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 |
1,125,092 |
G→A |
35.5% |
L182L (CTG→TTG) |
pheT ← |
phenylalanine tRNA synthetase, beta subunit |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,125,092 | 0 | G | A | 35.5%
| 49.8
/ 41.0
| 73 | L182L (CTG→TTG) | pheT | phenylalanine tRNA synthetase, beta subunit |
| Reads supporting (aligned to +/- strand): ref base G (27/20); new base A (15/11); total (42/31) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
GTCGTCGATGGTCGCACCAACCGGAACGATTTCCGGTTGAACCAGCGGCAGCTGGTTCAGCACGGCAACGTCACGCGCAACACCAATGATGCCTAAGCAGTCGGCACGGTTTGGCGTCACGCTGAT > minE/1125033‑1125158
|
gtcgtcGATGGTCGCACCAACCGGAACGATTTCCGGTTGAACCAGCGGCAGCTGGTTCAGCACGGCAAc < 1:3246033/69‑1 (MQ=255)
gtcgtcGATGGTCGCACCAACCGGAACGATTTCCGGTTGAACCAGCGGCAGCTGGTTCAGCACGGCAAc < 1:2720542/69‑1 (MQ=255)
tcgtcgATGGTCGCACCAACCGGAACGATTTCCGGTTGAACCAGCGGCAGCTGGTTCAGCACGGCAAc < 1:1264605/68‑1 (MQ=255)
tcgtcgATGGTCGCACCAACCGGAACGATTTCCGGTTGAACCAGCGGCAGCTGGTTCAGCACGGCAAc > 1:1977787/1‑68 (MQ=255)
tcgtcgATGGTCGCACCAACCGGAACGATTTCCGGTTGAACCAGCGGCAGCTGGTTCAGCACGGCAAc > 1:1332469/1‑68 (MQ=255)
tcgtcgATGGTCGCACCAACCGGAACGATTTCCGGTTGAACCAGCGGCAGCTGGTTCAGCACGGCAAc > 1:2433135/1‑68 (MQ=255)
tcgtcgATGGTCGCACCAACCGGAACGATTTCCGGTTGAACCAGCGGCAGCTGGTTCAGCACGGCAAc > 1:305899/1‑68 (MQ=255)
gtcgATGGTCGCACCAACCGGAACGATTTCCGGTTGAACCAGCGGCAGCTGGTTCAGCACGGCAACGTc > 1:2117906/1‑69 (MQ=255)
gtcgATGGTCGCACCAACCGGAACGATTTCCGGTTGAACCAGCGGCAGCTGGTTCAGCACGGCAACGTc > 1:3372192/1‑69 (MQ=255)
gtcgATGGTCGCACCAACCGGAACGATTTCCGGTTGAACCAGCGGCAGCTGGTTCAGCACGGCAACGTc > 1:3024084/1‑69 (MQ=255)
ggTCGCACCAACCGGAACGATTTCCGGTTGAACCAGCGGCAGCTGGTTCAGCACGGCAACGTCACgcgc > 1:2172309/1‑69 (MQ=255)
ggTCGCACCAACCGGAACGATTTCCGGTTGAACCAGCGGCAGCTGGTTCAGCACGGCAACGTCACgcgc > 1:2180302/1‑69 (MQ=255)
ggTCGCACCAACCGGAACGATTTCCGGTTGAACCAGCGGCAGCTGGTTCAGCACGGCAACGTCACgcgc > 1:2210105/1‑69 (MQ=255)
ggTCGCACCAACCGGAACGATTTCCGGTTGAACCAGCGGCAGCTGGTTCAGCACGGCAACGTCACgcgc > 1:2798365/1‑69 (MQ=255)
