Sample Resequencing Stats
Note: The mutation counts shown below represent unfiltered mutation sets.
| ALE, Flask, Isolate |
Predicted Mutations |
Mean Coverage |
Total Reads |
Percent Mapped |
Mapped Reads |
Average Read Length |
|
A1 F2 I194 R1
|
197 |
32.2 |
1845014 |
95.2% |
1756453 |
85.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
3,011,010 |
A→G |
E531G (GAA→GGA) |
ygfK → |
putative selenate reductase subunit YgfK |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 3,011,010 | 0 | A | G | 97.5%
| 135.9
/ ‑5.5
| 40 | E531G (GAA→GGA) | ygfK | putative selenate reductase subunit YgfK |
| Reads supporting (aligned to +/- strand): ref base A (0/0); major base G (23/16); minor base C (0/1); total (23/17) |
| Fisher's exact test for biased strand distribution p-value = 4.25e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
CGATCACCAGTGCCAATACAACTGTACCCGCCTGGATTACGACAGTGCGCTGAATATCCGCGAACTGAAAAAAGTCGCGCTGGAAAAAGGTTGGGATGAATATAAGCAACGCTGGCACAAACCAGCCGGTTCTGGTTCACGCCATCCGGTTGCCGTGAT > NZ_CP009273/3010927‑3011085
|
cGATCACCAGTGCCAATACAACTGTACCCGCCTGGATTACGACAGTGCGCTGAATATCCGCGAACTGAAAAAAGTCGCGCTGGGAAAAgg > 2:502760/1‑90 (MQ=255)
gATCACCAGTGCCAATACAACTGTACCCGCCTGGATTACGACAGTGCGCTGAATATCCGCGAACTGAAAAAAGTCGCGCTGGGAAAAGGt > 1:50175/1‑90 (MQ=255)
cACCAGTGCCAATACAACTGTACCCGCCTGGATTACGACAGTGCGCTGAATATCCGCGAACTGAAAAAAGTCGCGCTGGGAAAAGGTTgg > 2:319407/1‑90 (MQ=255)
cACCAGTGCCAATACAACTGTACCCGCCTGGATTACGACAGTGCGCTGAATATCCGCGAACTGAAAAAAGTCGCGCTGGGAAAAGGTTgg > 2:587017/1‑90 (MQ=255)
cAGTGCAAATAAAACTGTCCCCGCCTGGATTACGACAGTGCGCTGAATATCCGCGAACTGAAAAAAGTCGCGCTGGGAAAAGGTTGGGAt < 1:676376/90‑1 (MQ=255)
cAGTCCCAATAAACCTGTCCCCGCCTGGATTACGACAGTGCGCTGAATATCCGCGAACTGAAAAAAGTCGCGCTGGGAAAAGGTTGGGAt < 2:747185/90‑1 (MQ=255)
gCCAATACAACTGTACCCGCCTGGATTACGACAGTGCGCTGAATATCCGCGAACTGAAAAAAGTCGCGCTGGGAAAAGGTTGGGATGAat > 1:307223/1‑90 (MQ=255)
gTACCCGCCTGGATTACGACAGTGCGCTGAATATCCGCGAACTGAAAAAAGTCGCGCTGGGAAAAGGTTGGGATGAATATAAGCAACGCt > 1:475341/1‑90 (MQ=255)
