BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082664.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 3,197,676 number of mapped reads = 2,818,288 (88.14%) number of supplementary alignments = 12,627 (0.39%) number of secondary alignments = 0 number of mapped bases = 188,016,250 bp number of sequenced bases = 187,943,430 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 110,364 duplication rate = 3.13% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.2829 >>>>>>> ACTG content number of A's = 52,143,530 bp (27.74%) number of C's = 32,772,178 bp (17.44%) number of T's = 62,055,482 bp (33.02%) number of G's = 40,920,269 bp (21.77%) number of N's = 51,971 bp (0.03%) GC percentage = 39.21% >>>>>>> Mismatches and indels general error rate = 0.0096 number of mismatches = 1,778,671 number of insertions = 17,001 mapped reads with insertion percentage = 0.6% number of deletions = 44,943 mapped reads with deletion percentage = 1.58% homopolymer indels = 49.65% >>>>>>> Coverage mean coverageData = 0.0607X std coverageData = 0.4141X There is a 5.03% of reference with a coverageData >= 1X There is a 0.77% of reference with a coverageData >= 2X There is a 0.14% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 14338384 0.05752597101854362 0.6043745261103902 chr2 243199373 16932924 0.06962568937215147 0.5228457800184654 chr3 198022430 12898753 0.06513783817318068 0.3009360404371111 chr4 191154276 12588110 0.06585314366705561 0.32160135653819405 chr5 180915260 13043025 0.0720946646512848 0.31402075997446643 chr6 171115067 10332401 0.06038276570934575 0.3449526725353762 chr7 159138663 9541010 0.05995406659913939 0.5438943951888248 chr8 146364022 10711155 0.07318161153018875 0.48487666510062916 chr9 141213431 7155898 0.050674344142236726 0.4216644547270392 chr10 135534747 8965357 0.06614803361089389 0.4213148369917981 chr11 135006516 8731040 0.06467124890475656 0.37726943224417175 chr12 133851895 7829527 0.058493957070985064 0.28692102610063314 chr13 115169878 6954404 0.06038387919452341 0.2851119525684762 chr14 107349540 5766173 0.053713998215548946 0.30044995529390933 chr15 102531392 4727634 0.046109136994843494 0.24883470155477197 chr16 90354753 5624822 0.062252640987242806 0.3355950806724731 chr17 81195210 4094415 0.05042680473392457 0.2900756619444639 chr18 78077248 5133335 0.06574687417261428 0.7775882273142821 chr19 59128983 2910782 0.04922766894198062 0.4991987557085054 chr20 63025520 3842937 0.06097430056903934 0.30405372059566355 chr21 48129895 2624747 0.054534650449580245 0.2878414821766114 chr22 51304566 2113652 0.04119812649813664 0.23352696918016935 chrMT 16571 5427 0.32749984913402935 0.5692080873713883 chrX 155270560 10697415 0.06889532052953246 0.33402406562386744 chrY 59373566 452923 0.007628361079070103 0.17446279728073516