ggTCGCACCAACCGGAACGATTTCCGGTTGAACCAGCGGCAGCTGGTTCAGCACGGCAACGTCACgcgc > 1:2807485/1‑69 (MQ=255)
ggTCGCACCAACCGGAACGATTTCCGGTTGAACCAGCGGCAGCTGGTTCAGCACGGCAACGTCACgcgc > 1:3286779/1‑69 (MQ=255)
ggTCGCACCAACCGGAACGATTTCCGGTTGAACCAGCGGCAGCTGGTTCAGCACGGCAACGTCACgcgc > 1:723087/1‑69 (MQ=255)
ggTCGCACCAACCGGAACGATTTCCGGTTGAACCAGCGGCAGCTGGTTCAGCACGGCAACGTCACgcgc > 1:799620/1‑69 (MQ=255)
tCGCACCAACCGGAACGATTTCCGGTTGAACCAGCGGCAGCTGGTTCAGCACGGCAACGTCACGCGCaa > 1:2253249/1‑69 (MQ=255)
aCCAACCGGAACGATTTCCGGTTCAACCAGCGGCAGCTGGTTGAACACGGCAACGTCGCGCGCAACAcc > 1:3241539/1‑69 (MQ=255)
aCCAACCGGAACGATTTCCGGTTCAACCAGCGGCAGCTGGTTCAACa > 1:650535/1‑47 (MQ=38)
aCCAACCGGAACGATTTCCGGTTCAACCAGCGGCAGCTGGTTCAACACGGCAACGTcgc > 1:1119682/1‑57 (MQ=255)
aCCAACCGGAACGATTTCCGGTTCAACCAGCGGCAGCTGGTTCAACACGGCAACGTCGCGCGCAacac > 1:2187984/1‑68 (MQ=255)
aCCAACCGGAACGATTTCCGGTTCAACCAGCGGCAGCTGGTTCAACACGGCAACGTCGCGCGCAACAcc > 1:1659409/1‑69 (MQ=255)
aCCAACCGGAACGATTTCCGGTTCAACCAGCGGCAGCTGGTTCAACACGGCAACGTCGCGCGCAACAcc > 1:88472/1‑69 (MQ=255)
aCCAACCGGAACGATTTCCGGTTCAACCAGCGGCAGCTGGTTCAACACGGCAACGTCGCGCGCAACAcc > 1:616876/1‑69 (MQ=255)
aCCAACCGGAACGATTTCCGGTTCAACCAGCGGCAGCTGGTTCAACACGGCAACGTCGCGCGCAACAcc > 1:1197273/1‑69 (MQ=255)
aCCAACCGGAACGATTTCCGGTTCAACCAGCGGCAGCTGGTTCAACACGGCAACGTCGCGCGCAACAcc > 1:3357169/1‑69 (MQ=255)
aCCAACCGGAACGATTTCCGGTTCAACCAGCGGCAGCTGGTTCAACACGGCAACGTCGCGCGCAACAcc > 1:1404104/1‑69 (MQ=255)
aCCAACCGGAACGATTTCCGGTTCAACCAGCGGCAGCTGGTTCAACACGGCAACGTCGCGCGCAACAcc > 1:2167796/1‑69 (MQ=255)
aCCAACCGGAACGATTTCCGGTTCAACCAGCGGCAGCTGGTTCAACACGGCAACGTCGCGCGCAACAcc > 1:2934512/1‑69 (MQ=255)
aCCAACCGGAACGATTTCCGGTTCAACCAGCGGCAGCTGGTTCAACACGGCAACGTCGCGCGCAACAcc > 1:2798925/1‑69 (MQ=255)
aCCAACCGGAACGATTTCCGGTTCAACCAGCGGCAGCTGGTTCAACACGGCAACGTCGCGCGCAACAcc > 1:1812798/1‑69 (MQ=255)
aCCAACCGGAACGATTTCCGGTTCAACCAGCGGCAGCTGGTTCAACACGGCAACGTCGCGCGCAACAcc > 1:2327500/1‑69 (MQ=255)