gTACCCGCCTGGATTACGACAGTGCGCTGAATATCCGCGAACTGAAAAAAGTCGCGCTGGGAAAAGGTTGGGATGAATATAAGCAACGCt > 2:100757/1‑90 (MQ=255)
aCCCGCCTGGATTACGACAGTGCGCTGAATATCCGCGAACTGAAAAAAGTCGCGCTGGGAAAAGGTTGGGAt > 2:215427/1‑72 (MQ=255)
aCCCGCCTGGATTACGACAGTGCGCTGAATATCCGCGAACTGAAAAAAGTCGCGCTGGGAAAAGGTTGGGAt < 1:215427/72‑1 (MQ=255)
aCCCGCCTGGATTACGACAGTGCGCTGAATATCCGCGAACTGAAAAAAGTCGCGCTGGGAAAAGGTTGGGATGAATATAAGCAACGCTgg > 1:98455/1‑90 (MQ=255)
aCCCGCCTGGATTACGACAGTGCGCTGAATATCCGCGAACTGAAAAAAGTCGCGCTGGGAAAAGGTTGGGATGAATATAAGCAACGCTgg > 2:382273/1‑90 (MQ=255)
cGCCTGGATTACGACAGTGCGCTGAATATCCGCGAACTGAAAAAAGTCGCGCTGGGAAAAGGtt > 1:362944/1‑64 (MQ=255)
cGCCTGGATTACGACAGTGCGCTGAATATCCGCGAACTGAAAAAAGTCGCGCTGGGAAAAGGtt < 2:362944/64‑1 (MQ=255)
cGCCTGGATTACGACAGTGCGCTGAATATCCGCGAACTGAAAAAAGTCGCGCTGGGAAAAGGTTGGGATGAATATAAGc > 2:144094/1‑79 (MQ=255)
cGCCTGGATTACGACAGTGCGCTGAATATCCGCGAACTGAAAAAAGTCGCGCTGGGAAAAGGTTGGGATGAATATAAGc < 1:144094/79‑1 (MQ=255)
ccTGGATTACGACAGTGCGCTGAATATCCGCGAACTGAAAAAAGTCGCGCTGGGAAAAGGTTGGGATGAATATAAGCAACGCTGGCACaa > 1:864083/1‑90 (MQ=255)
aCGACAGTGCGCTGAATATCCGCGAACTGAAAAAAGTCGCGCTGGGAAAAGGTTGGGATGAATATAAGCAACGCTGGCACAAACCAGCCg < 1:132698/90‑1 (MQ=255)
cGACAGTGCGCTGAATATCCGCGAACTGAAAAAAGTCGCGCTGGGAAAAGGTTGGGATGAATATAAGCAACGCTGGCACAAACCAGCCgg > 2:219953/1‑90 (MQ=255)
cAGTGCACTGAATATCCGCGAACTGAAAAAAGTCGCGCTGGCAAAAGGTTGGGATGAATATAAGCAACGCTGGCACAAACCAGCCGGTTc < 2:200494/90‑1 (MQ=255)
gTGCGCTGAATATCCGCGAACTGAAAAAAGTCGCGCTGGGAAAAGGTTGGGATGAATATAAGCa > 1:25007/1‑64 (MQ=255)
gTGCGCTGAATATCCGCGAACTGAAAAAAGTCGCGCTGGGAAAAGGTTGGGATGAATATAAGCa < 2:25007/64‑1 (MQ=255)
gTGCGCTGAATATCCGCGAACTGAAAAAAGTCGCGCTGGGAAAAGGTTGGGATGAATATAAGCAACGCTGGCACAAACCAGcc < 2:689901/83‑1 (MQ=255)
gTGCGCTGAATATCCGCGAACTGAAAAAAGTCGCGCTGGGAAAAGGTTGGGATGAATATAAGCAACGCTGGCACAAACCAGcc > 1:689901/1‑83 (MQ=255)
tCCGCGAACTGAAAAAAGTCGCGCTGGGAAAAGGTTGGGATGAATATAAGCa < 1:522176/52‑1 (MQ=255)
tCCGCGAACTGAAAAAAGTCGCGCTGGGAAAAGGTTGGGATGAATATAAGCa > 2:522176/1‑52 (MQ=255)
