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 |
2,902,623 |
A→G |
33.3% |
D474D (GAT→GAC) |
nrdD ← |
anaerobic ribonucleoside‑triphosphate reductase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,902,623 | 0 | A | G | 33.3%
| 44.2
/ 30.6
| 60 | D474D (GAT→GAC) | nrdD | anaerobic ribonucleoside‑triphosphate reductase |
| Reads supporting (aligned to +/- strand): ref base A (14/26); new base G (12/8); total (26/34) |
| Fisher's exact test for biased strand distribution p-value = 9.75e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
TAACCCAGCGAAATAGACGCACGACCGTTTTTGAAGATTTCAGAAACATCATCGTCAGCATTGAGACGCACGCCACAAGCACCTTCCATATAGAGGATCGGGGC > minE/2902573‑2902676
|
tAACCCAGCGAAATAGACGCACGACCGTTTTTGAAGATTTCAGAAACATCATCGTCAGCATTGAGacgc > 1:2354542/1‑69 (MQ=255)
tAACCCAGCGAAATAGACGCACGACCGTTTTTGAAGATTTCAGAAACATCATCGTCAGCATTGAGacgc > 1:3108634/1‑69 (MQ=255)
tAACCCAGCGAAATAGACGCACGACCGTTTTTGAAGATTTCAGAAACATCATCGTCAGCATTGAGacg > 1:2730867/1‑68 (MQ=255)
gCGAAATAGACGCACGACCGTTTTTGAAGATTTCAGAAACATCATCGTCAGCATTGAGACTCACGCcac < 1:2769164/69‑1 (MQ=255)
gCGAAATAGACGCACGACCGTTTTTGAAGATTTCAGAAACATCATCGTCAGCATTGAGACGCACGCcac < 1:1098645/69‑1 (MQ=255)
gCGAAATAGACGCACGACCGTTTTTGAAGATTTCAGAAACATCATCGTCAGCATTGAGACGCACGCcac < 1:2328591/69‑1 (MQ=255)
gCGAAATAGACGCACGACCGTTTTTGAAGATTTCAGAAACATCATCGTCAGCATTGAGACGCACGCcac < 1:188325/69‑1 (MQ=255)
gCGAAATAGACGCACGACCGTTTTTGAAGATTTCAGAAACATCATCGTCAGCATTGAGACGCACGCcac < 1:508800/69‑1 (MQ=255)
gCGAAATAGACGCACGACCGTTTTTGAAGATTTCAGAAACATCATCGTCAGCATTGAGACGCACGCcac < 1:597067/69‑1 (MQ=255)
taaaTAGACGCACGACCGTTTTTGAAGATTTCAGAAACATCATCGTc < 1:1768439/46‑1 (MQ=255)
gAAATAGACGCACGACTGTTTTTGAAGATTTCAGAAACATCATCGTCAGCATTGAGACGCACGCcaca > 1:2296278/1‑68 (MQ=255)
gAAATAGACGCACGACCGTTTTTGAAGATTTCAGAAACATCATCGTc < 1:3123569/47‑1 (MQ=255)
gAAATAGACGCACGACCGTTTTTGAAGATTTCAGAAACATCATCGTc < 1:3208568/47‑1 (MQ=255)
gAAATAGACGCACGACCGTTTTTGAAGATTTCAGAAACATCATCGTc < 1:2277516/47‑1 (MQ=255)
gAAATAGACGCACGACCGTTTTTGAAGATTTCAGAAACATCATCGTc < 1:2648086/47‑1 (MQ=255)
gAAATAGACGCACGACCGTTTTTGAAGATTTCAGAAACATCATCGTc < 1:174294/47‑1 (MQ=255)
gAAATAGACGCACGACCGTTTTTGAAGATTTCAGAAACATCATCGTc < 1:3370504/47‑1 (MQ=255)
