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 |
1,404,287 |
A→G |
37.2% |
A164A (GCA→GCG) |
yejA → |
predicted oligopeptide transporter subunit |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,404,287 | 0 | A | G | 37.2%
| 52.6
/ 59.7
| 94 | A164A (GCA→GCG) | yejA | predicted oligopeptide transporter subunit |
| Reads supporting (aligned to +/- strand): ref base A (22/37); new base G (22/13); total (44/50) |
| Fisher's exact test for biased strand distribution p-value = 1.97e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.80e-01 |
TTTATGACCGAAGGCGTGCCGCAATTTCGTCTGGTCTACAAAGGCACCACCGTCAAAGCCATTGCACCGTTAACCGTGCGCATTGAGTTAGCTAAACCCGGCAAAGAAGATATGCTGAGTCTGTTTT > minE/1404222‑1404348
|
tttATGACCGAAGGCGTGCCGCAATTTCGTCTGGTCTACAAAGGCACCACCGTCAAAGCCATTGCAcc > 1:3078492/1‑68 (MQ=255)
tttATGACCGAAGGCGTGCCGCAATTTCGTCTGGTCTACAAAGGCACCACCGTCAAAGCCATTGCAcc > 1:173250/1‑68 (MQ=255)
tttATGACCGAAGGCGTGCCGCAATTTCGTCTGGTCTACAAAGGCACCACCGTCAAAGCCATTGCAcc > 1:3294941/1‑68 (MQ=255)
tttATGACCGAAGGCGTGCCGCAATTTCGTCTGGTCTACAAAGGCACCACCGTCAAAGCCATTGCAcc > 1:2456577/1‑68 (MQ=255)
tttATGACCGAAGGCGTGCCGCAATTTCGTCTGGTCTACAAAGGCACCACCGTCAAAGCCATTGCAcc > 1:1427737/1‑68 (MQ=255)
gTGCCGCAATTTCGTCTGGTCTACAAAGGCACCACCGTCAAAGCCATTGCGCCGTTAACCGTGCGCAtt < 1:100402/69‑1 (MQ=255)
gTGCCGCAATTTCGTCTGGTCTACAAAGGCACCACCGTCAAAGCCATTGCGCCGTTAACCGTGCGCAtt < 1:1960502/69‑1 (MQ=255)
gTGCCGCAATTTCGTCTGGTCTACAAAGGCACCACCGTCAAAGCCATTGCGCCGTTAACCGTGCGCAtt < 1:607313/69‑1 (MQ=255)
gTGCCGCAATTTCGTCTGGTCTACAAAGGCACCACCGTCAAAGCCATTGCGCCGTTAACCGTGCGCAtt < 1:2306747/69‑1 (MQ=255)
gTGCCGCAATTTCGTCTGGTCTACAAAGGCACCACCGTCAAAGCCATTGCGCCGTTAACCGTGCGCAtt < 1:2515820/69‑1 (MQ=255)
gTGCCGCAATTTCGTCTGGTCTACAAAGGCACCACCGTCAAAGCCATTGCGCCGTTAACCGTGCGCAtt < 1:1095427/69‑1 (MQ=255)
gTGCCGCAATTTCGTCTGGTCTACAAAGGCACCACCGTCAAAGCCATTGCGCCGTTAACCGTGCGCAtt < 1:903059/69‑1 (MQ=255)
gTGCCGCAATTTCGTCTGGTCTACAAAGGCACCACCGTCAAAGCCATTGCGCCGTTAACCGTGCGCAtt < 1:2628724/69‑1 (MQ=255)
gTGCCGCAATTTCGTCTGGTCTACAAAGGCACCACCGTCAAAGCCATTGCGCCGTTAACCGTGCCCAtt < 1:1114713/69‑1 (MQ=255)
gTGCCACAATTTCGTCTGGTCTACAAAGGCACCACCGTCAAAGCCATTGCGCCGTTAACCGTGCGCAtt < 1:1944167/69‑1 (MQ=255)
tGCCGCAATTTCGTCTGGTCTACAAAGGCACCACCGTCAAAGCCATTGCGCCGTTAACCGTGCGCAtt < 1:2646627/68‑1 (MQ=255)
