4 191154276 6660161 0.034841810182681975 0.22891178131734505 chr5 180915260 9398074 0.05194738133201146 0.25408643139146175 chr6 171115067 8951932 0.05231527624624663 0.35244000881767934 chr7 159138663 8401999 0.0527967172879918 0.7656930530794359 chr8 146364022 5133566 0.0350739610038866 0.3840952142339143 chr9 141213431 4317525 0.03057446426607962 0.4140765729618171 chr10 135534747 3947260 0.029123601787518 0.33286003877361087 chr11 135006516 4186157 0.03100707376227678 0.2981563213611669 chr12 133851895 7901608 0.05903247017907367 0.27714925085927844 chr13 115169878 1830067 0.015890153152719324 0.13815690085443164 chr14 107349540 3986211 0.03713300494813485 0.26199439152752674 chr15 102531392 3261369 0.03180849236885421 0.20578145912740234 chr16 90354753 4180765 0.0462705597789637 0.27166299987965187 chr17 81195210 3077649 0.03790431726206509 0.22981521634605928 chr18 78077248 3944265 0.0505174695706488 0.7482061896770337 chr19 59128983 1989180 0.03364137008749161 0.4446591431842558 chr20 63025520 3055515 0.04848059960473154 0.25146256581340354 chr21 48129895 1540945 0.03201637984042974 0.2298866578493862 chr22 51304566 1516270 0.029554289573368576 0.19126200034750854 chrMT 16571 9082 0.5480658982559894 0.8090431510981859 chrX 155270560 6671421 0.04296642583114275 0.2709919150146808 chrY 59373566 330363 0.005564142803886834 0.1346667709750226