gAAATAGACGCACGACCGTTTTTGAAGATTTCAGAAACATCATCGTCAGCATTGAGACGCACGCcaca > 1:2817401/1‑68 (MQ=255)
gAAATAGACGCACGACCGTTTTTGAAGATTTCAGAAACATCATCGTCAGCATTGAGACGCACGCcaca > 1:1937821/1‑68 (MQ=255)
gAAATAGACGCACGACCGTTTTTGAAGATTTCAGAAACATCATCGTCAGCATTGAGACGCACGCcaca > 1:1922111/1‑68 (MQ=255)
gAAATAGACGCACGACCGTTTTTGAAGATTTCAGAAACATCATCGTCAGCATTGAGACGCACGCcaca > 1:1287307/1‑68 (MQ=255)
gAAATAGACGCACGACCGTTTTTGAAGATTTCAGAAACATCATCGTCAGCATTGAGACGCACGCcaca > 1:3064935/1‑68 (MQ=255)
gAAATAGACGCACGACCGTTTTTGAAGATTTCAGAAACATCATCGTCAGCATTGAGACGCACGCcaca > 1:474307/1‑68 (MQ=255)
gAAATAGACGCACGACCGTTTTTGAAGATTTCAGAAACATCATCGTCAGCATTGAGACGCACGCcaca > 1:2413330/1‑68 (MQ=255)
gAAATAGACGCACGACCGTTTTTGAAGATTTCAGAAACATCATCGTCAGCATAGAGACGCACGCcac > 1:2167549/1‑67 (MQ=255)
aaTAGACGCACGACCGTTTTTGAAGATTTCAGAAACATCATCGTCAGCATTGAGACGCACGCCACAAGc < 1:784270/69‑1 (MQ=255)
aTAGACGCACGACCGTTTTTGAAGATTTCAGAAACATCATCGTCAGCATTGAGACGCACGCCACAAGCa < 1:703003/69‑1 (MQ=255)
aTAGACGCACGACCGTTTTTGAAGATTTCAGAAACATCATCGTCAGCATTGAGACGCACGCCACAAGCa < 1:984427/69‑1 (MQ=255)
aTAGACGCACGACCGTTTTTGAAGATTTCAGAAACATCATCGTCAGCATTGAGACGCACGCCACAAGCa < 1:356284/69‑1 (MQ=255)
aTAGACGCACGACCGTTTTTGAAGATTTCAGAAACATCATCGTCAGCATTGAGACGCACGCCACAAGCa < 1:1438916/69‑1 (MQ=255)
aTAGACGCACGACCGTTTTTGAAGATTTCAGAAACATCATCGTCAGCATTGAGACGCACGCCACAAGCa < 1:2708224/69‑1 (MQ=255)
tAGACGCACGACCGTTTTTGAAGATTTCAGAAACATCATCGTCAGCATTGAGACGCACGCCACAAGCa < 1:2144843/68‑1 (MQ=255)
tAGACGCACGACCGTTTTTGAAGATTTCAGAAACATCATCGTCAGCATTGAGACGCACGCCACAAGCa < 1:206935/68‑1 (MQ=255)
gACGCACGACCGTTTTTGAAGATTTCAGAAACATCATCGTc < 1:2906150/41‑1 (MQ=255)
cGCACGACCGTTTTTGAAGATTTCAGAAACATCATCGTCAGCATTGAGACGCACGCCACAAGCACCTTc < 1:1723993/69‑1 (MQ=255)
gCACGACCGTTTTTGAAGATTTCAGAAACATCATCGTCAGCATTGAGACGCACGCCACAAGCACCTTc < 1:2848847/68‑1 (MQ=255)
cGTTTTTGAAGATTTCAGAAACATCATCGTCAGCATTga < 1:176952/39‑1 (MQ=255)
tttGAAGATTTCAGAAACATCATCGTCAGCATTGAGACGCACGCCACAAGCACCTTCCa > 1:915212/1‑59 (MQ=255)
tttGAAGATTTCAGAAACATCATCGTCAGCATTGAGACGCACGCCACAAGCACCTTCCa > 1:1224992/1‑59 (MQ=255)
gAAGATTTCAGAAACGTCGTCGTCAGTATTCAGACGCACGCCACAAGCGCCTTCCATATAGAGGATCg < 1:733500/68‑1 (MQ=255)
