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 |
1,790,943 |
C→T |
44.9% |
I263I (ATC→ATT) |
gabD → |
succinate‑semialdehyde dehydrogenase I, NADP‑dependent |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,790,943 | 0 | C | T | 44.9%
| 13.9
/ 53.7
| 69 | I263I (ATC→ATT) | gabD | succinate‑semialdehyde dehydrogenase I, NADP‑dependent |
| Reads supporting (aligned to +/- strand): ref base C (31/7); new base T (18/13); total (49/20) |
| Fisher's exact test for biased strand distribution p-value = 3.77e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.80e-01 |
GAACAGTGCGCGAAAGACATCAAGAAAGTGTCGCTGGAGCTGGGCGGTAACGCGCCGTTTATCGTCTTTGACGATGCCGACCTCGACAAAGCCGTGGAAGGCGCGCTGGCCTCGAAATTCCGC > minE/1790881‑1791003
|
gAACAGTGCGCGAAAGACATCAAGAAAGTGTCGCTGGAGCTGGGCGGTAACGCGCCGTTTATCGTCttt > 1:818765/1‑69 (MQ=255)
gAACAGTGCGCGAAAGACATCAAGAAAGTGTCGCTGGAGCTGGGCGGTAACGCGCCGTTTATCGTCttt > 1:1243871/1‑69 (MQ=255)
gAACAGTGCGCGAAAGACATCAAGAAAGTGTCGCTGGAGCTGGGCGGTAACGCGCCGTTTATCGTCttt > 1:445960/1‑69 (MQ=255)
gAACAGTGCGCGAAAGACATCAAGAAAGTGTCGCTGGAGCTGGGCGGTAACGCGCCGTTTATCGTCttt > 1:3374374/1‑69 (MQ=255)
gAACAGTGCGCGAAAGACATCAAGAAAGTGTCGCTGGAGCTGGGCGGTAACGCGCCGTTTATCGTCttt > 1:32485/1‑69 (MQ=255)
gAACAGTGCGCGAAAGACATCAAGAAAGTGTCGCTGGAGCTGGGCGGTAACGCGCCGTTTATCGTCttt > 1:1508329/1‑69 (MQ=255)
gAACAGTGCGCGAAAGACATCAAGAAAGTGTCGCTGGAGCTGGGCGGTAACGCGCCGTTTATCGTCttt > 1:3008204/1‑69 (MQ=255)
gAACAGTGCGCGAAAGACATCAAGAAAGTGTCGCTGGAGCTGGGCGGTAACGCGCCGTTTATCGTCttt > 1:2961302/1‑69 (MQ=255)
gAACAGTGCGCGAAAGACATCAAGAAAGTGTCGCTGGAGCTGGGCGGTAACGCGCCGTTTATCGTCttt > 1:2188829/1‑69 (MQ=255)
gAACAGTGCGCGAAAGACATCAAGAAAGTGTCGCTGGAGCTGGGCGGTAACGCGCCGTTTATCGTCttt > 1:1848769/1‑69 (MQ=255)
cAGTGCGCGAAAGACATCAAGAAAGTGTCGCTGGAGCTGGGCGGTAACGCGCCGTTTATCGTCTTTGAc > 1:1086978/1‑69 (MQ=255)
cAGTGCGCGAAAGACATCAAGAAAGTGTCGCTGGAGCTGGGCGGTAACGCGCCGTTTATCGTCTTTGAc < 1:739734/69‑1 (MQ=255)
