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 |
1,427,948 |
T→C |
31.5% |
P786P (CCA→CCG) |
napA ← |
nitrate reductase, periplasmic, large subunit |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,427,948 | 0 | T | C | 31.5%
| 29.0
/ 16.0
| 38 | P786P (CCA→CCG) | napA | nitrate reductase, periplasmic, large subunit |
| Reads supporting (aligned to +/- strand): ref base T (12/14); new base C (7/5); total (19/19) |
| Fisher's exact test for biased strand distribution p-value = 7.28e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.83e-01 |
TCGCATCCAGCGTCAGTTTGTTAACCAACTGTGCGGCGTCGAAGAACGGCATGTACACCAGGCCCTGTGGCGGACGGTTACGACCGCGCGTTTCAACAATCGAGATCACTTCGCCACGGCGAGAAACCACTTTCA > minE/1427881‑1428015
|
tCGCATCCAGCGTCAGTTTGTTAACCAACTGTGCGGCGTCGAAGAACGGCATGTACACCAGGCCCtgtg < 1:750970/69‑1 (MQ=255)
tCGCATCCAGCGTCAGTTTGTTAACCAACTGTGCGGCGTCGAAGAACGGCATGTACACCAGGCCCtgtg < 1:621436/69‑1 (MQ=255)
tCGCATCCAGCGTCAGTTTGTTAACCAACTGTGCGGCGTCGAAGAACGGCATGTACACCAGGCCCtgtg < 1:2758508/69‑1 (MQ=255)
tCGCATCCAGCGTCAGTTTGTTAACCAACTGTGCGGCGTCGAAGAACGGCATGTACACCAGGCCCtgtg < 1:241101/69‑1 (MQ=255)
tCGCATCCAGCGTCAGTTTGTTAACCAACTGTGCGGCGTCGAAGAACGGCATGTACACCAGGCCCtgtg < 1:2363436/69‑1 (MQ=255)
cAGCGTCAGTTTGTTAACCAACTGTGCGGCGTCGAAGAACGGCATGTACACCAGGCCCTGTGGCGGACg > 1:1070632/1‑69 (MQ=255)
cAGCGTCAGTTTGTTAACCAACTGTGCGGCGTCGAAGAACGGCATGTACACCAGGCCCTGTGGCGGACg > 1:3223144/1‑69 (MQ=255)
cAGCGTCAGTTTGTTAACCAACTGTGCGGCGTCGAAGAACGGCATGTACACCAGGCCCTGTGGCGGACg > 1:1729401/1‑69 (MQ=255)
tGTTAAGCAACTGTGCGGCGTCGAAGAACGGCATGTACACCAGGCCCTGTGGCGGACg < 1:185815/58‑1 (MQ=255)
tGTTAACCAACTGTGCGGCGTCGAAGAACGGCATGTACACCAGGCCCTGTGGCGGACg > 1:316859/1‑58 (MQ=255)
tGTTAACCAACTGTGCGGCGTCGAAGAACGGCATGTACACCAGGCCCTGTGGCGGACg < 1:1670304/58‑1 (MQ=255)
tGTTAACCAACTGTGCGGCGTCGAAGAACGGCATGTACACCAGGCCCTGTGGCGGACg > 1:1707322/1‑58 (MQ=255)
tGTTAACCAACTGTGCGGCGTCGAAGAACGGCATGTACACCAGGCCCTGTGGCGGACg < 1:1217899/58‑1 (MQ=255)
tGTTAACCAACTGTGCGGCGTCGAAGAACGGCATGTACACCAGGCCCTGTGGCGGACg > 1:777311/1‑58 (MQ=255)
tGTTAACCAACTGTGCGGCGTCGAAGAACGGCATGTACACCAGGCCCTGTGGCGGACg > 1:1882940/1‑58 (MQ=255)
tGTTAACCAACTGTGCGGCGTCGAAGAACGGCATGTACACCAGGCCCTGTGGCGGACg < 1:191647/58‑1 (MQ=255)
tGTTAACCAACTGTGCGGCGTCGAAGAACGGCATGTACACCAGGCCCTGTGGCGGACg > 1:696385/1‑58 (MQ=255)
tGTTAACCAACTGTGCGGCGTCGAAGAACGGCATGTACACCAGGCCCTGTGGCGGACg < 1:2036171/58‑1 (MQ=255)
cagcTGTGCGGCGTCGAAGAACGGCATGTACACCAGGCCCTGCGGCGGACGGTTACGACCGCGCGTTTc < 1:985437/66‑1 (MQ=255)
cagcTGTGCGGCGTCGAAGAACGGCATGTACACCAGGCCCTGCGGCGGACGGTTACGACCGCGCGTTTc < 1:1152157/66‑1 (MQ=255)
cagcTGTGCGGCGTCGAAGAACGGCATGTACACCAGGCCCTGCGGCGGACGGTTACGACCGCGCGTTTc < 1:515814/66‑1 (MQ=255)
