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 |
1,448,347 |
T→C |
57.7% |
N251N (AAT→AAC) |
atoS → |
sensory histidine kinase in two‑component regulatory system with AtoC |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,448,347 | 0 | T | C | 57.7%
| 19.1
/ 41.5
| 59 | N251N (AAT→AAC) | atoS | sensory histidine kinase in two‑component regulatory system with AtoC |
| Reads supporting (aligned to +/- strand): ref base T (18/7); new base C (31/3); total (49/10) |
| Fisher's exact test for biased strand distribution p-value = 7.96e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
ACAAAATATTCCCACTCGATTACCACAATTGCCCGGTGAAATGGGGCAAATCAGTCAGAGTGTTAATAACCTCGCCCAGGCACTGCGTGAAACGCGGACACTTAACGATCTGATTATTGAAAACGCTGCCGAT > minE/1448281‑1448413
|
acaAAATATTCCCACTCGATTACCACAATTGCCCGGTGAAATGGGGCAAATCAGTCAGAGTGTtaat < 1:2644382/67‑1 (MQ=255)
ttCCCACTCGATTACCACAATTGCCCGGTGAAATGGGGCAAATCAGTCAGAGTGTTAATAACCTCGccc > 1:1071615/1‑69 (MQ=255)
ttCCCACTCGATTACCACAATTGCCCGGTGAAATGGGGCAAATCAGTCAGAGTGTTAATAACCTCGccc > 1:1964210/1‑69 (MQ=255)
ttCCCACTCGATTACCACAATTGCCCGGTGAAATGGGGCAAATCAGTCAGAGTGTTAATAACCTCGccc > 1:132493/1‑69 (MQ=255)
ttCCCACTCGATTACCACAATTGCCCGGTGAAATGGGGCAAATCAGTCAGAGTGTTAATAACCTCGccc > 1:1913620/1‑69 (MQ=255)
ttCCCACTCGATTACCACAATTGCCCGGTGAAATGGGGCAAATCAGTCAGAGTGTTAATAACCTCGccc > 1:1613648/1‑69 (MQ=255)
ttCCCACTCGATTACCACAATTGCCCGGTGAAATGGGGCAAATCAGTCAGAGTGTTAATAACCTCGccc > 1:757033/1‑69 (MQ=255)
cACTCGATTACCACAATTGCCCGGTGAAATGGGGCAAATCAGTCAGAGTGTTAATAACCTCGCCCAgg < 1:459247/68‑1 (MQ=255)
cGATTACCACAATTGCCCGGTGAAATGGGGCAAATCAGTCAGAGTGTTAATAACCTCGCCCAGGCACTg > 1:2891184/1‑69 (MQ=255)
cGATTACCACAATTGCCCGGTGAAATGGGGCAAATCAGTCAGAGTGTTAATAACCTCGCCCAGGCACTg > 1:841066/1‑69 (MQ=255)
ttACCACAATTGCCCGGTGAAATGGGGCAAATCAGTCAGAGTGTTAACAACCTCG‑‑CAGGCACTGCGTGa < 1:1201894/69‑1 (MQ=255)
aCCACAATTGCCCGGTGAAATGGGGCAAATCAGTCAGAGTGTTAATAACCTCGCCCa > 1:3171416/1‑57 (MQ=255)
aCCACAATTGCCCGGTGAAATGGGGCAAATCAGTCAGAGTGTTAATAACCTCGCCCAGGCACTGCGTGa > 1:273607/1‑69 (MQ=255)
aCCACAATTGCCCGGTGAAATGGGGCAAATCAGTCAGAGTGTTAATAACCTCGCCCAGGCACTGCGTGa > 1:1898287/1‑69 (MQ=255)
aCCACAATTGCCCGGTGAAATGGGGCAAATCAGTCAGAGTGTTAACAACCTCGCCCAGGCACTGCGTGa < 1:1674084/69‑1 (MQ=255)
aCCACAATTGCCCGGTGAAATGGGGCAAATCAGTCAGAGTGTTAACAAACTCGCCCAGGCACTGCGTGa < 1:885086/69‑1 (MQ=255)
caATTGCCCGGTGAAATGGGGCAAATCAGTCAGAGTGTTAACACCCTCGCCCAGGCACTGCGTGaaa > 1:1691417/1‑67 (MQ=255)
caATTGCCCGGTGAAATGGGGCAAATCAGTCAGAGTGTTAACAACCTCGCCCAGGCACTGCGTGaaa > 1:2425752/1‑67 (MQ=255)