cAGTGCGCGAAAGACATCAAGAAAGTGTCGCTGGAGCTGGGCGGTAACGCGCCGTTTATCGTCTTTGAc > 1:1358848/1‑69 (MQ=255)
cAGTGCGCGAAAGACATCAAGAAAGTGTCGCTGGAGCTGGGCGGTAACGCGCCGTTTATCGTCTTTGAc > 1:1626798/1‑69 (MQ=255)
cAGTGCGCGAAAGACATCAAGAAAGTGTCGCTGGAGCTGGGCGGTAACGCGCCGTTTATCGTCTTTGAc > 1:2044673/1‑69 (MQ=255)
cAGTGCGCGAAAGACATAAAGAAAGTGTCGCTGGAGCTGGGCGGTAACGCGCCGTTTATCGTCTTTGAc < 1:2748442/69‑1 (MQ=255)
aGTGCGCGAAAGACATCAAGAAAGTGTCGCTGGAGCTGGGCGGTAACGCGCCGTTTATCGTCTTTGAc < 1:1796792/68‑1 (MQ=255)
tGCGCGAAAGACATCAAGAAAGTGTCGCTGGAGCTGGGCGGTAACGCGCCGTTTATCGTCTTTGACGAt > 1:2747708/1‑69 (MQ=255)
tGCGCGAAAGACATCAAGAAAGTGTCGCTGGAGCTGGGCGGTAACGCGCCGTTTATCGTCTTTGACGAt > 1:1713926/1‑69 (MQ=255)
tGCGCGAAAGACATCAAGAAAGTGTCGCTGGAGCTGGGCGGTAACGCGCCGTTTATCGTCTTTGACGAt > 1:226912/1‑69 (MQ=255)
tGCGCGAAAGACATCAAGAAAGTGTCGCTGGAGCTGGGCGGTAACGCGCCGTTTATCGTCTTTGACGAt > 1:2635783/1‑69 (MQ=255)
cgAAAGACATCAAGAAAGTGTCGCTGGAGCTGGGCGGTAACGCGCCGTTTATCGTCTTTGACGATGcc < 1:2490223/68‑1 (MQ=255)
gAAAGACATCAAGAAAGTGTCGCTGGAGCTGGGCGGTAACGCGCCGTTTATCGTCTTTGACGATGcc < 1:576542/67‑1 (MQ=255)
tCGCTGGAGCTGGGCGGTAACGCGCCGTTTATCGTCTTTGACGATGCCGACCTCGACAAAGCCGTGGaa > 1:286710/1‑69 (MQ=255)
tCGCTGGAGCTGGGCGGTAACGCGCCGTTTATCGTCTTTGACGATGCCGACCTCGACAAAGCCGTGGaa > 1:829803/1‑69 (MQ=255)
tCGCTGGAGCTGGGCGGTAACGCGCCGTTTATCGTCTTTGACGATGCCGACCTCGACAAAGCCGTGGaa > 1:1570853/1‑69 (MQ=255)
tCGCTGGAGCTGGGCGGTAACGCGCCGTTTATCGTCTTTGACGATGCCGACCTCGACAAAGCCGTGGaa > 1:1160102/1‑69 (MQ=255)
tCGCTGGAGCTGGGCGGTAACGCGCCGTTTATCGTCTTTGACGATGCCGACCTCGACAAAGCCGTGGaa > 1:1460439/1‑69 (MQ=255)
tCGCTGGAGCTGGGCGGTAACGCGCCGTTTATCGTCTTTGACGATGCCGACCTCGACAAAGCCGTGGaa > 1:1180497/1‑69 (MQ=255)
tCGCTGGAGCTGGGCGGTAACGCGCCGTTTATCGTCTTTGACGATGCCGACCTCGACAAAGCCGTGGa > 1:845870/1‑68 (MQ=255)
cGCTGGAGCTGGGCGGTAACGCGCCGTTTATCGTCTTTGAc < 1:355110/41‑1 (MQ=255)
tGGAGCTGGGCGGCTACGCACCGTTTATTGTCTTTGACGATGCCGATCTCGATAAAGCCGTGGAAGgcg > 1:2097898/1‑69 (MQ=255)
