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 |
|
A69 F1 I1 R1
|
20 |
59.3 |
3764421 |
95.9% |
3610079 |
75.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
REL606 |
3,488,896 |
T→G |
E104A (GAA→GCA) |
glpR ← |
DNA‑binding transcriptional repressor |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | REL606 | 3,488,896 | 0 | T | G | 94.0%
| 194.8
/ 1.3
| 50 | E104A (GAA→GCA) | glpR | DNA‑binding transcriptional repressor |
| Reads supporting (aligned to +/- strand): ref base T (3/0); new base G (27/20); total (30/20) |
| Fisher's exact test for biased strand distribution p-value = 2.65e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.77e-01 |
CGTGTTAGCAACATTGAGATTGTTGGTGACAATACGCAAATTGCTGTGATTAAGCAGCGCGTGCGCCACCGCTTCCGGCGTGGTGCCGATATCGATAAACAGTGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCAA > REL606/3488823‑3488965
|
cGTGTTAGCAACATTGAGATTGTTGGTGACAATACGCAAATTGCTGTGATTAAGCAGCGCGTGCGCCACCGCTGcc > 1:1571097/1‑76 (MQ=255)
ttAGCAACATTGAGATTGTTGGTGACAATACGCAAATTGCTGTGATTAAGCCGCGCGTGCGCCACCGCTGCCcgcg > 2:627926/1‑76 (MQ=255)
ttAGCAACATTGAGATTGTTGGTGACAATACGCAAATTGCTGTGATTAAGCAGCGCGTGCGCCACCGCTGCCGGCg > 1:330757/1‑76 (MQ=255)
gCAACATTGAGATTGTTGGTGACAATACGCAAATTGCTGTGATTAAGCAGCGCGTGCGCCACCGCTGCCGGCgtgg < 2:1489231/76‑1 (MQ=255)
gCAACATTGAGATTGTTGGTGAAAATACGCAAATTGTTGTGATTAAGCAGCGCGTGCGCCACCGCTGCCGGCgtgg < 2:1864168/76‑1 (MQ=255)
cAACATTGAGATTGTTGGTGACAATACGCAAATTGCTGTGATTAAGCAGCGCGTGCGCCACCGCTGCCGGCgtggt > 2:1004800/1‑76 (MQ=255)
aaCATTGAGATTGTTGGTGACAATACGCAAATTGCTGTGATTAAGCAGCGCGTGCGCCACCGCTGCCGGCgtggtg < 2:724699/76‑1 (MQ=255)
aaCATTGAGATTGTTGGTGACAATACGCAAATTGCTGTGATTAAGCAGCGCGTGCGCCACCGCTGCCGGCgtggtg < 2:1528202/76‑1 (MQ=255)
aaCATTGAGATTGGTGGTGACAATACGCAAATTGCTGTGATTAAGCAGCGCGTGCGCCACCGCTGCCGGCgtggtg < 2:171632/76‑1 (MQ=255)
aCATTGAGATTGTTGGTGACAATACGCAAATTGCTGTGATTAAGCAGCGCGTGCGCCACCGCTGCCGGCGTGGTGc > 1:1218819/1‑76 (MQ=255)
aCATTGAGATTGTTGGTGACAATACGCAAATTGCTGTGATTAAGCAGCGCGTGCGCCACCGCTGCCGGCGTGGTGc < 2:753839/76‑1 (MQ=255)
aCATTGAGATTGTTGGTGACAATACGCAAATTGCTGTGATTAAGCAGCGCGTGCGCCACCGCTGCCGGCGTGGTGc > 1:1437700/1‑76 (MQ=255)