tGCCGCAATTTCGTCTGGTCTACAAAGGCACCACCGTCAAAGCCATTGCGCCGTTAACCGTGCGCAtt < 1:1374733/68‑1 (MQ=255)
tGCCGCAATTTCGTCTGGTCTACAAAGGCACCACCGTCAAAGCCATTGCGCCGTTAACCGTGCGCAtt < 1:1481108/68‑1 (MQ=255)
gCAATTTCGTCTGGTCTACAAAGGCACCACCGTCAAAGCCATTGCACCGTTAACCGTGCGCATTGAGtt < 1:287036/69‑1 (MQ=255)
gCAATTTCGTCTGGTCTACAAAGGCACCACCGTCAAAGCCATTGCACCGTTAACCGTGCGCATTGAGtt < 1:3061027/69‑1 (MQ=255)
gCAATTTCGTCTGGTCTACAAAGGCACCACCGTCAAAGCCATTGCACCGTTAACCGTGCGCATTGAGtt < 1:1803581/69‑1 (MQ=255)
gCAATTTCGTCTGGTCTACAAAGGCACCACCGTCAAAGCCATTGCACCGTTAACCGTGCGCATTGAGtt < 1:3009974/69‑1 (MQ=255)
cTACAAAGGCACCACCGTCAAAGCCATTGCGCCGTTAACCGTGGGCATTGAGTTAGCTAAACCCgg > 1:2744508/1‑66 (MQ=255)
cTACAAAGGCACCACCGTCAAAGCCATTGCGCCGTTAACCGTGCGCATTGAGTTAGCTAAACCCgg > 1:1994687/1‑66 (MQ=255)
cTACAAAGGCACCACCGTCAAAGCCATTGCGCCGTTAACCGTGCGCATTGAGTTAGCTAAACCCgg > 1:19810/1‑66 (MQ=255)
cTACAAAGGCACCACCGTCAAAGCCATTGCGCCGTTAACCGTGCGCATTGAGTTAGCTAAACCCgg > 1:2381864/1‑66 (MQ=255)
cTACAAAGGCACCACCGTCAAAGCCATTGCGCCGTTAACCGTGCGCATTGAGTTAGCTAAACCCgg > 1:2228176/1‑66 (MQ=255)
cTACAAAGGCACCACCGTCAAAGCCATTGCGCCGTTAACCGTGCGCATTGAGTTAGCTAAACCCgg > 1:2292597/1‑66 (MQ=255)
cTACAAAGGCACCACCGTCAAAGCCATTGCGCCGTTAACCGTGCGCATTGAGTTAGCTAAACCCgg > 1:2623311/1‑66 (MQ=255)
cTACAAAGGCACCACCGTCAAAGCCATTGCGCCGTTAACCGTGCGCATTGAGTTAGCTAAACCCgg > 1:2339912/1‑66 (MQ=255)
cTACAAAGGCACCACCGTCAAAGCCATTGCGCCGTTAACCGTGCGCATTGAGTTAGCTAAACCCgg > 1:983280/1‑66 (MQ=255)
cTACAAAGGCACCACCGTCAAAGCCATTGCGCCGTTAACCGTGCGCATTGAGTTAGCTAAACCCgg > 1:1190895/1‑66 (MQ=255)
cTACAAAGGCACCACCGTCAAAGCCATTGCGCCGTTAACCGTGCGCATTGAGTTAGCTAAACCCgg > 1:874117/1‑66 (MQ=255)
cTACAAAGGCACCACCGTCAAAGCCATTGCGCCGTTAACCGTGCGCATTGAGTTAGCTAAACCCgg > 1:674937/1‑66 (MQ=255)
cTACAAAGGCACCACCGTCAAAGCCATTGCGCCGTTAACCGTGCGCATTGAGTTAGCTAAACCCgg > 1:1147138/1‑66 (MQ=255)
cTACAAAGGCACCACCGTCAAAGCCATTGCGCCGTTAACCGTGCGCATTGAGTTAGCTAAACCCgg > 1:66074/1‑66 (MQ=255)
cTACAAAGGCACCACCGTCAAAGCCATTGCGCCGTTAACCGTGCGCATTGAGTTAGCTAAACCCgg > 1:149984/1‑66 (MQ=255)
cTACAAAGGCACCACCGTCAAAGCCATTGCGCCGTTAACCGTGCGCATTGAGTTAGCTAAACCCgg > 1:967859/1‑66 (MQ=255)
cTACAAAGGCACCACCGTCAAAGCCATTGCGCCGTTAACCGTGCGCATTGAGTTAGCTAAACCCgg > 1:490442/1‑66 (MQ=255)