tGGAGCTGGGCGGCAACGCACCGTTTATTGTCTTTGACGATGCCGATCTCGATAAAGCCGTGGAAGgcg > 1:625603/1‑69 (MQ=255)
tGGAGCTGGGCGGCAACGCACCGTTTATTGTCTTTGACGATGCCGATCTCGATAAAGCCGTGGAAGgcg > 1:1610090/1‑69 (MQ=255)
tGGAGCTGGGCGGCAACGCACCGTTTATTGTCTTTGACGATGCCGATCTCGATAAAGCCGTGGAAGgcg > 1:3042160/1‑69 (MQ=255)
tGGAGCTGGGCGGCAACGCACCGTTTATTGTCTTTGACGATGCCGATCTCGATAAAGCCGTGGAAGgcg > 1:806034/1‑69 (MQ=255)
tGGAGCTGGGCGGCAACGCACCGTTTATTGTCTTTGACGATGCCGATCTCGATAAAGCCGTGGAAGgcg > 1:2599106/1‑69 (MQ=255)
tGGAGCTGGGCGGCAACGCACCGTTTATTGTCTTTGACGATGCCGATCTCGATAAAGCCGTGGAAGgcg > 1:2504501/1‑69 (MQ=255)
tGGAGCTGGGCGGCAACGCACCGTTTATTGTCTTTGACGATGCCGATCTCGATAAAGCCGTGGAAGgcg > 1:975901/1‑69 (MQ=255)
tGGAGCTGGGCGGCAACGCACCGTTTATTGTCTTTGACGATGCCGATCTCGATAAAGCCGTGGAAGgcg > 1:1896726/1‑69 (MQ=255)
ggAGCTGGGCGGTAACGCACCGTTTATTGTCTTTGACGATGCCGATCTCGATAAAGCCGTGGAAGgcg > 1:393170/1‑68 (MQ=255)
ggAGCTGGGCGGCAACGCACCGTTTATTGTCTTTGACGATGCCGATCTCGATAAAGCCGTGGAAGgcgc > 1:770560/1‑69 (MQ=255)
ggAGCTGGGCGGCAACGCACCGTTTATTGTCTTTGACGATGCCGATCTCGATAAAGCCGTGGAAGgcgc > 1:2887420/1‑69 (MQ=255)
ggAGCTGGGCGGCAACGCACCGTTTATTGTCTTTGACGATGCCGATCTCGATAAAGCCGTGGAAGgcgc > 1:3118033/1‑69 (MQ=255)
ggAGCTGGGCGGCAACGCACCGTTTATTGTCTTTGACGATGCCGATCTCGATAAAGCCGTGGAAGgcgc > 1:3099176/1‑69 (MQ=255)
ggAGCTGGGCGGCAACGCACCGTTTATTGTCTTTGACGATGCCGATCTCGATAAAGCCGTGGAAGgcgc > 1:2379560/1‑69 (MQ=255)
ggAGCTGGGCGGCAACGCACCGTTTATTGTCTTTGACGATGCCGATCTCGATAAAGCCGTGGAAGgcgc > 1:919578/1‑69 (MQ=255)
ggAGCTGGGCGGCAACGCACCGTTTATTGTCTTTGACGATGCCGATCTCGATAAAGCCGTGGAAGgcg > 1:408654/1‑68 (MQ=255)
ggAGCTGGGCGGCAACGCACCGTTTATTGTCTTTGACGATGCCGATCTAGATAAAGCCGTGGAAGgcgc > 1:1922696/1‑69 (MQ=255)
aaCGCGCCGTTTATCGTCTTTGACGATGCCGACCTCGACAAAGCCGTGGAAGGCGCGCTGGCCTCGaaa > 1:2921916/1‑69 (MQ=255)
aaCGCGCCGTTTATCGTCTTTGACGATGCCGACCTCGACAAAGCCGTGGAAGGCGCGCTGGCCTCGaaa > 1:3267708/1‑69 (MQ=255)
aaCGCGCCGTTTATCGTCTTTGACGATGCCGACCTCGACAAAGCCGTGGAAGGCGCGCTGGCCTCGaaa > 1:754711/1‑69 (MQ=255)