cATTGAGATTGTTGGTGACAATACGCAAATTGCTGTGATTAAGCAGCGCGTGCGCCACCGCTGCCGGCGTGGTGcc > 2:1368185/1‑76 (MQ=255)
aTTGAGATTGTTGGTGACAATACGCAAATTGCTGTGATTAAGCAGCGCGTGCGCCACCGCTGCCGGCGTGGTGCCg < 2:1403407/76‑1 (MQ=255)
tGAGATTGTTGGTGACAATACGCAAATTGCTGTGATTAAGCAGCGCGTGCGCCACCGCTGCCGGCGTGGTGCCGat < 1:580066/76‑1 (MQ=255)
agtttgttgGTGACAATACGCAAATTGCTGTGATTAAGCAGCGCGTGCGCCACCGCTGCCGGCGTGGTGCCGatat < 2:1165940/73‑1 (MQ=255)
agaTTGTTGGTGACAATACGCAAATTGCTGTGATTAAGCAGCGCGTGCGCCACCGCTGCCGGCGTGGTGCCGatat > 2:976752/1‑76 (MQ=255)
tgttgGTGACAATACGCAAATTGCTGTGATTAAGCAGCGCGTGCGCCACCGCTGCCGGCGTGGTGCCGATATCGAt > 1:732570/1‑76 (MQ=255)
ttgGTGACAATACGCAAATTGCTGTGATTAAGCAGCGCGTGCGCCACCGCTGCCGGCGTGGTGCCGATATCGATaa < 2:118552/76‑1 (MQ=255)
tgGTGACAATACGCAAATTGCTGTGATTAAGCAGCGCGTGCGCCACCGCTGCCGGCGTGGTGCCGATATCGATaaa > 1:1533039/1‑76 (MQ=255)
tgGTGACAATACGCAAATTGCTGTGATTAAGCAGCGCGTGCGCCACCGCTGCCGGCGTGGTGCCGATATCGATaaa > 1:1668101/1‑76 (MQ=255)
tGACAATACGCAAATTGCTGTGATTAAGCAGCGCGTGCGCCACCGCTGCCGGCGTGGTGCCGATATCGATAAACAg > 1:369054/1‑76 (MQ=255)
tGACAATACGCAAATTGCTGTGATTAAGCAGCGCGAGCGCCACCGCTGCCGGCGTGGTGCCGATATCGATAAACAg > 2:481278/1‑76 (MQ=255)
gACAATACGCAAATTGCTGTGATTAAGCAGCGCGTGCGCCACCGCTGCCGGCGTGGTGCCGATATCGATAAACAgt > 1:1219216/1‑76 (MQ=255)
aCAATACGCAAATTGCTGTGATTAAGCAGCGCGTGCGCCACCGCTGCCGGCGTGGTGCCGATATCGATAAACAgtg > 2:508546/1‑76 (MQ=255)
cAATACGCAAATTGCTGTGATTAAGCAGCGCGTGCGCCACCGCTTCCGGCGCGGTGCCGCTATCGATAAACAgtgt > 2:1205192/1‑76 (MQ=255)
aaTACGCAAATTGCTGTGATTAAGCAGCGCGTGCGCCACCGCTGCCGGCGTGGTGCCGATATCGATAAACAGTGTc > 2:1570195/1‑76 (MQ=255)
aTACGCAAATTGCTGTGATTAAGCAGCGCGTGCGCCACCGCTGCCGGCGTGGTGCCGATATCGATAAACAGTGTCg > 1:1873005/1‑76 (MQ=255)
tACGCAAATTGCTGTGATTAAGCAGCGCGTGCGCCACCGCTGCCGGCGTGGTGCCGATATCGATAAACAGTGTCGa < 1:765748/76‑1 (MQ=255)
tACGCAAATTGCTGTGATTAAGCAGCGCGTGCGCCACCGCTGCCGGCGTGGTGCCGATATCGATAAACAGTGTCGa < 2:1876647/76‑1 (MQ=255)
tACGCAAATTGCTGTGATTAAGCAGCGCGTGCGCCACCGCTGCCGGCGTGGTGCCGATATCGATAAACAGTGTCGa < 1:1123877/76‑1 (MQ=255)
aCGCAAATTGCTGTGATTAAGCAGCGCGTGCGCCACCGCTGCCGGCGTGGTGCCGATATCGATAAACAGTGTCGAg < 1:635346/76‑1 (MQ=255)
aCGCAAATTGCTGTGATTAAGCAGCGCGTGCGCCACCGCTGCCGGCGTGGTGCCGATATCGATAAACAGTGTCGAg > 2:683470/1‑76 (MQ=255)
