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 |
|
A6 F21 I0 R1
|
2169 |
63.0 |
3952800 |
76.2% |
3012033 |
62.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
834,449 |
G→C |
12.7% |
V969V (GTG→GTC) |
narG → |
nitrate reductase 1, alpha subunit |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 834,449 | 0 | G | C | 12.7%
| 143.9
/ 11.0
| 55 | V969V (GTG→GTC) | narG | nitrate reductase 1, alpha subunit |
| Reads supporting (aligned to +/- strand): ref base G (12/36); new base C (3/4); total (15/40) |
| Fisher's exact test for biased strand distribution p-value = 3.76e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.53e-01 |
ACACCGCAATTGATGCGGCAGAGATGATCCTGACACTGGCACCGGAAACCAACGGTCAGGTAGCCGTGAAAGCCTGGGCTGCCCTGAGCGAATTTACCGGTCGTGACCATACGCATCTGGCGCTGAATAAAGAAGA > minE/834382‑834517
|
acacCGCAATTGATGCGGCAGAGATGATCCTGACACTGGCACCGGAAACCAACGGTCAGGTAGCCGTGaaa < 1:2051503/71‑1 (MQ=255)
acacCGCAATTGATGCCGCAGAGATGATCCTGACACTGGCACCGGAAACCAACGGTCAGGTAGCCGTGaaa < 1:2554568/71‑1 (MQ=255)
acCGCAATTGATGCGGCAGAGATGATCCTGACACTGGCACCGGAAACCAACGGTCAGGTAGCCGTGAAAGc < 1:2230757/71‑1 (MQ=255)
acCGCAATTGATGCGGCAGAGATGATCCTGACACTGGCACCGGAAACCAACGGTCAGGTAGCCGTGAAAGc < 1:429588/71‑1 (MQ=255)
ccGCCATTGACGCTTCAGAAGTGATTCTGGCACTGGCACCGGAAACCAACGGTCATGTTGCAGTCAAAGcg < 1:3944539/71‑2 (MQ=255)
ccGCCATTGACGCTTCAGAAGTGATTCTGGCACTGGCACCGGAAACCAACGGTCATGTTGCAGTCAAAGcg < 1:2130776/71‑2 (MQ=255)
ccaTTGACGCTTCAGAAGTGATTCTGGCACTGGCACCGGAAACCAACGGTCATGTTGCAGTCAAAGCGTgg > 1:3805666/3‑71 (MQ=255)
aTTGATGCGGCAGAGATGATCCTGACACTGGCACCGGAAACCAACGGTCAGGTAGCCGTGAAAGCCTGGGc > 1:687598/1‑71 (MQ=255)
aTTGACGCTTCAGAAGTGATTCTGGCACTGGCACCGGAAACCAACGGTCATGTTGCAGTCAAAGCGTggc < 1:3499303/70‑2 (MQ=255)
aTGCGGCAGAGATGATCCTGACACTGGCACCGGAAACCAACGGTCAGGTAGCCGTGAAAGCCTGGGCTGcc < 1:3659694/71‑1 (MQ=255)
cGGCAGAGATGATCCTGACACTGGCACCGGAAACCAACGGTCAGGTAGCCGTGAAAGCCTGGGCTGCCCt < 1:3012662/70‑1 (MQ=255)
cGGCAGAGATGATCCTGACACTGGCACCGGAAACCAACGGTCAGGTAGCCGTGAAAGCCTGGGCTGCCCTg < 1:3552959/71‑1 (MQ=255)
ggCAGAGATGATCCTGACACTGGCACCGGAAACCAACGGTCAGGTAGCCGTGAAAGCCTGGGCTGCCCt > 1:1773243/1‑69 (MQ=255)