agccGGAACGATTTCCGGTTGAACCAGCGGCAGCTGGTTCAGCACGGCAACGTCACGCGCAACACCAat < 1:1884758/67‑1 (MQ=255)
aaCCGGAACGATTTCCTGTTGAACCAGCGGCAGCTGGTTCAGCACGGCAACGTCACGCGCAACACCAat < 1:2819441/69‑1 (MQ=255)
aaCCGGAACGATTTCCGGTTTAACCAGCGGCAGCTGGTTCAGCACGGCAACGTCACGCGCAACACCAat < 1:2180433/69‑1 (MQ=255)
aaCCGGAACGATTTCCGGTTGAACCAGCGGCAGCTGGTTCAGCACGGCAACGTCACGCGCAACACCAat < 1:3016695/69‑1 (MQ=255)
aaCCGGAACGATTTCCGGTTGAACCAGCGGCAGCTGGTTCAGCACGGCAACGTCACGCGCAACACCAat < 1:3298333/69‑1 (MQ=255)
aaCCGGAACGATTTCCGGTTGAACCAGCGGCAGCTGGTTCAGCACGGCAACGTCACGCGCAACACCAat < 1:337432/69‑1 (MQ=255)
aaCCGGAACGATTTCCGGTTGAACCAGCGGCAGCTGGTTCAGCACGGCAACGTCACGCGCAACACCAat < 1:393408/69‑1 (MQ=255)
aaCCGGAACGATTTCCGGTTGAACCAGCGGCAGCTGGTTCAGCACGGCAACGTCACGCGCAACACCAat < 1:196456/69‑1 (MQ=255)
aaCCGGAACGATTTCCGGTTGAACCAGCGGCAGCTGGTTCAGCACGGCAACGTCACGCGCAACACCAat < 1:1156618/69‑1 (MQ=255)
aaCCGGAACGATTTCCGGTTGAACCAGCGGCAGCTGGTTCAGCACGGCAACGTCACGCGCAACACCAat < 1:1483432/69‑1 (MQ=255)
aaCCGGAACGATTTCCGGTTGAACCAGCGGCAGCTGGTTCAGCACGGCAACGTCACGCGCAACACCAat < 1:305769/69‑1 (MQ=255)
aaCCGGAACGATTTCCGGTTGAACCAGCGGCAGCTGGTTCAGCACGGCAACGTCACGCGCAACACCAat < 1:300631/69‑1 (MQ=255)
aaCCGGAACGATTTCCGGTTGAACCAGCGGCAGCTGGTTCAGCACGGCAACGTCACGCGCAACACCAat < 1:2817411/69‑1 (MQ=255)
aaCCGGAACGATTTCCGGTTGAACCAGCGGCAGCTGGTTCAGCACGGCAACGTCACGCGCAACACCAat < 1:2730926/69‑1 (MQ=255)
aaCCGGAACGATTTCCGGTTGAACCAGCGGCAGCTGGTTCAGCACGGCAACGTCACGCGCAACACCAat < 1:2331151/69‑1 (MQ=255)
aaCCGGAACGATTTCCGGTTGAACCAGCGGCAGCTGGTTCAGCACGGCAACGGCACGCGCAACACCAat < 1:1127110/69‑1 (MQ=255)
tGAACCAGCGGCAGCTGGTTCAGCACGGCAACGTCACGCGCAACACCAat < 1:1764894/50‑1 (MQ=255)
tGAACCAGCGGCAGCTGGTTCAGCACGGCAACGTCACGCGCAACACCAATGATGCCTAAGCAGTCGGCa > 1:22615/1‑69 (MQ=255)
tGAACCAGCGGCAGCTGGTTCAGCACGGCAACGTCACGCGCAACACCAATGATGCCTAAGCAGTCGGCa > 1:2019938/1‑69 (MQ=255)
ggCAGCTGGTTCAACACGGCAACGTCGCGCGCAACACCAATGATACCTAAGCAGTCGGCACGGTTTGGc < 1:2530924/69‑1 (MQ=255)
ggCAGCTGGTTCAACACGGCAACGTCGCGCGCAACACCAATGATACCTAAGCAGTCGGCACGGTTTGGc < 1:728402/69‑1 (MQ=255)
