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 |
2,343,982 |
G→A |
29.9% |
A216A (GCG→GCA) |
glnG → |
fused DNA‑binding response regulator in two‑component regulatory system with GlnL, nitrogen regulator I (NRI) |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,343,982 | 0 | G | A | 29.9%
| 58.8
/ 25.4
| 60 | A216A (GCG→GCA) | glnG | fused DNA‑binding response regulator in two‑component regulatory system with GlnL, nitrogen regulator I (NRI) |
| Reads supporting (aligned to +/- strand): ref base G (12/30); new base A (15/3); total (27/33) |
| Fisher's exact test for biased strand distribution p-value = 1.45e-04 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.94e-01 |
GCTGAATATGGCAGCTATCCCAAAAGATTTGATCGAATCAGAACTGTTTGGCCACGAGAAAGGCGCGTTTACTGGCGCGAATACCATTCGTCAGGGGCGTTTTGAACAGGCCGATGGCGGTACAT > minE/2343916‑2344040
|
gcTGAATATGGCAGCTATCCCAAAAGATTTGATCGAATCAGAACTGTTTGGCCACGAGAAAGGCGCGtt < 1:2125558/69‑1 (MQ=255)
gcTGAATATGGCAGCTATCCCAAAAGATTTGATCGAATCAGAACTGTTTGGCCACGAGAAAGGCGCGtt < 1:852066/69‑1 (MQ=255)
gcTGAATATGGCAGCTATCCCAAAAGATTTGATCGAATCAGAACTGTTTGGCCACGAGAAAGGCGCGtt < 1:2133681/69‑1 (MQ=255)
gCAGCTATCCCAAAAGATTTGATCGAATCAGAACTGTTTGGCCACGAGAAAGGCGCGTTTACTGGcgcg < 1:2774305/69‑1 (MQ=255)
gCAGCTATCCCAAAAGATTTGATCGAATCAGAACTGTTTGGCCACGAGAAAGGCGCGTTTACTGGcgcg < 1:2340768/69‑1 (MQ=255)
gCAGCTATCCCAAAAGATTTGATCGAATCAGAACTGTTTGGCCACGAGAAAGGCGCGTTTACTGGcgcg < 1:29761/69‑1 (MQ=255)
gCAGCTATCCCAAAAGATTTGATCGAATCAGAACTGTTTGGCCACGAGAAAGGCGCGTTTACTGGcgcg < 1:3273378/69‑1 (MQ=255)
gCAGCTATCCCAAAAGATTTGATCGAATCAGAACTGTTTGGCCACGAGAAAGGCGCGTTTACTGGcgcg < 1:3407160/69‑1 (MQ=255)
gCAGCTATCCCAAAAGATTTGATCGAATCAGAACTGTTTGGCCACGAGAAAGGCGCGTTTACTGGcgcg < 1:653244/69‑1 (MQ=255)
gCAGCTATCCCAAAAGATTTGATCGAATCAGAACTGTTTGGCCACGAGAAAGGCGCGTTTACTGGcgcg < 1:1157286/69‑1 (MQ=255)
tATCCCAAAAGATTTGATCGAATCAGAACTGTTTGGCCACGAGAAAGGCGCGTTTACTGGCGCGAATAc < 1:2514510/69‑1 (MQ=255)
aTCCCGAAGGATTTGATCGAATCCGAACTGTTTGGTCACGAGAAAGGCGCATTTACCGGCGCGAATAcc > 1:3076302/1‑69 (MQ=25)
aTCCCGAAGGATTTGATCGAATCCGAACTGTTTGGTCACGAGAAAGGCGCATTTACCGGCGCGAATAcc > 1:2982820/1‑69 (MQ=25)
aTCCCGAAGGATTTGATCGAATCCGAACTGTTTGGTCACGAGAAAGGCGCATTTACCGGCGCGAATAcc > 1:2896671/1‑69 (MQ=25)