cTACAAAGGCACCACCGTCAAAGCCATTGCGCCGTTAACCGTGCGCATTGAGTTAGCTAAACCCgg > 1:1093892/1‑66 (MQ=255)
cTACAAAGGCACCACCGTCAAAGCCATTGCGCCGTTAACCGTGCGCATTGAGTTAGCTAAACCCgg > 1:488640/1‑66 (MQ=255)
cTACAAAGGCACCACCGTCAAAGCCATTGCGCCGTTAACCGTGCGCATTGAGTTAGCTAAACCCgg > 1:469759/1‑66 (MQ=255)
cTACAAAGGCACCACCGTCAAAGCCATTGCGCCGTTAACCGTGCGCATTGAGTTAGCTAAACCCgg > 1:422299/1‑66 (MQ=255)
cTACAAAGGCACCACCGTCAAAGCCATTGCGCCGTTAACCGTGCGCATTGAGTTAGCTAAACCCg > 1:2052065/1‑65 (MQ=255)
aaGGCACCACCGTCAAAGCCATTGCACCGTTAACCGTGCGCATTGAg > 1:1774675/1‑47 (MQ=255)
aaGGCACCACCGTCAAAGCCATTGCACCGTTAACCGTGCGCATTGAGt > 1:1034710/1‑48 (MQ=255)
aaGGCACCACCGTCAAAGCCATTGCACCGTTAACCGTGCGCATTGAGt > 1:2635993/1‑48 (MQ=255)
aaGGCACCACCGTCAAAGCCATTGCACCGTTAACCGTGCGCATTGAGt > 1:872537/1‑48 (MQ=255)
aaGGCACCACCGTCAAAGCCATTGCACCGTTAACCGTGCGCATTGAGt > 1:2732593/1‑48 (MQ=255)
aaGGCACCACCGTCAAAGCCATTGCACCGTTAACCGTGCGCATTGAGt > 1:2813611/1‑48 (MQ=255)
aaGGCACCACCGTCAAAGCCATTGCACCGTTAACCGTGCGCATTGAGt > 1:2866199/1‑48 (MQ=255)
aaGGCACCACCGTCAAAGCCATTGCACCGTTAACCGTGCGCATTGAGt > 1:2953167/1‑48 (MQ=255)
aaGGCACCACCGTCAAAGCCATTGCACCGTTAACCGTGCGCATTGAGt > 1:318385/1‑48 (MQ=255)
aaGGCACCACCGTCAAAGCCATTGCACCGTTAACCGTGCGCATTGAGt > 1:2512710/1‑48 (MQ=255)
aaGGCACCACCGTCAAAGCCATTGCACCGTTAACCGTGCGCATTGAGt > 1:1606853/1‑48 (MQ=255)
aaGGCACCACCGTCAAAGCCATTGCACCGTTAACCGTGCGCATTGAGt > 1:2249688/1‑48 (MQ=255)
aaGGCACCACCGTCAAAGCCATTGCACCGTTAACCGTGCGCATTGAGt > 1:1256978/1‑48 (MQ=255)
aaGGCACCACCGTCAAAGCCATTGCACCGTTAACCGTGCGCATTGAGt > 1:2109074/1‑48 (MQ=255)
aaGGCACCACCGTCAAAGCCATTGCACCGTTAACCGTGCGCATTGAGt > 1:2108175/1‑48 (MQ=255)
aaGGCACCACCGTCAAAGCCATTGCACCGTTAACCGTGCGCATTGAGt > 1:1496386/1‑48 (MQ=255)
aaGGCACCACCGTCAAAGCCATTGCACCGTTAACCGTGCGCATTGAGTTAGCTAAACCCGGCAaagaa < 1:139385/68‑1 (MQ=255)
aaGGCACCACCGTCAAAGCCATTGCACCGTTAACCGTGCGCATTGAGTTAGCTAAACCCGGCAaagaa < 1:445866/68‑1 (MQ=255)
aaGGCACCACCGTCAAAGCCATTGCACCGTTAACCGTGCGCATTGAGTTAGCTAAACCCGGCAaagaa < 1:3229361/68‑1 (MQ=255)
aaGGCACCACCGTCAAAGCCATTGCACCGTTAACCGTGCGCATTGAGTTAGCTAAACCCGGCAaagaa < 1:1659032/68‑1 (MQ=255)
aaGGCACCACCGTCAAAGCCATTGCACCGTTAACCGTGCGCATTGAGTTAGCTAAACCCGGCAaagaa < 1:3100404/68‑1 (MQ=255)
aaGGCACCACCGTCAAAGCCATTGCACCGTTAACCGTGCGCATTGAGTTAGCTAAACCCGGCAaagaa < 1:1883354/68‑1 (MQ=255)