cagcTGTGCGGCGTCGAAGAACGGCATGTACACCAGGCCCTGCGGCGGACGGTTACGACCGCGCGTTTc < 1:1325944/66‑1 (MQ=255)
cagcTGTGCGGCGTCGAAGAACGGCATGTACACCAGGCCCTGCGGCGGACGGTTACGACCGCGCGTTTc < 1:1702584/66‑1 (MQ=255)
tgtgCGGCGTCGAAGAACGGCATGTACACCAGGCCCtgtg < 1:1447151/40‑1 (MQ=255)
cgTCGAAGAACGGCATGTACACCAGGCCCTGCGGCGGACGGTTACGACCGCGCGTTTCGACAATCgag > 1:1089049/1‑68 (MQ=255)
cgTCGAAGAACGGCATGTACACCAGGCCCTGCGGCGGACGGTTACGACCGCGCGTTTCGACAATCgag > 1:3261608/1‑68 (MQ=255)
cgTCGAAGAACGGCATGTACACCAGGCCCTGCGGCGGACGGTTACGACCGCGCGTTTCGACAATCgag > 1:2738965/1‑68 (MQ=255)
cgTCGAAGAACGGCATGTACACCAGGCCCTGCGGCGGACGGTTACGACCGCGCGTTTCGACAATCgag > 1:3032957/1‑68 (MQ=255)
cgTCGAAGAACGGCATGTACACCAGGCCCTGCGGCGGACGGTTACGACCGCGCGTTTCGACAATCgag > 1:2857396/1‑68 (MQ=255)
cgTCGAAGAACGGCATGTACACCAGGCCCTGCGGCGGACGGTTACGACCGCGCGTTTCGACAATCgag > 1:1523712/1‑68 (MQ=255)
cgTCGAAGAACGGCATGTACACCAGGCCCTGCGGCGGACGGTTACGACCGCGCGTTTCGACAATCgag > 1:2700861/1‑68 (MQ=255)
aCGGCATGTACACCAGGCCCTGTGGCGGACGGTTACGACCGCGCGTTTCAACAATCGAGATCACTTCGc < 1:400255/69‑1 (MQ=255)
aCGGCATGTACACCAGGCCCTGTGGCGGACGGTTACGACCGCGCGTTTCAACAATCGAGATCACTTCGc < 1:1604619/69‑1 (MQ=255)
aCGGCATGTACACCAGGCCCTGTGGCGGACGGTTACGACCGCGCGTTTCAACAATCGAGATCACTTCGc < 1:1730402/69‑1 (MQ=255)
aCGGCATGTACACCAGGCCCTGTGGCGGACGGTTACGACCGCGCGTTTCAACAATCGAGATCACTTCGc < 1:1029098/69‑1 (MQ=255)
aCGGCATGTACACCAGGCCCTGTGGCGGACGGTTACGACCGCGCGTTTCAACAATCGAGATCACTTCGc < 1:2365436/69‑1 (MQ=255)
aCGGCATGTACACCAGGCCCTGTGGCGGACGGTTACGACCGCGCGTTTCAACAATCGAGATCACTTCGc < 1:2672538/69‑1 (MQ=255)
aCGGCATGTACACCAGGCCCTGTGGCGGACGGTTACGACCGCGCGTTTCAACAATCGAGATCACTTCGc < 1:1157821/69‑1 (MQ=255)
tACACCAGGCCCTGTGGCGGACGGTTACGACCGCGCGTTTCAACAATCGAGATCACTTCGCCACGGc > 1:3130760/1‑67 (MQ=255)
tACACCAGGCCCTGTGGCGGACGGTTACGACCGCGCGTTTCAACAATCGAGATCACTTCGCCACGGCg > 1:2792998/1‑68 (MQ=255)
tACACCAGGCCCTGTGGCGGACGGTTACGACCGCGCGTTTCAACAATCGAGATCACTTCGCCACGGCg > 1:2089670/1‑68 (MQ=255)
tACACCAGGCCCTGTGGCGGACGGTTACGACCGCGCGTTTCAACAATCGAGATCACTTCGCCACGGCg > 1:2906400/1‑68 (MQ=255)
ggCCCTGTGGCGGACGGTTACGACCGCGCGTTTCAACAATCGAGATCACTTCGCCACGGCGAGAAACca < 1:2646292/69‑1 (MQ=255)
ggCCCTGTGGCGGACGGTTACGACCGCGCGTTTCAACAATCGAGATCACTTCGCCACGGCGAGAAACca < 1:862361/69‑1 (MQ=255)
gtgGCGGACGGTTACGACCGCGCGTTTCAACAATCGAGATCACTTCGCCACGGCGAGAAACcactttca > 1:559853/1‑69 (MQ=255)
gtgGCGGACGGTTACGACCGCGCGTTTCAACAATCGAGATCACTTCGCCACGGCGAGAAACcactttca > 1:2004469/1‑69 (MQ=255)
|
TCGCATCCAGCGTCAGTTTGTTAACCAACTGTGCGGCGTCGAAGAACGGCATGTACACCAGGCCCTGTGGCGGACGGTTACGACCGCGCGTTTCAACAATCGAGATCACTTCGCCACGGCGAGAAACCACTTTCA > minE/1427881‑1428015
|
| 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
