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 I227 R1
|
223 |
21.3 |
1167702 |
97.0% |
1132670 |
86.4 |
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 | 97.2%
| 110.7
/ ‑4.0
| 36 | T467P (ACG→CCG) | yidK | solute:sodium symporter family transporter |
| Reads supporting (aligned to +/- strand): ref base T (1/0); new base G (16/19); total (17/19) |
| Fisher's exact test for biased strand distribution p-value = 4.72e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.94e-01 |
CCGCAAACGCATCTTTGAAGGTGAACGGCGTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGTACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGATAGTTGATGGTGATGTAGCTGATTATGCCAATCCCCATCGCTA > NZ_CP009273/3851991‑3852164
|
ccGCAAACGCATCTTTGAAGGTGAACGGCGTGGCGCGCGGTTTGATAAAACCGATCACTAGCATCACGACCACGTTGATGCAGAACGGAc > 2:474287/1‑90 (MQ=255)
ccGCAAACGCATCTTTGAAGGTGAACGGCGTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGAc < 2:514727/90‑1 (MQ=255)
ccGCAAACGCATCTTTGAAGGTGAACGGCGTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGAc < 2:218809/90‑1 (MQ=255)
ccGCAAACGCATCTTTGAAGGTGAACGGCGTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGAc < 2:269784/90‑1 (MQ=255)
ccGCAAACGCATCTTTGAAGGTGAACGGCGTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGAc > 1:269784/1‑90 (MQ=255)
aaaCGCATCTTTGAAGGTGAACGGCGTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGc < 1:234518/90‑1 (MQ=255)
aaCGCATCTTTGAAGGTGAACGGCGTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGcc > 1:211993/1‑90 (MQ=255)
cGCATCTTTGAAGGTGAACGGCGTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGGCAGGCCAg < 1:19326/90‑1 (MQ=255)
ttGAAGGTGAACGGCGTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATag < 1:430950/90‑1 (MQ=255)
tGAACGGCGTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAAt > 1:192137/1‑90 (MQ=255)
gAACGGCGTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATg > 1:218671/1‑90 (MQ=255)
gTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCCCGACCACGTTGATGCAGAACGGACAGGCCAGCACATa < 2:269237/74‑1 (MQ=255)
gTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGTACAGGCCAGCACATAGAGGAAATGGAAGTCg > 2:160752/1‑90 (MQ=255)
gTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATa > 1:269237/1‑74 (MQ=255)
gTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTc > 1:158469/1‑89 (MQ=255)
gTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTc < 2:158469/89‑1 (MQ=255)
tGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGa < 1:275404/90‑1 (MQ=255)
gcgcgGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACtt < 1:306237/90‑1 (MQ=255)
gcgGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCa > 2:379656/1‑90 (MQ=255)
cgGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCAc > 1:80061/1‑90 (MQ=255)
tGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGGAATGGAAGTCGAACTTCACCAGAt < 2:18794/90‑1 (MQ=255)
tGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGAt < 2:426208/90‑1 (MQ=255)
tGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGAt < 2:181331/90‑1 (MQ=255)
tGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGAt < 1:454294/90‑1 (MQ=255)
aaaCCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGATAGTTg > 2:140946/1‑90 (MQ=255)
aaaCCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGATAGTTg < 1:379656/90‑1 (MQ=255)
aTCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGACGAACTTCACCAGATAGATGATGGTg > 1:547431/1‑90 (MQ=255)
gCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGATAGTTGATGGTGATGTAGc < 1:242364/90‑1 (MQ=255)
aCGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGATAGTTGATGGTGATGTAGCTGAtt < 1:349635/90‑1 (MQ=255)
cACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGATAGTTGATGGTGATGTAGCTGATTATGcc > 2:130506/1‑90 (MQ=255)
aCGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGAt < 1:314839/61‑1 (MQ=255)
aCGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGAt > 2:314839/1‑61 (MQ=255)
gAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGAt < 2:74657/50‑1 (MQ=255)
gAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGAt > 1:74657/1‑50 (MQ=255)
gAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGATAGTTGATGGTGATGTAGCTGATTATGCCAATCCCCATCGc > 2:279097/1‑90 (MQ=255)
aCGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGATAGTTGATGGTGATGTAGCTGATTATGCCAATCCCCATCGCTa > 1:567339/1‑90 (MQ=255)
|
CCGCAAACGCATCTTTGAAGGTGAACGGCGTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGTACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGATAGTTGATGGTGATGTAGCTGATTATGCCAATCCCCATCGCTA > NZ_CP009273/3851991‑3852164
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 32 ≤ 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
GTTTCATGTCCACCGCAAACGCATCTTTGAAGGTGAACGGCGTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGTACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGATAGTTGATGGTGATGTAGCTGATTATGCCAATCCCCATCGCTA > NZ_CP009273/3851979‑3852164
|
GTTTCATGTCCACCGCAAACGCATCTTTGAAGGTGAACGGCGTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGG > SRR3722111.183600/1‑100 (MQ=60)
GTTTCATGTCCACCGCAAACGCATCTTTGAAGGTGAACGGCGTGGCGCGCGGTTTGATAAAACCGATCACCAGCAGCACGACCACGTTGATGCAGAACGG > SRR3722111.380240/1‑100 (MQ=60)
TTCATGTCCACCGCAAACGCATCTTTGAAGGTGAACGGCGTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGAC > SRR3722111.273055/1‑100 (MQ=60)
GTCCACCGCAAACGCATCTTTGAAGGTGAACGGCGTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCC > SRR3722111.214579/1‑100 (MQ=60)
AAACGCATCTTTGAAGGTGAACGGCGTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAG < SRR3722111.237320/100‑1 (MQ=60)
CGCATCTTTGAAGGTGAACGGCGTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGGCAGGCCAGCACATAGAGG < SRR3722111.19561/100‑1 (MQ=60)
TCTTTGAAGGTGAACGGCGTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAAT > SRR3722111.194537/1‑100 (MQ=60)
CTTTGAAGGTGAACGGCGTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATG > SRR3722111.221327/1‑100 (MQ=60)
TTGAAGGTGAACGGCGTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGA < SRR3722111.437377/100‑1 (MQ=60)
GGTGAACGGCGTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGccgtct > SRR3722111.272496/1‑94 (MQ=60)
GGTGAACGGCGTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCG > SRR3722111.160473/1‑100 (MQ=60)
GCGTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCAC > SRR3722111.81036/1‑100 (MQ=60)
TGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAG < SRR3722111.278821/100‑1 (MQ=60)
GCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGATAG < SRR3722111.310213/100‑1 (MQ=60)
agatgtgtataagagaCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGATAGTTGATGGT < SRR3722111.318978/84‑1 (MQ=60)
TGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGATAGTTGATGGT < SRR3722111.461186/100‑1 (MQ=60)
GATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGACGAACTTCACCAGATAGATGATGGTG > SRR3722111.556038/1‑100 (MQ=60)
AAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGATAGTTGATGGTGATGT < SRR3722111.385092/100‑1 (MQ=60)
GCATCACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGATAGTTGATGGTGATGTAGCTGATTATGCC < SRR3722111.245241/100‑1 (MQ=60)
ACGACCACGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGATAGTTGATGGTGATGTAGCTGATTATGCCAATCC < SRR3722111.354373/100‑1 (MQ=60)
CGTTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGATAGTTGATGGTctgtctcttatacacatctgacgctgccga > SRR3722111.75559/1‑70 (MQ=60)
TTGATGCAGAACGGACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGATAGTTGATGGTGATGTAGCTGATTATGCCAATCCCCATCGCTA > SRR3722111.576262/1‑100 (MQ=60)
|
GTTTCATGTCCACCGCAAACGCATCTTTGAAGGTGAACGGCGTGGCGCGCGGTTTGATAAAACCGATCACCAGCATCACGACCACGTTGATGCAGAACGTACAGGCCAGCACATAGAGGAAATGGAAGTCGAACTTCACCAGATAGTTGATGGTGATGTAGCTGATTATGCCAATCCCCATCGCTA > NZ_CP009273/3851979‑3852164
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
