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 |
|
A2 F1 I0 R1
|
4577 |
57.4 |
3436498 |
77.7% |
2670158 |
63.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
894,957 |
A→C |
35.5% |
S370A (TCG→GCG) |
sapA ← |
predicted antimicrobial peptide transporter subunit |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 894,957 | 0 | A | C | 35.5%
| 42.4
/ 50.4
| 62 | S370A (TCG→GCG) | sapA | predicted antimicrobial peptide transporter subunit |
| Reads supporting (aligned to +/- strand): ref base A (11/29); new base C (12/10); total (23/39) |
| Fisher's exact test for biased strand distribution p-value = 5.40e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.06e-01 |
TTCCACGCCTGCGAACGTGTGGGCACCCACAGTTTCAGCGTTAAATTTTCCAGCCCCAACGACTTCAACTGTTCGCGCGATTTCGCCGGATTGTATTCAGTAATTTTAGCCTCGTTGTCA > minE/894896‑895015
|
ttCCACGCCTGCGAACGTGTGGGCACCCACAGTTTCAGCGTTAAATTTTCCAGCCCCAACGACTTCAAc < 1:824611/69‑1 (MQ=255)
ttCCACGCCTGCGAACGTGTGGGCACCCACAGTTTCAGCGTTAAATTTTCCAGCCCCAACGACTTCAAc < 1:3092184/69‑1 (MQ=255)
gCCTGCGAACGTGTGGGCACCCACAGTTTCAGCGTTAAATTTTCCAGCCCCAACGACTTCAACTGTTcg > 1:750606/1‑69 (MQ=255)
gCCTGCGAACGTGTGGGCACCCACAGTTTCAGCGTTAAATTTTCCAGCCCCAACGACTTCAACTGTTcg > 1:2249012/1‑69 (MQ=255)
aaCGTGTGGGCACCCACAGTTTCAGCGTTAAATTTTCCAGCCCCAACGACTTCAACTGTTCGCGCGAt < 1:1260075/68‑1 (MQ=255)
aaCGTGTGGGCACCCACAGTTTCAGCGTTAAATTTTCCAGCCCCAACGACTTCAACTGTTCGCGCGAt < 1:976226/68‑1 (MQ=255)
aaCGTGTGGGCACCCACAGTTTCAGCGTTAAATTTTCCAGCCCCAACGACTTCAACTGTTCGCGCGAt < 1:768366/68‑1 (MQ=255)
aaCGTGTGGGCACCCACAGTTTCAGCGTTAAATTTTCCAGCCCCAACGACTTCAACTGTTCGCGCGAt < 1:509672/68‑1 (MQ=255)
aaCGTGTGGGCACCCACAGTTTCAGCGTTAAATTTTCCAGCCCCAACGACTTCAACTGTTCGCGCGAt < 1:2698626/68‑1 (MQ=255)
aaCGTGTGGGCACCCACAGTTTCAGCGTTAAATTTTCCAGCCCCAACGACTTCAACTGTTCGCGCGAt < 1:2483690/68‑1 (MQ=255)
aaCGTGTGGGCACCCACAGTTTCAGCGTTAAATTTTCCAGCCCCAACGACTTCAACTGTTCGCGCGAt < 1:2464586/68‑1 (MQ=255)
aaCGTGTGGGCACCCACAGTTTCAGCGTTAAATTTTCCAGCCCCAACGACTTCAACTGTTCGCGCGAt < 1:2462326/68‑1 (MQ=255)
aaCGTGTGGGCACCCACAGTTTCAGCGTTAAATTTTCCAGCCCCAACGACTTCAACTGTTCGCGCGAt < 1:2429697/68‑1 (MQ=255)
aaCGTGTGGGCACCCACAGTTTCAGCGTTAAATTTTCCAGCCCCAACGACTTCAACTGTTCGCGCGAt < 1:2239100/68‑1 (MQ=255)
aCGTGTGGGCACCCACAGTTTCAGCGTTAAGTTTTCCAGCGCCAACGCCTTCAACTGTTCGCGCGAt > 1:3290727/1‑67 (MQ=255)