caATTGCCCGGTGAAATGGGGCAAATCAGTCAGAGTGTTAACAACCTCGCCCAGGCACTGCGTGaaa > 1:2751452/1‑67 (MQ=255)
caATTGCCCGGTGAAATGGGGCAAATCAGTCAGAGTGTTAACAACCTCGCCCAGGCACTGCGTGaaa > 1:2762573/1‑67 (MQ=255)
caATTGCCCGGTGAAATGGGGCAAATCAGTCAGAGTGTTAACAACCTCGCCCAGGCACTGCGTGaaa > 1:97651/1‑67 (MQ=255)
caATTGCCCGGTGAAATGGGGCAAATCAGTCAGAGTGTTAACAACCTCGCCCAGGCACTGCGTGaaa > 1:2338966/1‑67 (MQ=255)
caATTGCCCGGTGAAATGGGGCAAATCAGTCAGAGTGTTAACAACCTCGCCCAGGCACTGCGTGaaa > 1:3174459/1‑67 (MQ=255)
caATTGCCCGGTGAAATGGGGCAAATCAGTCAGAGTGTTAACAACCTCGCCCAGGCACTGCGTGaaa > 1:3236188/1‑67 (MQ=255)
caATTGCCCGGTGAAATGGGGCAAATCAGTCAGAGTGTTAACAACCTCGCCCAGGCACTGCGTGaaa > 1:3253043/1‑67 (MQ=255)
caATTGCCCGGTGAAATGGGGCAAATCAGTCAGAGTGTTAACAACCTCGCCCAGGCACTGCGTGaaa > 1:337410/1‑67 (MQ=255)
caATTGCCCGGTGAAATGGGGCAAATCAGTCAGAGTGTTAACAACCTCGCCCAGGCACTGCGTGaaa > 1:3421384/1‑67 (MQ=255)
caATTGCCCGGTGAAATGGGGCAAATCAGTCAGAGTGTTAACAACCTCGCCCAGGCACTGCGTGaaa > 1:356984/1‑67 (MQ=255)
caATTGCCCGGTGAAATGGGGCAAATCAGTCAGAGTGTTAACAACCTCGCCCAGGCACTGCGTGaaa > 1:36153/1‑67 (MQ=255)
caATTGCCCGGTGAAATGGGGCAAATCAGTCAGAGTGTTAACAACCTCGCCCAGGCACTGCGTGaaa > 1:483760/1‑67 (MQ=255)
caATTGCCCGGTGAAATGGGGCAAATCAGTCAGAGTGTTAACAACCTCGCCCAGGCACTGCGTGaaa > 1:787397/1‑67 (MQ=255)
caATTGCCCGGTGAAATGGGGCAAATCAGTCAGAGTGTTAACAACCTCGCCCAGGCACTGCGTGaaa > 1:937889/1‑67 (MQ=255)
caATTGCCCGGTGAAATGGGGCAAATCAGTCAGAGTGTTAACAACCTCGCCCAGGCACTGCGTGaaa > 1:2298869/1‑67 (MQ=255)
caATTGCCCGGTGAAATGGGGCAAATCAGTCAGAGTGTTAACAACCTCGCCCAGGCACTGCGTGaaa > 1:1394348/1‑67 (MQ=255)
caATTGCCCGGTGAAATGGGGCAAATCAGTCAGAGTGTTAACAACCTCGCCCAGGCACTGCGTGaaa > 1:1532119/1‑67 (MQ=255)
caATTGCCCGGTGAAATGGGGCAAATCAGTCAGAGTGTTAACAACCTCGCCCAGGCACTGCGTGaaa > 1:1578880/1‑67 (MQ=255)
caATTGCCCGGTGAAATGGGGCAAATCAGTCAGAGTGTTAACAACCTCGCCCAGGCACTGCGTGaaa > 1:2234753/1‑67 (MQ=255)
caATTGCCCGGTGAAATGGGGCAAATCAGTCAGAGTGTTAACAACCTCGCCCAGGCACTGCGTGaaa > 1:1748342/1‑67 (MQ=255)
caATTGCCCGGTGAAATGGGGCAAATCAGTCAGAGTGTTAACAACCTCGCCCAGGCACTGCGTGaaa > 1:1775545/1‑67 (MQ=255)
caATTGCCCGGTGAAATGGGGCAAATCAGTCAGAGTGTTAACAACCTCGCCCAGGCACTGCGTGaaa > 1:2156096/1‑67 (MQ=255)
caATTGCCCGGTGAAATGGGGCAAATCAGTCAGAGTGTTAACAACCTCGCCCAGGCACTGCGTGaaa > 1:1971302/1‑67 (MQ=255)
caATTGCCCGGTGAAATGGGGCAAATCAGTCAGAGTGTTAACAACCTCGCCCAGGCACTGCGTGaaa > 1:2326862/1‑67 (MQ=255)
caATTGCCCGGTGAAATGGGGCAAATCAGTCAGAGTGTTAACAACCTCGCCCAGGCACTGCGTGaaa > 1:2065066/1‑67 (MQ=255)
caATTGCCCGGTGAAATGGGGCAAATCAGTCAGAGTGTTAACAACCTCGCCCAGGAACTGCGTGaaa > 1:197394/1‑67 (MQ=255)
