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 I211 R1
|
223 |
18.0 |
1007644 |
96.3% |
970361 |
85.7 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
3,852,078 |
T→G |
T467P (ACG→CCG) |
yidK ← |
solute:sodium symporter family transporter |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 3,852,078 | 0 | T | G | 100.0%
| 37.7
/ NA
| 13 | T467P (ACG→CCG) | yidK | solute:sodium symporter family transporter |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base G (2/11); total (2/11) |
CCGCAAACGCATCTTTGAAGGTGAACGGCGTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGTACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGATAGTTGATGGTGATGTAGCTGATTA > NZ_CP009273/3851991‑3852146
|
ccGCAAACGCATCTTTGAAGGTGAACGGCGTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGAc < 1:335940/90‑1 (MQ=255)
ccGCAAACGCATCTTTGAAGGTGAACGGCGTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGAc < 1:44238/90‑1 (MQ=255)
ccGCAAACGCATCTTTGAAGGTGAACGGCGTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGAc < 2:85366/90‑1 (MQ=255)
aCGCATCTTTGAAGGTGAACGGCGTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCa < 2:310457/90‑1 (MQ=255)
aTCTTTGAAGGTGAACGGCGTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGcac > 1:284272/1‑90 (MQ=255)
ggggAACGGCGTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGaa > 1:485130/4‑90 (MQ=255)
ttGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGa < 1:126994/90‑1 (MQ=255)
aCCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGATAGTTGAt < 1:423151/90‑1 (MQ=255)
ccGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGATAGTTGATg < 2:284272/90‑1 (MQ=255)
ccGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGATAGTTGATg < 2:497269/90‑1 (MQ=255)
ccGATCACCAGCATCACGACCAAGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGATAGTTGATg < 1:4227/90‑1 (MQ=255)
gCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGATAGTTGATGGTGATGTAGc < 2:346478/90‑1 (MQ=255)
cGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGATAGTTGATGGTGATGTAGCTGATTa < 1:172456/90‑1 (MQ=255)
|
CCGCAAACGCATCTTTGAAGGTGAACGGCGTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGTACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGATAGTTGATGGTGATGTAGCTGATTA > NZ_CP009273/3851991‑3852146
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 28 ≤ 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
TTCATGTCCACCGCAAACGCATCTTTGAAGGTGAACGGCGTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGTACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGATAGTTGATGGTGATGTAGCTGATTATGCCAATCCC > NZ_CP009273/3851981‑3852156
|
TTCATTTCCACCGTAAACGCATCTTTGAAGGTGAACGGCGTGGCGCGCGGTTTGATAAACCCGATCACCAGCATCACGACCACGTTGATGCAGAACGGAC < SRR3722094.261817/100‑1 (MQ=60)
CCGCAAACGCATCTTTGAAGGTGAACGGCGTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCAC > SRR3722094.288549/1‑100 (MQ=60)
CCGCAAACGCATCTTTGAAGGTGAACGGCGTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCAC < SRR3722094.341454/100‑1 (MQ=60)
CCGCAAACGCATCTTTGAAGGTGAACGGCGTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCAC < SRR3722094.44867/100‑1 (MQ=60)
CATCTTTGAAGGGGAACGGCGTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAA > SRR3722094.493686/1‑100 (MQ=60)
TTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGATAGTTGATGG < SRR3722094.128817/100‑1 (MQ=60)
ACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGATAGTTGATGGTGATGTAG < SRR3722094.430539/100‑1 (MQ=60)
CCGATCACCAGCATCACGACCAAGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGATAGTTGATGGTGATGTAGC < SRR3722094.4293/100‑1 (MQ=60)
CGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGATAGTTGATGGTGATGTAGCTGATTATGCCAATCCC < SRR3722094.174856/100‑1 (MQ=60)
|
TTCATGTCCACCGCAAACGCATCTTTGAAGGTGAACGGCGTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGTACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGATAGTTGATGGTGATGTAGCTGATTATGCCAATCCC > NZ_CP009273/3851981‑3852156
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 11 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