gAAGATTTCAGAAACGTCGTCGTCAGCATTCAGACGCACGCCACAAGCGCCTTCCATATAGAGGATCg < 1:737630/68‑1 (MQ=255)
gAAGATTTCAGAAACGTCGTCGTCAGCATTCAGACGCACGCCACAAGCGCCTTCCATATAGAGGATCg < 1:992176/68‑1 (MQ=255)
gAAGATTTCAGAAACGTCGTCGTCAGCATTCAGACGCACGCCACAAGCGCCTTCCATATAGAGGATCg < 1:2553805/68‑1 (MQ=255)
gAAGATTTCAGAAACGTCGTCGTCAGCATTCAGACGCACGCCACAAGCGCCTTCCATATAGAGGATCg < 1:294318/68‑1 (MQ=255)
gAAGATTTCAGAAACGTCGTCGTCAGCATTCAGACGCACGCCACAAGCGCCTTCCATATAGAGGATCg < 1:2465496/68‑1 (MQ=255)
gAAGATTTCAGAAACGTCGTCGTCAGCATTCAGACGCACGCCACAAGCGCCTTCCATATAGAGGATCg < 1:2056036/68‑1 (MQ=255)
gAAGATTTCAGAAACGTCGTCGTCAGCATTCAGACGCACGCCACAAGCGCCTTCCATATAGAGGATCg < 1:1634957/68‑1 (MQ=255)
gATTTCAGAAACATCATCGTCAGCATTGAGACGCACGCCACAACCACCTTCCATATAGAGGATCGGGGc < 1:1213623/69‑1 (MQ=255)
ttCAGAAACGTCGTCGTCAGCATTCAGACGCACGCCACAAGcg > 1:2753276/1‑42 (MQ=37)
ttCAGAAACGTCGTCGTCAGCATTCAGACGCACGCCACAAGcg > 1:1370261/1‑42 (MQ=37)
ttCAGAAACGTCGTCGTCAGCATTCAGACGCACGCCACAAGcg > 1:1402142/1‑42 (MQ=37)
ttCAGAAACGTCGTCGTCAGCATTCAGACGCACGCCACAAGcg > 1:741693/1‑42 (MQ=37)
ttCAGAAACGTCGTCGTCAGCATTCAGACGCACGCCACAAGcg > 1:1458954/1‑42 (MQ=37)
ttCAGAAACGTCGTCGTCAGCATTCAGACGCACGCCACAAGcg > 1:1546488/1‑42 (MQ=37)
ttCAGAAACGTCGTCGTCAGCATTCAGACGCACGCCACAAGcg > 1:1573642/1‑42 (MQ=37)
ttCAGAAACGTCGTCGTCAGCATTCAGACGCACGCCACAAGcg > 1:3301833/1‑42 (MQ=37)
ttCAGAAACGTCGTCGTCAGCATTCAGACGCACGCCACAAGcg > 1:3144642/1‑42 (MQ=37)
ttCAGAAACGTCGTCGTCAGCATTCAGACGCACGCCACAAGcg > 1:3136689/1‑42 (MQ=37)
ttCAGAAACGTCGTCGTCAGCATTCAGACGCACGCCACAAGcg > 1:2600264/1‑42 (MQ=37)
ttCAGAAACGTCGTCGTCAGCATTCAGACGCACGCCACAAGcg > 1:3067725/1‑42 (MQ=37)
atcGTCAGCATTGAGACGCACGCCACAAGCACCTTCCata > 1:1718410/1‑40 (MQ=255)
atcGTCAGCATTGAGACGCACGCCACAAGCACCTTCCata > 1:373009/1‑40 (MQ=255)
atcGTCAGCATTGAGACGCACGCCACAAGCACCTTCCata > 1:1634319/1‑40 (MQ=255)
atcGTCAGCATTGAGACGCACGCCACAAGCACCTTCCata > 1:1812196/1‑40 (MQ=255)
atcGTCAGCATTGAGACGCACGCCACAAGCACCTTCCata > 1:21579/1‑40 (MQ=255)
atcGTCAGCATTGAGACGCACGCCACAAGCACCTTCCata > 1:1396698/1‑40 (MQ=255)
|
TAACCCAGCGAAATAGACGCACGACCGTTTTTGAAGATTTCAGAAACATCATCGTCAGCATTGAGACGCACGCCACAAGCACCTTCCATATAGAGGATCGGGGC > minE/2902573‑2902676
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