cGCAAATTGCTGTGATTAAGCAGCGCGTGCGCCACCGCTGCCGGCGTGGTGCCGATATCGATAAACAGTGTCGAGc < 2:944497/76‑1 (MQ=255)
cGCAAATTGCTGTGATTAAGCAGCGCGTGCGCCACCGCTGCCGGCGTGGTGCCGATATCGATAAACAGTGTCGAGc > 1:1342098/1‑76 (MQ=255)
cAAATTGCTGTGATTAAGCAGCGCGTGCGCCACCGCTGCCGGCGTGGTGCCGATATCGATAAACAGTGTCGAGCCa < 2:1621616/76‑1 (MQ=255)
cAAATTGCTGTGATTAAGCAGCGCGTGCGCCACCGCTGCCGGCGTGGTGCCGATATCGATAAACAGTGTCGAGCCa > 2:74722/1‑76 (MQ=255)
cAAATTGCTGTGATTAAGCAGCGCGTGCGCCACCGCTGCCGGCGTGGTGCCGATATCGATAAACAGTGTCGAGCCa > 1:1440878/1‑76 (MQ=255)
aaTTGCTGTGATTAAGCAGCGCGTGCGCCACCGCTGCCGGCGTGGTGCCGATATCGATAAACAGTGTCGAGCCAtt > 1:792881/1‑76 (MQ=255)
tgATTAAGCAGCGCGTGCGCCACCGCTTCCGGCGTGGTGCCGATATCGATAAACAGTGTCGAGCCATTGGGGAttt > 1:1595527/1‑76 (MQ=255)
gATTAAGCAGCGCGTGCGCCACCGCTGCCGGCGTGGTGCCGATATCGATAAACAGTGTCGAGCCATTGGGGATTTg > 2:4743/1‑76 (MQ=255)
aTTAAGCAGCGCGTGCGCCACCGCTGCCGGCGTGGTGCCGATATCGATAAACAGTGTCGAGCCATTGGGGATTTGc < 1:729695/76‑1 (MQ=255)
aTTAAGCAGCGCGTGCGCCACCGCTGCCGGCGTGGGGCCGATATCGATAAACAGTGTCGAGCCATTGGGGATTTGc > 2:1559184/1‑76 (MQ=255)
tAAGCAGCGCGTGCGCCACCGCTTCCGGCGTGGTGCCGCTATCGATAAACAGTGTCGAGCCATTGGGGATTTGCTc > 1:579621/1‑76 (MQ=255)
cgcgTGCGCCACCGCTGCCGGCGTGGTGCCGATATCGATAAACAGTGTCGAGCCATTGGGGATTTGCTCCGCCACt > 2:640877/1‑76 (MQ=255)
cgTGCGCCACCGCTGCCGGCGTGGTGCCGATATCGATAAACAGTGTCGAGCCATTGGGGATTTGCTCCGCCACttt < 2:518071/76‑1 (MQ=255)
cgTGCCCCCCCGCTGCCGGCGTGGTGCCGATATCGATAAACAGTGTCGAGCCATTGGGGATTTGCTCCGCCACttt < 2:551090/76‑1 (MQ=255)
ccACCGCTGCCGGCGTGGTGCCGATATCGATAAACAGTGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGc > 2:1876785/1‑76 (MQ=255)
cACCGCTGCCGGCGTGGTGCCGATATCGATAAACAGTGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCa > 2:1333098/1‑76 (MQ=255)
cACCGCTGCCGGCGTGGTGCCGATATCGATAAACAGTGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCa > 2:1879047/1‑76 (MQ=255)
cccGCTGCCGGCGTGGTGCCGATATCGATAAACAGTGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCaa < 2:754387/75‑1 (MQ=255)
|
CGTGTTAGCAACATTGAGATTGTTGGTGACAATACGCAAATTGCTGTGATTAAGCAGCGCGTGCGCCACCGCTTCCGGCGTGGTGCCGATATCGATAAACAGTGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCAA > REL606/3488823‑3488965
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