caATTGCCCGGTGAAATGGGGCAAATCAGTCAGAGTGTTAACAACCTCGCCAGGGCACTGCGTGaaa > 1:2813756/1‑67 (MQ=255)
caATTGCACGGTGAAATGGGGCAAATCAGTCAGAGTGTTAACAACCTCGCCCAGGCACTGCGTGaaa > 1:2153437/1‑67 (MQ=255)
caATTGACCGGTGAAATGGGGCAAATCAGTCAGAGTGTTAACAACCTCGCCCAGGCACTGCGTGaaa > 1:732771/1‑67 (MQ=255)
aTTGCCCGGTGAAATGGGGCAAATCAGTCAGAGTGTTAATAACCTCGCCCAGGCACTGCGTGAAAcgcg < 1:3069404/69‑1 (MQ=255)
aTTGCCCGGTGAAATGGGGCAAATCAGTCAGAGTGTTAATAACCTCGCCCAGGCACTGCGTGAAAcgcg < 1:3391857/69‑1 (MQ=255)
tcagtcagAGTGTTAATAACCTCGCCCAGGCACTGCGTGAAACGCGGACACTTAACGATCTGattatt > 1:126348/1‑68 (MQ=255)
tcagtcagAGTGTTAATAACCTCGCCCAGGCACTGCGTGAAACGCGGACACTTAACGATCTGattatt > 1:2353722/1‑68 (MQ=255)
tcagtcagAGTGTTAATAACCTCGCCCAGGCACTGCGTGAAACGCGGACACTTAACGATCTGattatt > 1:1570017/1‑68 (MQ=255)
tcagtcagAGTGTTAATAACCTCGCCCAGGCACTGCGTGAAACGCGGACACTTAACGATCTGattatt > 1:3347163/1‑68 (MQ=255)
tcagtcagAGTGTTAATAACCTCGCCCAGGCACTGCGTGAAACGCGGACACTTAACGATCTGattatt > 1:2055576/1‑68 (MQ=255)
tcagtcagAGTGTTAATAACCTCGCCCAGGCACTGCGTGAAACGCGGACACTTAACGATCTGattatt > 1:2083573/1‑68 (MQ=255)
agtcagAGTGTTAATAACCTCGCCCAGGCACTGCGTGAAACGCGGACACTTAACGATCTGATTATTGaa < 1:2198469/69‑1 (MQ=255)
gtcagAGTGTTAATAACCTCGCCCAGGCACTGCGTGAAACGCGGACACTTAACGATCTGATTATTGaa < 1:3013698/68‑1 (MQ=255)
agagTGTTAATAACCTCGCCCAGGCACTGCGTGAAACGCGGACACTTAACGATCTGATTATTGAAAACg > 1:2269244/1‑69 (MQ=255)
agTGTTAATAACCTCGCCCAGGCACTGCGTGAAACGCGGACACTTAACGATCTGATTATTGAAAACGc < 1:2390923/68‑1 (MQ=255)
agTGTTAATAACCTCGCCCAGGCACTGCGTGAAACGCGGACACTTAACGATCTGATTATTGAAAACGc < 1:1298154/68‑1 (MQ=255)
aataaCCTCGCCCAGGCACTGCGTGAAACGCGGACACTTAACGATCTGATTATTGAAAACGCTGCCGAt > 1:184759/1‑69 (MQ=255)
aataaCCTCGCCCAGGCACTGCGTGAAACGCGGACACTTAACGATCTGATTATTGAAAACGCTGCCGAt > 1:2212942/1‑69 (MQ=255)
aataaCCTCGCCCAGGCACTGCGTGAAACGCGGACACTTAACGATCTGATTATTGAAAACGCTGCCGAt > 1:372220/1‑69 (MQ=255)
aataaCCTCGCCCAGGCACTGCGTGAAACGCGGACACTTAACGATCTGATTATTGAAAACGCTGCCGAt > 1:1566827/1‑69 (MQ=255)
aataaCCTCGCCCAGGCACTGCGTGAAACGCGGACACTTAACGATCTGATTATTGAAAACGCTGCCGAt > 1:79961/1‑69 (MQ=255)
aataaCCTCGCCCAGGCACTGCGTGAAACGCGGACACTTAACGATCTGATTATTGAAAACGCTGCCGAt > 1:1325453/1‑69 (MQ=255)
aataaCCTCGCCCAGGCACTGCGTGAAACGCGGACACTTAACGATCTGATTATTGAAAACGCTGCCGAt > 1:3060589/1‑69 (MQ=255)
|
ACAAAATATTCCCACTCGATTACCACAATTGCCCGGTGAAATGGGGCAAATCAGTCAGAGTGTTAATAACCTCGCCCAGGCACTGCGTGAAACGCGGACACTTAACGATCTGATTATTGAAAACGCTGCCGAT > minE/1448281‑1448413
|
| 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