ggCAGAGATGATCCTGACACTGGCACCGGAAACCAACGGTCAGGTAGCCGTGAAAGCCTGGGCTGCCCTGa < 1:1390835/71‑1 (MQ=255)
ggCAGAGATGATCCTGACACTGGCACCGGAAACCAACGGTCAGGTAGCCGTGAAAGCCTGGGCTGCCCTGa < 1:810064/71‑1 (MQ=255)
agagATGATCCTGACACTGGCACCGGAAACCAACGGTCAGGTAGCCGTGAAAGCCTGGGCTGCCCTGAGCg < 1:96780/71‑1 (MQ=255)
agagATCATCCTGACACTGGCACCGGAAACCAACGGTCAGGTAGCCGTGAAAGCCTGGGCTGCCCTGAGCg < 1:101367/71‑1 (MQ=255)
agaTGATCCTGACACTGGCACCGGAAACCAACGGTCAGGTAGCCGTGAAAGCCTGGGCTGCCCTGAGCGaa < 1:73807/71‑1 (MQ=255)
atgatCCTGACACTGGCACCGGAAACCAACGGTCAGGTAGCCGTGAAAGc < 1:3776411/50‑1 (MQ=255)
atgatCCTGACACTGGCACCGGAAACCAACGGTCAGGTAGCCGTGAAAGCCTGGGCt < 1:920004/57‑1 (MQ=255)
atgatCCTGACACTGGCACCGGAAACCAACGGTCAGGTAGCCGTGAAAGCCTGGGCTGCCCTGAGCGAAtt > 1:927810/1‑71 (MQ=255)
tgatTCTGGCACTGGCACCGGAAACCAACGGTCATGTTGCAGTCAAAg < 1:1362179/48‑1 (MQ=255)
tgatCCTGACACTGGCACCGGAAACCAACGGTCAGGTAGCCGTGAAAGCCTGGGCTGCCCTGAGCGAAttt < 1:3740928/71‑1 (MQ=255)
tgatCCTGACACTGGCACCGGAAACCAACGGTCAGGTAGCCGTGAAAGCCTGGGCTGCCCTGAGCGAAttt < 1:3262197/71‑1 (MQ=255)
gatCCTGACACTGGCACCGGAAACCAACGGTCAGGTAGCCGTGAAAGCCTGGGCTGCCCTGAGCGAAttt < 1:2664816/70‑1 (MQ=255)
tCCTGACACTGGCACCGGAAACCAACGGTCAGGTAGCCGTGAAAGCCTGGGCTGCCCTGAGCGaa > 1:3335422/1‑65 (MQ=255)
tCCTGACACTGGCACCGGAAACCAACGGTCAGGTAGCCGTGAAAGCCTGGGCTGCCCTGAGCGAAt > 1:1154044/1‑66 (MQ=255)
cTGACACTGGCACCGGAAACCAACGGTCAGGTAGCCGTGAAAGCCTGGGCTGCCCTGAGCGAATTTACCgg > 1:3104904/1‑71 (MQ=255)
gACACTGGCACCGGAAACCAACGGTCAGGTAGCCGTGAAAGCCTGGGCTGCCCTGAGCGAAtt < 1:1590634/63‑1 (MQ=255)
cacTGGCACCGGAAACCAACGGTCAGGTAGCCGTGAAAGCCTGGGCTGCCCTGAGCGa < 1:2247197/58‑1 (MQ=255)
cTGGCACCGGAAACCAACGGTCAGGTAGCCGTGAAAGCCTGGGCTGCCCTGAGCGAATTTACCGGTCGt < 1:2422971/69‑1 (MQ=255)
aCCGGAAACCAACGGTCAGGTAGCCGTGAAAGCCTGGGCTGCCCTGAGCGAATTTACCGGTCGTGACCATa > 1:779164/1‑71 (MQ=255)
cGGAAACCAACGGTCAGGTAGCCGTGAAAGCCTGGGCTGCCCTGAGCGAATTTACCGGTCGTGACCATAc < 1:3126901/70‑1 (MQ=255)
ggAAACCAACGGTCAGGTAGCCGTGAAAGCCTGGGCTGCCCTGAGCGAATTTACCGGt < 1:493808/58‑1 (MQ=255)
ggAAACCAACGGTCAGGTAGCCGTGAAAGCCTGGGCTGCCCTGAGCGAATTTACCGGTCGTGACCATACGc < 1:2134806/71‑1 (MQ=255)