aCGTGTGGGCACCCACAGTTTCAGCGTTAAGTTTTCCAGCCCCACCGCCTTCAACTGTTCGCGCGAt > 1:545167/1‑67 (MQ=255)
aCGTGTGGGCACCCACAGTTTCAGCGTTAAGTTTTCCAGCCCCAACGCCTTCAACTGTTCGCGCGAt > 1:968131/1‑67 (MQ=255)
aCGTGTGGGCACCCACAGTTTCAGCGTTAAGTTTTCCAGCCCCAACGCCTTCAACTGTTCGCGCGAt > 1:1319065/1‑67 (MQ=255)
aCGTGTGGGCACCCACAGTTTCAGCGTTAAGTTTTCCAGCCCCAACGCCTTCAACTGTTCGCGCGAt > 1:1372205/1‑67 (MQ=255)
aCGTGTGGGCACCCACAGTTTCAGCGTTAAGTTTTCCAGCCCCAACGCCTTCAACTGTTCGCGCGAt > 1:3294333/1‑67 (MQ=255)
aCGTGTGGGCACCCACAGTTTCAGCGTTAAGTTTTCCAGCCCCAACGCCTTCAACTGTTCGCGCGAt > 1:1386512/1‑67 (MQ=255)
aCGTGTGGGCACCCACAGTTTCAGCGTTAAGTTTTCCAGCCCCAACGCCTTCAACTGTTCGCGCGAt > 1:368844/1‑67 (MQ=255)
aCGTGTGGGCACCCACAGTTTCAGCGTTAAGTTTTCCAGCCCCAACGCCTTCAACTGTTCGCGCGAt > 1:597728/1‑67 (MQ=255)
aCGTGTGGGCACCCACAGTTTCAGCGTTAAGTTTTCCAGCCCCAACGCCTT‑AACTGTTCGCGCGAt > 1:3037842/1‑66 (MQ=255)
aCGTGTGGGCACCCACAGTTTCAGCGTTAAGTTTTACAGCCCCAACGCCTTCAACTGTTCGCGCGAt > 1:2002982/1‑67 (MQ=255)
aCGTGTGGGCAACCACAGTTTCAGCGTTAAGTTTTCCAGCCCCAACGCCTTCAACTGTTCGCGCGAt > 1:2446437/1‑67 (MQ=255)
cACCCACAGTTTCAGCGTTAAATTTTCCAGCCCCACCGACTTCAACTGTTCGCGCGATTTCGCCGGAt > 1:3037316/1‑68 (MQ=255)
cACCCACAGTTTCAGCGTTAAATTTTCCAGCCCCAACGACTTCAACTGTTCGCGCGATTTCGCCGGAt > 1:1419130/1‑68 (MQ=255)
cACCCACAGTTTCAGCGTTAAATTTTCCAGCCCCAACGACTTCAACTGTTCGCGCGATTTCGCCGGAt > 1:3245585/1‑68 (MQ=255)
cACCCACAGTTTCAGCGTTAAATTTTCCAGCCCCAACGACTTCAACTGTTCGCGCGATTTCGCCGGAt > 1:1403401/1‑68 (MQ=255)
cACCCACAGTTTCAGCGTTAAATTTTCCAGCCCCAACGACTTCAACTGTTCGCGCGATTTCGCCGGAt > 1:1777709/1‑68 (MQ=255)
aCCCACAGTTTCAGCGTTAAATTTTCCAGCCCCAACGACTTCAACTGTTCGCGCGATTTCGCCGGATTg < 1:449951/69‑1 (MQ=255)
aCCCACAGTTTCAGCGTTAAATTTTCCAGCCCCAACGACTTCAACTGTTCGCGCGATTTCGCCGGATTg < 1:2821479/69‑1 (MQ=255)
aCCCACAGTTTCAGCGTTAAATTTTCCAGCCCCAACGACTTCAACTGTTCGCGCGATTTCGCCGGATTg < 1:1814116/69‑1 (MQ=255)
aCCCACAGTTTCAGCGTTAAATTTTCCAGCCCCAACGACTTCAACTGTTCGCGCGATTTCGCCGGATTg < 1:2290120/69‑1 (MQ=255)
aCCCACAGTTTCAGCGTTAAATTTTCCAGCCCCAACGACTTCAACTGTTCGCGCGATTTCGCCGGATTg < 1:3239030/69‑1 (MQ=255)
aCCCACAGTTTCAGCGTTAAATTTTCCAGCCCCAACGACTTCAACTGTTCGCGCGATTTCGCCGGATTg < 1:2288560/69‑1 (MQ=255)
aCCCACAGTTTCAGCGTTAAATTTTCCAGCCCCAACGACTTCAACTGTTCGCGCGATTTCGCCGGATTg < 1:2059928/69‑1 (MQ=255)
cacaGTTTCAGCGTTAAATTTTCCAGCCCCAACGACTTCAACTGTTCGCGCGATTTCGCCGGATTGTa > 1:673538/1‑68 (MQ=255)
cacaGTTTCAGCGTTAAATTTTCCAGCCCCAACGACTTCAACTGTTCGCGCGATTTCGCCGGATTGTa > 1:2084434/1‑68 (MQ=255)