ccGCGAACTGAAAAAAGTCGCGCTGGGAAAAGGTTGGGATGAATATAAGCAACGCTGGCACAAACCAGCCGGTTCTGGTTCACGCCATcc < 1:604041/90‑1 (MQ=255)
gcgAACTGAAAAAAGTCGCGCTGGGAAAAGGTTGGGATGAATATAAGCAACGCTGGCACAAACCAGCCGGTTCTGGTTCACGCCATcc > 1:144020/1‑88 (MQ=255)
gcgAACTGAAAAAAGTCGCGCTGGGAAAAGGTTGGGATGAATATAAGCAACGCTGGCACAAACCAGCCGGTTCTGGTTCACGCCATcc < 2:144020/88‑1 (MQ=255)
gAACTGAAAAAAGTCGCGCTGGGAAAAGGTTGGGATGAATATAAGCAACGCTGGCACAAACCAGCCGGTTCTGGTTCACGCCATCCGGtt > 2:551021/1‑90 (MQ=255)
aCTGAAAAAAGTCGCGCTGGGAAAAGGTTGGGATGAATATAAGCAACGCTGGCACAAACCAGCCGGTTCTGGTTCACGCCATCCGGt < 2:256772/87‑1 (MQ=255)
aCTGAAAAAAGTCGCGCTGGGAAAAGGTTGGGATGAATATAAGCAACGCTGGCACAAACCAGCCGGTTCTGGTTCACGCCATCCGGt > 1:256772/1‑87 (MQ=255)
aCTGAAAAAAGTCGCGCTGGGAAAAGGTTGGGATGAATATAAGCAACGCTGGCACAAACCAGCCGGTTCTGGGTCACGCCATCCGGTTGc > 2:214341/1‑90 (MQ=255)
tGAAAAAAGTCGCGCTGGGAAAAGGTTGGGATGAATATAAGCAACGCTGGCACAAACCAGCCGGTTCTGGTTCACGCCATCCGGTTGCCg < 2:864083/90‑1 (MQ=255)
aaaaGTCGCGCTGGGAAAAGGTTGGGATGAATATAAGCAACGCTGGCACAAACCAGCCGGTTCTGGTTCACGCCATCCGGTTGCCGTGAt < 2:17628/90‑1 (MQ=255)
aGTCGCGCTGGGAAAAGGTTGGGATGAATATAAGCAACGCTGGCACAAACCAGCCGGTTCTGGTTCAc > 2:609041/1‑68 (MQ=255)
aGTCGCGCTGGGAAAAGGTTGGGATGAATATAAGCAACGCTGGCACAAACCAGCCGGTTCTGGTTCAc < 1:609041/68‑1 (MQ=255)
gcgcTGGGAAAAGGTTGGGATGAATATAAGCAACGCTGGCACAAACCAGCCGGTTCTGGTTCACGCCATCCGGt < 1:612999/74‑1 (MQ=255)
gcgcTGGGAAAAGGTTGGGATGAATATAAGCAACGCTGGCACAAACCAGCCGGTTCTGGTTCACGCCATCCGGt > 2:612999/1‑74 (MQ=255)
|
CGATCACCAGTGCCAATACAACTGTACCCGCCTGGATTACGACAGTGCGCTGAATATCCGCGAACTGAAAAAAGTCGCGCTGGAAAAAGGTTGGGATGAATATAAGCAACGCTGGCACAAACCAGCCGGTTCTGGTTCACGCCATCCGGTTGCCGTGAT > NZ_CP009273/3010927‑3011085
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 19 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
GTCATATTTGCGATCACCAGTGCCAATACAACTGTACCCGCCTGGATTACGACAGTGCGCTGAATATCCGCGAACTGAAAAAAGTCGCGCTGGAAAAAGGTTGGGATGAATATAAGCAACGCTGGCACAAACCAGCCGGTTCTGGTTCACGCCATCCGGTTGCCGTGATTGGTGCAGGTCCGGCGGGTCTGGC > NZ_CP009273/3010917‑3011109