aTCCCGAAGGATTTGATCGAATCCGAACTGTTTGGTCACGAGAAAGGCGCATTTACCGGCGCGAATAcc > 1:2408691/1‑69 (MQ=25)
aTCCCGAAGGATTTGATCGAATCCGAACTGTTTGGTCACGAGAAAGGCGCATTTACCGGCGCGAATAcc > 1:27543/1‑69 (MQ=25)
aTCCCGAAGGATTTGATCGAATCCGAACTGTTTGGTCACGAGAAAGGCGCATTTACCGGCGCGAATAcc > 1:2623740/1‑69 (MQ=25)
aTCCCGAAGGATTTGATCGAATCCGAACTGTTTGGTCACGAGAAAGGCGCATTTACCGGCGCGAATAcc > 1:1031823/1‑69 (MQ=25)
aTCCCGAAGGATTTGATCGAATCCGAACTGTTTGGTCACGAGAAAGGCGCATTTACCGGCGCGAATAcc > 1:2326230/1‑69 (MQ=25)
aTCCCGAAGGATTTGATCGAATCCGAACTGTTTGGTCACGAGAAAGGCGCATTTACCGGCGCGAATAcc > 1:2289714/1‑69 (MQ=25)
aTCCCGAAGGATTTGATCGAATCCGAACTGTTTGGTCACGAGAAAGGCGCATTTACCGGCGCGAATAcc > 1:1957089/1‑69 (MQ=25)
aTCCCGAAGGATTTGATCGAATCCGAACTGTTTGGTCACGAGAAAGGCGCATTTACCGGCGCGAATAcc > 1:1551141/1‑69 (MQ=25)
aTCCCGAAGGATTTGATCGAATCCGAACTGTTTGGTCACGAGAAAGGCGCATTTACCGGCGCGAATAcc > 1:1741576/1‑69 (MQ=25)
aTCCCGAAGGATTTGATCGAATCCGAACTGTTTGGTCACGAGAAAGGCGCATTTACCGGCGCGAATAcc > 1:1827942/1‑69 (MQ=25)
aTCCCGAAGGATTTGATCGAATCCGAACTGTTTGGTCACGAGAAAGGCGCATTTACCGGCGCGAATAcc > 1:1781850/1‑69 (MQ=25)
aTCCCGAAGGATTTGATCGAATCCGAACTGTTTGGTCACGAGAAAGGCGCATTTACCGGCGCGAATAc > 1:2671945/1‑68 (MQ=25)
ccAAAAGATTTGATCGAATCAGAACTGTTTGGCCACGAGAAAGGCGCGTTTACTGGCGCGAATACCAtt > 1:118690/1‑69 (MQ=255)
ccAAAAGATTTGATCGAATCAGAACTGTTTGGCCACGAGAAAGGCGCGTTTACTGGCGCGAATACCAtt > 1:647299/1‑69 (MQ=255)
ccAAAAGATTTGATCGAATCAGAACTGTTTGGCCACGAGAAAGGCGCGTTTACTGGCGCGAATACCAtt > 1:386046/1‑69 (MQ=255)
ccAAAAGATTTGATCGAATCAGAACTGTTTGGCCACGAGAAAGGCGCGTTTACTGGCGCGAATACCAtt > 1:3347594/1‑69 (MQ=255)
ccAAAAGATTTGATCGAATCAGAACTGTTTGGCCACGAGAAAGGCGCGTTTACTGGCGCGAATACCAtt > 1:2963908/1‑69 (MQ=255)
ccAAAAGATTTGATCGAATCAGAACTGTTTGGCCACGAGAAAGGCGCGTTTACTGGCGCGAATACCAtt > 1:2798457/1‑69 (MQ=255)
tttGATCGAATCAGAACTGTTTGGCCACGAGAAAGGCGCGTTTACTGGCGCGAATACCATTCGTCAggg > 1:208336/1‑69 (MQ=255)
tttGATCGAATCAGAACTGTTTGGCCACGAGAAAGGCGCGTTTACTGGCGCGAATACCATTCGTCAggg > 1:955934/1‑69 (MQ=255)
tttGATCGAATCAGAACTGTTTGGCCACGAGAAAGGCGCGTTTACTGGCGCGAATACCATTCGTCAggg > 1:679080/1‑69 (MQ=255)
attGATCGAATCAGAACTGTTTGGCCACGAGAAAGGCGCGTTTACTGGCGCGAATACCATTCGTCAggg > 1:942335/2‑69 (MQ=255)
tcgATCGAATCCGAACTGTTTGGTCACGAGAAAGGCGCATTTACCGGCGCGAATACCAt < 1:1782663/57‑1 (MQ=25)
tGATCGAATCCGAACTGTTTGGTCACGAGAAAGGCGCATTTACCGGCGCGAATACCAt < 1:2146601/58‑1 (MQ=25)