ggAAACCAACGGTCAGGTAGCCGTGAAAGCCTGGGCTGCCCTGAGCGAATTTACCGGTCGTGACCATACGc < 1:2654637/71‑1 (MQ=255)
gAAACCAACGGTCATGTTGCAGTCAAAGCGTGGCAGGCGCTGGGCGAGATCACCGGGCGCGAACATACCCa > 1:1739912/1‑71 (MQ=255)
aaaCCAACGGTCAGGTAGCCGTGAAAGCCTGGGCTGCCCTGAGCGAAttt > 1:2353246/1‑50 (MQ=255)
aaaCCAACGGTCAGGTAGCCGTGAAAGCCTGGGCTGACCTGAGCGAATTTAc < 1:3307540/52‑1 (MQ=255)
aaCCAACGGTCATGTTGCAGTCAAAGCGTGGCAGGCGCTGGGCGAGATCACCGGGCGCGAACATACCCATc > 1:2476558/1‑71 (MQ=255)
cAACGGTCAGGTAGCCGTGAAAGCCTGGGCTGCCCTGAGCGAATTTACCGGTCGTg < 1:1609248/56‑1 (MQ=255)
cAACGGTCAGGTAGCCGTGAAAGCCTGGGCTGCCCTGAGCGAATTTACCGGTCGTGACCATa > 1:1111526/1‑62 (MQ=255)
cAACGGTCAGGAAGCCGTGAAAGCCTGGGCTGCCCTGAGCGAATTTAc < 1:1499716/48‑1 (MQ=255)
aCGGTCAGGTAGCCGTGAAAGCCTGGGCTGCCCTGAGCGAATTTACCGGTCGTGACCATACGCATCTGgcg < 1:98880/71‑1 (MQ=255)
cGGTCAGGTAGCCGTGAAAGCCTGGGCTGCCCTGAGCGAATTTACCGGTCGt < 1:1740392/52‑1 (MQ=255)
tCAGGTAGCCGTGAAAGCCTGGGCTGCCCTGAGCGAATTTACCGGTCGTGACCATACGCATCTGGCGCt < 1:1918581/69‑1 (MQ=255)
ggTAGCCGTGAAAGCCTGGGCTGCCCTGAGCGAATTTACCGGTCGTGACCATACGCATCTGGCGCTGAATa < 1:3896094/71‑1 (MQ=255)
gTAGCCGTGAAAGCCTGGGCTGCCCTGAGCGAATTTACCGGTCGTGACCATACGCATCTGGCGCTGAATa > 1:1021293/1‑70 (MQ=255)
aGCCGTGAAAGCCTGGGCTGCCCTGAGCGAATTTACCGGTCGTGACCATACGCATCTGGCGCTGAATa > 1:2346364/1‑68 (MQ=255)
gCCGTGAAAGCCTGGGCTGCCCTGAGCGAATTTACCGGTCGTGACCATACGCATCTGGCGCTGAATAaag < 1:2065168/70‑1 (MQ=255)
ccGTGAAAGCCTGGGCTGCCCTGAGCGAATTTACCGGTCGTGACCa < 1:2867127/46‑1 (MQ=255)
gTGAAAGCCTGGGCTGCCCTGAGCGAATTTACCGGTCGTGACCATACGCATCTGGCGCTGAATaa > 1:2907642/1‑65 (MQ=255)
gTGAAAGCCTGGGCTGCCCTGAGCGAATTTACCGGTCGTGACCATACGCATCTGGCGCTGAATAAagaaga < 1:2445255/71‑1 (MQ=255)
tGAAAGCCTGGGCTGCCCTGAGCGAATTTACCGGTCGTGACCATACGCATCTgg < 1:2459053/54‑1 (MQ=255)
tGAAAGCCTGGGCTGCCCTGAGCGAATTTACCGGTCGTGACCATACGCATCTGGCGCTGAAt < 1:3687186/62‑1 (MQ=255)
|
ACACCGCAATTGATGCGGCAGAGATGATCCTGACACTGGCACCGGAAACCAACGGTCAGGTAGCCGTGAAAGCCTGGGCTGCCCTGAGCGAATTTACCGGTCGTGACCATACGCATCTGGCGCTGAATAAAGAAGA > minE/834382‑834517
|
| 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