|
ttcattttggcacccccgggccccaaaacatgTGTACCCGCCTGGATTACGACAGTGCGCTGAATATCCGCGAACTGAAAAAAGTCGCGCTGGGAAAAGG < SRR3722072.336718/68‑1 (MQ=60)
taatatttgcaaccccccgtgcaaaaaaAACTGTCCCCGCCTGGATTACGACAGTGCGCTGAATATCCGCGAACTGAAAAAAGTCGCGCTGGGAAAAGGT < SRR3722072.680648/72‑1 (MQ=60)
TCATATTTGCGATCACCAGTGCCAATACAACTGTACCCGCCTGGATTACGACAGTGCGCTGAATATCCGCGAACTGAAAAAAGTCGCGCTGGGAAAAGGT > SRR3722072.51094/1‑100 (MQ=60)
tgcaacccccagtccaaaaacacctgccCCCGCCTGGATTACGACAGTGCGCTGAATATCCGCGAACTGAAAAAAGTCGCGCTGGGAAAAGGTTGGGATG < SRR3722072.630916/72‑1 (MQ=60)
gacccCCAGTGCAAATACAACTGTACCCGCCTGGATTACGACAGTGCGCTGAATATCCGCGAACTGAAAAAAGTCGCGCTGGGAAAAGGTTGGGATGAAT < SRR3722072.213812/95‑1 (MQ=60)
GATCACCAGTGCCAATACAACTGTACCCGCCTGGATTACGACAGTGCGCTGAATATCCGCGAACTGAAAAAAGTCGCGCTGGGAAAAGGTTGGGATGAAT > SRR3722072.312553/1‑100 (MQ=60)
acgagataatcggacgtctcgtgggctcggagatgtgtataagagacagGAATATCCGCGAACTGAAAAAAGTCGCGCTGGGAAAAGGTTGGGATGAATA < SRR3722072.5308/51‑1 (MQ=60)
CACCAGTGCCAATACAACTGTACCCGCCTGGATTACGACAGTGCGCTGAATATCCGCGAACTGAAAAAAGTCGCGCTGGGAAAAGGctgtctcttataca > SRR3722072.429097/1‑86 (MQ=60)
aaagacaaaaaaacttgtcCCCGCCTGGATTACGACAGTGCGCTGAATATCCGCGAACTGAAAAAAGTCGCGCTGGGAAAAGGTTGGGATGAATATAAGC < SRR3722072.219086/81‑1 (MQ=60)
CAGTGCAAATAAAACTGTCCCCGCCTGGATTACGACAGTGCGCTGAATATCCGCGAACTGAAAAAAGTCGCGCTGGGAAAAGGTTGGGATGAATATAAGC < SRR3722072.688478/100‑1 (MQ=60)
CAATACAACTGTACCCGCCTGGATTACGACAGTGCGCTGAATATCCGCGAACTGAAAAAAGTCGCGCTGGGAAAAGGTTGGGATGAATATAAGCAACGCT > SRR3722072.483998/1‑100 (MQ=60)
ATACAACTGTACCCGCCTGGATTACGACAGTGCGCTGAATATCCGCGAACTGAAAAAAGTCGCGCTGGGAAAAGGTTGGGATGAATATAAGCAACGCTGG > SRR3722072.100277/1‑100 (MQ=60)
caAACTGTCCCCGCCTGGATTACGACAGTGCGCTGAATATCCGCGAACTGAAAAAAGTCGCGCTGGGAAAAGGTTGGGATGAATATAAGCAACGCTGGCA < SRR3722072.146667/98‑1 (MQ=60)
tgggctcggagatgtgtataagagacagGCGCTGAATATCCGCGAACTGAAAAAAGTCGCGCTGGGAAAAGGTTGGGATGAATATAAGCAACGCTGGCAC < SRR3722072.531572/72‑1 (MQ=60)
CAACTGTACCCGCCTGGATTACGACAGTGCGCTGAATATCCGCGAACTGAAAAAAGTCGCGCTGGGAAAAGGTTGGGATGAATActgtctcttatacaca > SRR3722072.369385/1‑84 (MQ=60)
