BamQC report
-----------------------------------
>>>>>>> Input
bam file = ERR2094100.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/ERP024468/ERP024468.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 = 379,056
number of mapped reads = 355,390 (93.76%)
number of supplementary alignments = 25,204 (6.65%)
number of secondary alignments = 0
number of mapped paired reads (first in pair) = 178,479
number of mapped paired reads (second in pair) = 176,911
number of mapped paired reads (both in pair) = 352,568
number of mapped paired reads (singletons) = 2,822
number of mapped bases = 45,024,324 bp
number of sequenced bases = 44,134,869 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 335,149
duplication rate = 50.16%
>>>>>>> Insert size
mean insert size = 1,629,509.0251
std insert size = 11,208,662.3956
median insert size = 155
>>>>>>> Mapping quality
mean mapping quality = 41.2992
>>>>>>> ACTG content
number of A's = 13,031,089 bp (29.53%)
number of C's = 9,170,020 bp (20.78%)
number of T's = 12,197,898 bp (27.64%)
number of G's = 9,735,420 bp (22.06%)
number of N's = 442 bp (0%)
GC percentage = 42.84%
>>>>>>> Mismatches and indels
general error rate = 0.0366
number of mismatches = 1,549,759
number of insertions = 30,427
mapped reads with insertion percentage = 8.41%
number of deletions = 126,382
mapped reads with deletion percentage = 34.2%
homopolymer indels = 28.42%
>>>>>>> Coverage
mean coverageData = 0.0145X
std coverageData = 2.7755X
There is a 0.02% of reference with a coverageData >= 1X
There is a 0.01% of reference with a coverageData >= 2X
There is a 0.01% 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 0.01% of reference with a coverageData >= 6X
There is a 0.01% of reference with a coverageData >= 7X
There is a 0.01% 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 0.01% of reference with a coverageData >= 11X
There is a 0.01% of reference with a coverageData >= 12X
There is a 0.01% of reference with a coverageData >= 13X
There is a 0.01% 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 0.01% of reference with a coverageData >= 21X
There is a 0.01% of reference with a coverageData >= 22X
There is a 0.01% of reference with a coverageData >= 23X
There is a 0.01% of reference with a coverageData >= 24X
There is a 0.01% of reference with a coverageData >= 25X
There is a 0.01% of reference with a coverageData >= 26X
There is a 0.01% of reference with a coverageData >= 27X
There is a 0.01% of reference with a coverageData >= 28X
There is a 0.01% of reference with a coverageData >= 29X
There is a 0.01% of reference with a coverageData >= 30X
There is a 0.01% of reference with a coverageData >= 31X
There is a 0.01% of reference with a coverageData >= 32X
There is a 0.01% of reference with a coverageData >= 33X
There is a 0.01% of reference with a coverageData >= 34X
There is a 0.01% of reference with a coverageData >= 35X
There is a 0.01% of reference with a coverageData >= 36X
There is a 0.01% of reference with a coverageData >= 37X
There is a 0.01% of reference with a coverageData >= 38X
There is a 0.01% of reference with a coverageData >= 39X
There is a 0.01% of reference with a coverageData >= 40X
There is a 0.01% of reference with a coverageData >= 41X
There is a 0.01% of reference with a coverageData >= 42X
There is a 0.01% of reference with a coverageData >= 43X
There is a 0.01% of reference with a coverageData >= 44X
There is a 0.01% of reference with a coverageData >= 45X
There is a 0.01% of reference with a coverageData >= 46X
There is a 0.01% of reference with a coverageData >= 47X
There is a 0.01% 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 1112835 0.004464723078864466 1.63412469857757
chr2 243199373 2048536 0.008423278295211722 2.3373462802075315
chr3 198022430 790036 0.003989628851640696 1.1498740712584554
chr4 191154276 1365209 0.00714192237059871 1.93052828823735
chr5 180915260 806148 0.004455942522482625 1.6539240140907912
chr6 171115067 1008508 0.005893741665659401 1.598230569292081
chr7 159138663 1236042 0.007767075434082288 2.3337228320249137
chr8 146364022 1284620 0.008776883707117586 2.876665511862717
chr9 141213431 714290 0.005058229907323759 1.5026448515244009
chr10 135534747 1024097 0.007555973819761511 2.132786827736208
chr11 135006516 1323889 0.009806111876851929 2.309111267575719
chr12 133851895 1272706 0.009508315141896198 2.563902706343696
chr13 115169878 930292 0.00807756347540804 1.9914116193170217
chr14 107349540 117084 0.0010906800345860822 0.3044087715753464
chr15 102531392 272795 0.002660599789769752 0.5938198555770777
chr16 90354753 153433 0.0016981176408063447 0.6587596617645546
chr17 81195210 369129 0.004546191825847855 1.2017946421202579
chr18 78077248 165065 0.0021141242068367983 0.4773088596641064
chr19 59128983 89189 0.001508380416419474 0.4110711613631407
chr20 63025520 199859 0.003171080540073291 1.3154697491712355
chr21 48129895 201240 0.0041811851033541625 1.235989273347794
chr22 51304566 60670 0.0011825458186314256 0.30486476154978676
chrMT 16571 838230 50.58415303844065 241.43055714991738
chrX 155270560 26731748 0.1721623725708209 9.09323666698925
chrY 59373566 908674 0.015304352782179193 3.2032690098711325