ggCAGCTGGTTCAACACGGCAACGTCGCGCGCAACACCAATGATACCTAAGCAGTCGGCACGGTTTGGc < 1:2115104/69‑1 (MQ=255)
ggCAGCTGGTTCAACACGGCAACGTCGCGCGCAACACCAATGATACCTAAGCAGTCGGCACGGTTTGGc < 1:1110785/69‑1 (MQ=255)
ggCAGCTGGTTCAACACGGCAACGTCGCGCGCAACACCAATGATACCTAAGCAGTCGGCACGGTTTGGc < 1:3380884/69‑1 (MQ=255)
ggCAGCTGGTTCAACACGGCAACGTCGCGCGCAACACCAATGATACCTAAGCAGTCGGCACGGTTTGGc < 1:2133777/69‑1 (MQ=255)
ggCAGCTGGTTCAACACGGCAACGTCGCGCGCAACACCAATGATACCTAAGCAGTCGGCACGGTTTGGc < 1:1293628/69‑1 (MQ=255)
ggCAGCTGGTTCAACACGGCAACGTCGCGCGCAACACCAATGATACCTAAGCAGTCGGCACGGTTTGGc < 1:3262722/69‑1 (MQ=255)
ggCAGCTGGTTCAACACGGCAACGTCGCGCGCAACACCAATGATACCTAAGCAGTCGGCACGGTTTGGc < 1:3137979/69‑1 (MQ=255)
ggCAGCTGGTTCAACACGGCAACGTCGCGCGCAACACCAATGATACCTAAGCAGTCGGCACGGTTTGGc < 1:3103916/69‑1 (MQ=255)
gCAGCTGGTTCAACACGGCAACGTCGCGCGCAACACCAATGATACCTAAGCAGTCGGCACGGTTTGGc < 1:2575739/68‑1 (MQ=255)
cAGCACGGCAACGTCACGCGCAACACCAATGATGCCTAAGCAGTCGGCACGGTTTGGCGTCACGCTGa > 1:509062/1‑68 (MQ=255)
cAGCACGGCAACGTCACGCGCAACACCAATGATGCCTAAGCAGTCGGCACGGTTTGGCGTCACGCTGAt > 1:3354816/1‑69 (MQ=255)
cAGCACGGCAACGTCACGCGCAACACCAATGATGCCTAAGCAGTCGGCACGGTTTGGCGTCACGCTGAt > 1:1347890/1‑69 (MQ=255)
cAGCACGGCAACGTCACGCGCAACACCAATGATGCCTAAGCAGTCGGCACGGTTTGGCGTCACGCTGAt > 1:475504/1‑69 (MQ=255)
cAGCACGGCAACGTCACGCGCAACACCAATGATGCCTAAGCAGTCGGCACGGTTTGGCGTCACGCTGAt > 1:605953/1‑69 (MQ=255)
cAGCACGGCAACGTCACGCGCAACACCAATGATGCCTAAGCAGTCGGCACGGTTTGGCGTCACGCTGAt > 1:2302479/1‑69 (MQ=255)
cAGCACGGCAACGTCACGCGCAACACCAATGATGCCTAAGCAGTCGGCACGGTTTGGCGTCACGCTGAt > 1:2827767/1‑69 (MQ=255)
cAGCACGGCAACGTCACGCGCAACACCAATGATGCCTAAGCAGTCGGCACGGTTTGGCGTCACGCTGAt > 1:1758570/1‑69 (MQ=255)
cAGCACGGCAACGTCACGCGCAACACCAATGATGCCTAAGCAGTCGGCACGGTTTGGCGTCACGCTGAt > 1:801611/1‑69 (MQ=255)
|
GTCGTCGATGGTCGCACCAACCGGAACGATTTCCGGTTGAACCAGCGGCAGCTGGTTCAGCACGGCAACGTCACGCGCAACACCAATGATGCCTAAGCAGTCGGCACGGTTTGGCGTCACGCTGAT > minE/1125033‑1125158
|
| 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