aaCGCGCCGTTTATCGTCTTTGACGATGCCGACCTCGACAAAGCCGTGGAAGGCGCGCTGGCCTCGaaa > 1:2591422/1‑69 (MQ=255)
aaCGCGCCGTTTATCGTCTTTGACGATGCCGACCTCGACAAAGCCGTGGAAGGCGCGCTGGCCTCGaaa > 1:2219268/1‑69 (MQ=255)
aaCGCGCCGTTTATCGTCTTTGACGATGCCGACCTCGACAAAGCCGTGGAAGGCGCGCTGGCCTCGaa > 1:1302270/1‑68 (MQ=255)
cgcaCCGTTTATTGTCTTTGACGATGCCGATCTCGATAAAGCCGTGGAAGGCGCGCTGGCCTCGAAAtt < 1:998311/69‑1 (MQ=255)
cgcaCCGTTTATTGTCTTTGACGATGCCGATCTCGATAAAGCCGTGGAAGGCGCGCTGGCCTCGAAAtt < 1:719934/69‑1 (MQ=255)
cgcaCCGTTTATTGTCTTTGACGATGCCGATCTCGATAAAGCCGTGGAAGGCGCGCTGGCCTCGAAAtt < 1:565898/69‑1 (MQ=255)
cgcaCCGTTTATTGTCTTTGACGATGCCGATCTCGATAAAGCCGTGGAAGGCGCGCTGGCCTCGAAAtt < 1:1392563/69‑1 (MQ=255)
cgcaCCGTTTATTGTCTTTGACGATGCCGATCTCGATAAAGCCGTGGAAGGCGCGCTGGCCTCGAAAtt < 1:3318204/69‑1 (MQ=255)
cgcaCCGTTTATTGTCTTTGACGATGCCGATCTCGATAAAGCCGTGGAAGGCGCGCTGGCCTCGAAAtt < 1:3272219/69‑1 (MQ=255)
cgcaCCGTTTATTGTCTTTGACGATGCCGATCTCGATAAAGCCGTGGAAGGCGCGCTGGCCTCGAAAtt < 1:307270/69‑1 (MQ=255)
cgcaCCGTTTATTGTCTTTGACGATGCCGATCTCGATAAAGCCGTGGAAGGCGCGCTGGCCTCGAAAtt < 1:2893443/69‑1 (MQ=255)
cgcaCCGTTTATTGTCTTTGACGATGCCGATCTCGATAAAGCCGTGGAAGGCGCGCTGGCCTCGAAAtt < 1:1030367/69‑1 (MQ=255)
cgcaCCGTTTATTGTCTTTGACGATGCCGATCTCGATAAAGCCGTGGAAGGCGCGCTGGCCTCGAAAtt < 1:2435857/69‑1 (MQ=255)
cgcaCCGTTTATTGTCTTTGACGATGCCGATCTCGATAAAGCCGTGGAAGGCGCGCTGGCCTCGAAAtt < 1:1924411/69‑1 (MQ=255)
cgcaCCGTTTATTGTCTTTGACGATGCCGATCTCGATAAAGCCGTGGAAGGCGCCCTGGCCTCGAAAtt < 1:2152383/69‑1 (MQ=255)
gcaccGTTTATTGTCTTTGACGATGCCGATCTCGATAAAGCCGTGGAAGGCGCGCTGGCCTCGAAAtt < 1:2294241/65‑1 (MQ=255)
ccGTTTATCGTCTTTGACGATGCCGACCTCGACAAAGCCGTGGAAGGCGCGCTGGCCTCGAAATTCCGc < 1:805299/69‑1 (MQ=255)
|
GAACAGTGCGCGAAAGACATCAAGAAAGTGTCGCTGGAGCTGGGCGGTAACGCGCCGTTTATCGTCTTTGACGATGCCGACCTCGACAAAGCCGTGGAAGGCGCGCTGGCCTCGAAATTCCGC > minE/1790881‑1791003
|
| 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