ACTGTACCCGCCTGGATTACGACAGTGCGCTGAATATCCGCGAACTGAAAAAAGTCGCGCTGGGAAAAGGTTGGGATGAATATAAGCAACGCTGGCACAA > SRR3722072.878987/1‑100 (MQ=60)
GATTACGACAGTGCGCTGAATATCCGCGAACTGAAAAAAGTCGCGCTGGGAAAAGGTTGGGATGAATATAAGCAACGCTGGCACctgtctcttatacaca > SRR3722072.25446/1‑84 (MQ=60)
GATTACGACAGTGCGCTGAATATCCGCGAACTGAAAAAAGTCGCGCTGGGAAAAGGTTGGGATGAATATAAGCAACGCTGGCACAAACCAGCCGGTTCTG > SRR3722072.702239/1‑100 (MQ=60)
TACGACAGTGCGTTGAATACCCGCGAACTGAAAAAAGTCGCGCTGGGAAAAGGTTGGGATGAATATAAGCAACGCTGGCACAAACCAGCCGGTTCTGGTT < SRR3722072.105762/100‑1 (MQ=60)
ACGACAGTGCGCTGAATATCCGCGAACTGAAAAAAGTCGCGCTGGGAAAAGGTTGGGATGAATATAAGCAACGCTGGCACAAACCAGCCGGTTCTGGTTC < SRR3722072.135079/100‑1 (MQ=60)
CTGAATATCCGCGAACTGAAAAAAGTCGCGCTGGGAAAAGGTTGGGATGAATATAAGCAACGCTGGCACAAACCAGCCGGTTCTGGTTCACGCCATCCGG > SRR3722072.146592/1‑100 (MQ=60)
tataagagacaGAACTGAAAAAAGTCGCGCTGGGAAAAGGTTGGGATGAATATAAGCAACGCTGGCACAAACCAGCCGGTTCTGGTTCACGCCATCCGGT < SRR3722072.619896/89‑1 (MQ=60)
ATATCCGCGAACTGAAAAAAGTCGCGCTGGGAAAAGGTTGGGATGAATATAAGCAACGCTGGCACAAACCAGCCGGTTCTGGTTCACGCCATCCGGTTGC > SRR3722072.261127/1‑100 (MQ=60)
CCGCGAACTGAAAAAAGTCGCGCTGGGAAAAGGTTGGGATGAATATAAGCAACGCTGGCACAAACCAGCCGGTTCTGGTTCACGCCATCCGGTTGCCGTG < SRR3722072.614823/100‑1 (MQ=60)
agacagGAAAAAAGTCGCGCTGGGAAAAGGTTGGGATGAATATAAGCAACGCTGGCACAAACCAGCCGGTTCTGGTTCACGCCATCCGGTTGCCGTGATT < SRR3722072.623925/94‑1 (MQ=60)
GGGAAAAGGTTGGGATGAATATAAGCAACGCTGGCACAAACCAGCCGGTTCTGGTTCACGCCATCCGGTTGCCGTGATTGGTGCAGGTCCGGCGGGTCTG > SRR3722072.243895/1‑100 (MQ=60)
GAAAAGGTTGGGATGAATATAAGCAACGCTGGCACAAACCAGCCGGTTCTGGTTCACGCCATCCGGTTGCCGTGATTGGTGCAGGTCCGGCGGGTCTGGC < SRR3722072.809441/100‑1 (MQ=60)
|
GTCATATTTGCGATCACCAGTGCCAATACAACTGTACCCGCCTGGATTACGACAGTGCGCTGAATATCCGCGAACTGAAAAAAGTCGCGCTGGAAAAAGGTTGGGATGAATATAAGCAACGCTGGCACAAACCAGCCGGTTCTGGTTCACGCCATCCGGTTGCCGTGATTGGTGCAGGTCCGGCGGGTCTGGC > NZ_CP009273/3010917‑3011109
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