tAAATTTTCCAGCCCCAACGACTTCAACTGTTCGCGCGATTTCGCCGGATTGTATTCAGTAATTTTAGc < 1:2262968/69‑1 (MQ=255)
tAAATTTTCCAGCCCCAACGACTTCAACTGTTCGCGCGATTTCGCCGGATTGTATTCAGTAATTTTAGc < 1:2848284/69‑1 (MQ=255)
tAAATTTTCCAGCCCCAACGACTTCAACTGTTCGCGCGATTTCGCCGGATTGTATTCAGTAATTTTAGc < 1:2493656/69‑1 (MQ=255)
aaaTTTTCCAGCCCCAACGACTTCAACTGTTCGCGCGATTTCGCCGGATTGTATTCAGTAATTTTAGcc > 1:3004349/1‑69 (MQ=255)
aaaTTTTCCAGCCCCAACGACTTCAACTGTTCGCGCGATTTCGCCGGATTGTATTCAGTAATTTTAGcc > 1:3425907/1‑69 (MQ=255)
cAGCCCCAACGACTTCAACTGTTCGCGCGATTTCGCCGGATTGTATTCAGTAATTTTAGCCTCGTTGt < 1:1617620/68‑1 (MQ=255)
gCCCCAACGACTTCAACTGTTCGCGCGATTTCGCCGGATTGTATTCAGTAATTTTAGCCTCGTTGTCa < 1:1050681/68‑1 (MQ=255)
gCCCCAACGACTTCAACTGTTCGCGCGATTTCGCCGGATTGTATTCAGTAATTTTAGCCTCGTTGTCa < 1:3061292/68‑1 (MQ=255)
gCCCCAACGACTTCAACTGTTCGCGCGATTTCGCCGGATTGTATTCAGTAATTTTAGCCTCGTTGTCa < 1:2419062/68‑1 (MQ=255)
gCCCCAACGACTTCAACTGTTCGCGCGATTTCGCCGGATTGTATTCAGTAATTTTAGCCTCGTTGTCa < 1:516038/68‑1 (MQ=255)
gCCCCAACGACTTCAACTGTTCGCGCGATTTCGCCGGATTGTATTCAGTAATTTTAGCCTCGTTGTCa < 1:160872/68‑1 (MQ=255)
gCCCCAACGACTTCAACTGTTCGCGCGATTTCGCCGGATTGTATTCAGTAATTTTAGCCTAGTTGTCa < 1:2049457/68‑1 (MQ=255)
ccAACGCCTTCAACTGTTCGCGCGATTTTGCCGGATTGTATTCAGTAATTTTAGCCTCGTTGTCa < 1:484323/65‑1 (MQ=255)
ccAACGCCTTCAACTGTTCGCGCGATTTTGCCGGATTGTATTCAGTAATTTTAGCCTCGTTGTCa < 1:2619602/65‑1 (MQ=255)
ccAACGCCTTCAACTGTTCGCGCGATTTTGCCGGATTGTATTCAGTAATTTTAGCCTCGTTGTCa < 1:376623/65‑1 (MQ=255)
ccAACGCCTTCAACTGTTCGCGCGATTTTGCCGGATTGTATTCAGTAATTTTAGCCTCGTTGTCa < 1:2790060/65‑1 (MQ=255)
ccAACGCCTTCAACTGTTCGCGCGATTTTGCCGGATTGTATTCAGTAATTTTAGCCTCGTTGTCa < 1:2476982/65‑1 (MQ=255)
ccAACGCCTTCAACTGTTCGCGCGATTTTGCCGGATTGTATTCAGTAATTTTAGCCTCGTTGTCa < 1:1644419/65‑1 (MQ=255)
ccAACGCCTTCAACTGTTCGCGCGATTTTGCCGGATTGTATTCAGTAATTTTAGCCTCGTTGTCa < 1:3317160/65‑1 (MQ=255)
ccAACGCCTTCAACTGTTCGCGCGATTTTGCCGGATTGTATTCAGTAATTTTAGCCTCGTTGTCa < 1:85309/65‑1 (MQ=255)
ccAACGCCTTCAACTGTTCGCGCGATTTTGCCGGATTGTATTCAGTAATTTTAGCCTCGTTGTCa < 1:2967740/65‑1 (MQ=255)
aCGCCTTCAACTGTTCGCGTGATTTTGCCGGATTGTATTCAGTAATTTTAGCCTCGTTGTCa < 1:29203/62‑1 (MQ=255)
|
TTCCACGCCTGCGAACGTGTGGGCACCCACAGTTTCAGCGTTAAATTTTCCAGCCCCAACGACTTCAACTGTTCGCGCGATTTCGCCGGATTGTATTCAGTAATTTTAGCCTCGTTGTCA > minE/894896‑895015
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