aTCAGAACTGTTTGGCCACGAGAAAGGCGCGTTTACTGGCGCGAATACCATTCGTCAGGGGCGTTTTg < 1:3211704/68‑1 (MQ=255)
aTCAGAACTGTTTGGCCACGAGAAAGGCGCGTTTACTGGCGCGAATACCATTCGTCAGGGGCGTTTTg < 1:1199424/68‑1 (MQ=255)
aTCAGAACTGTTTGGCCACGAGAAAGGCGCGTTTACTGGCGCGAATACCATTCGTCAGGGGCGTTTTg < 1:1940411/68‑1 (MQ=255)
aTCAGAACTGTTTGGCCACGAGAAAGGCGCGTTTACTGGCGCGAATACCATTCGTCAGGGGCGTTTTg < 1:631143/68‑1 (MQ=255)
aTCAGAACTGTTTGGCCACGAGAAAGGCGCGTTTACTGGCGCGAATACCATTCGTCAGGGGCGTTTTg < 1:2214205/68‑1 (MQ=255)
aTCAGAACTGTTTGGCCACGAGAAAGGCGCGTTTACTGGCGCGAATACCATTCGTCAGGGGCGTTTTg < 1:1322134/68‑1 (MQ=255)
aTCAGAACTGTTTGGCCACGAGAAAGGCGCGTTTACTGGCGCGAATACCATTCGTCAGGGGCGTTTTg < 1:1869235/68‑1 (MQ=255)
aTCAGAACTGTTTGGCCACGAGAAAGGCGCGTTTACTGGCGCGAATACCATTCGTCAGGGGCGTTTTg < 1:3314843/68‑1 (MQ=255)
aTCAGAACTGTTTGGCCACGAGAAAGGCGCGTTTACTGGCGCGAATACCATTCGTCAGGGGCGTTTTg < 1:3115739/68‑1 (MQ=255)
aTCAGAACTGTTTGGCCACGAGAAAGGCGCGTTTACTGGCGCGAATACCATTCGTCAGGGGCGTTTTg < 1:1967097/68‑1 (MQ=255)
aTCAGAACTGTTTGGCCACGAGAAAGGCGCGTTTACTGGCGCGAATACCATTCGTCAGGGGCGTTTTg < 1:1843907/68‑1 (MQ=255)
aTCAGAACTGTTTGGCCACGAGAAAGGCGCGTTTACTGGCGCGAATACCATTCGTCAGGGGCGTTTTg < 1:1766870/68‑1 (MQ=255)
aTCAGAACTGTTTGGCCACGAGAAAGGCGCGTTTACTGGCGCGAATACCATTCGTCAGGGGCGTTTTg < 1:1823854/68‑1 (MQ=255)
aTCAGAACTGTATGGCCACGAGAAAGGCGCGTTTACTGGCGCGAATACCATTCGTCAGGGGCGTTTTg < 1:464777/68‑1 (MQ=255)
tCAGAACTGTTTGGCCACGAGAAAGGCGCGTTTACTGGCGCGAATACCATTCGTCAGGGGCGTTTTg < 1:2687079/67‑1 (MQ=255)
cAGAACTGTTTGGCCACGAGAAAGGCGCGTTTACTGGCGCGAATACCATTCGTCAGGGGCGTTTTGAAc > 1:2478355/1‑69 (MQ=255)
aGAACTGTTTGGCCACGAGAAAGGCGCGTTTACTGGCGCGAATACCATTCGTCAGGGGCGTTTTGAACa > 1:1796866/1‑69 (MQ=255)
tcACGAGAAAGGCGCATTTACCGGCGCGAATACCAt < 1:1664700/35‑1 (MQ=37)
gagaAAGGCGCGTTTACTGGCGCGAATACCATTCGTCAGGGGCGTTTTg < 1:2688780/49‑1 (MQ=255)
agaAAGGCGCGTTTACTGGCGCGAATACCATTCGTCAGGGGCGTTTTGAACAGGCCGATGGCGGTACat < 1:186061/69‑1 (MQ=255)
agaAAGGCGCGTTTACTGGCGCGAATACCATTCGTCAGGGGCGTTTTGAACAGGCCGATGGCGGTACat < 1:1709739/69‑1 (MQ=255)
gaAAGGCGCGTTTACTGGCGCGAATACCATTCGTCAGGGGCGTTTTGAACAGGCCGATGGCGGTACat < 1:221346/68‑1 (MQ=255)
|
GCTGAATATGGCAGCTATCCCAAAAGATTTGATCGAATCAGAACTGTTTGGCCACGAGAAAGGCGCGTTTACTGGCGCGAATACCATTCGTCAGGGGCGTTTTGAACAGGCCGATGGCGGTACAT > minE/2343916‑2344040
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