aaGGCACCACCGTCAAAGCCATTGCACCGTTAACCGTGCGCATTGAGTTAGCTAAACCCGGCAaagaa < 1:3073072/68‑1 (MQ=255)
aaGGCACCACCGTCAAAGCCATTGCACCGTTAACCGTGCGCATTGAGTTAGCTAAACCCGGCAaagaa < 1:1887244/68‑1 (MQ=255)
aaGGCACCACCGTCAAAGCCATTGCACCGTTAACCGTGCGCATTGAGTTAGCTAAACCCGGCAaagaa < 1:3025625/68‑1 (MQ=255)
aaGGCACCACCGTCAAAGCCATTGCACCGTTAACCGTGCGCATTGAGTTAGCTAAACCCGGCAaagaa < 1:27363/68‑1 (MQ=255)
aaGGCACCACCGTCAAAGCCATTGCACCGTTAACCGTGCGCATTGAGTTAGCTAAACCCGGCAaagaa < 1:2289236/68‑1 (MQ=255)
aaGGCACCACCGTCAAAGCCATTGCACCGTTAACCGTGCGCATTGAGTTAGCTAAACCCGGCAaagaa < 1:2369287/68‑1 (MQ=255)
aGGCACCACCGTCAAAGCCATTGCACCGTTAACCGTGCGCATTGAGTTAGCTAAACCCGGCAAagaaga < 1:2538485/69‑1 (MQ=255)
ccGTCAAAGCCATTGCACCGTTAACCGTGCGCATTGAGTTAGCTAAACCCGGCAAAGAAGATATGCTGa < 1:2131381/69‑1 (MQ=255)
ccGTCAAAGCCATTGCACCGTTAACCGTGCGCATTGAGTTAGCTAAACCCGGCAAAGAAGATATGCTGa < 1:1528076/69‑1 (MQ=255)
ccGTCAAAGCCATTGCACCGTTAACCGTGCGCATTGAGTTAGCTAAACCCGGCAAAGAAGATATGCTGa < 1:3104342/69‑1 (MQ=255)
cAAAGCCATTGCACCGTTAACCGTGCGCATTGAGTTAGCTAAACCCGGCAAAGAAGATATGCTGAGTCt < 1:3096195/69‑1 (MQ=255)
cAAAGCCATTGCACCGTTAACCGTGCGCATTGAGTTAGCTAAACCCGGCAAAGAAGATATGCTGAGTCt < 1:1347492/69‑1 (MQ=255)
cAAAGCCATTGCACCGTTAACCGTGCGCATTGAGTTAGCTAAACCCGGCAAAGAAGATATGCTGAGTCt < 1:1233153/69‑1 (MQ=255)
cAAAGCCATTGCACCGTTAACCGTGCGCATTGAGTTAGCTAAACCCGGCAAAGAAGATATGCTGAGTCt < 1:112183/69‑1 (MQ=255)
cAAAGCCATTGCACCGTTAACCGTGCGCATTGAGTTAGCTAAACCCGGCAAAGAAGATATGCTGAGTCt < 1:156682/69‑1 (MQ=255)
cAAAGCCATTGCACCGTTAACCGTGCGCATTGAGTTAGCTAAACCCGGCAAAGAAGATATGCTGAGTCt < 1:1586668/69‑1 (MQ=255)
cAAAGCCATTGCACCGTTAACCGTGCGCATTGAGTTAGCTAAACCCGGCAAAGAAGATATGCTGAGTCt < 1:460173/69‑1 (MQ=255)
cAAAGCCATTGCACCGTTAACCGTGCGCATTGAGTTAGCTAAACCCGGCAAAGAAGATATGCTGAGTCt < 1:3405088/69‑1 (MQ=255)
cAAAGCCATTGCACCGTTAACCGTGCGCATTGAGTTAGCTAAACCCGGCAAAGAAGATATGCTGAGTCt < 1:1627318/69‑1 (MQ=255)
cAAAGCCATTGCACCGTTAACCGTGCGCATTGAGTTAGCTAAACCCGGCAAAGAAGATATGCTGAGTCt < 1:3034964/69‑1 (MQ=255)
cAAAGCCATTGCACCGTTAACCGTGCGCATTGAGTTAGCTAAACCCGGCAAAGAAGATATGCTGAGTCt < 1:2019039/69‑1 (MQ=255)
cAAAGCCATTGCACCGTTAACCGTGCGCATTGAGTTAGCTAAACCCGGCAAAGAAGATATGCTGAGTCt < 1:2033879/69‑1 (MQ=255)
cAAAGCCATTGCACCGTTAACCGTGCGCATTGAGTTAGCTAAACCCGGCAAAGAAGATATGCTGAGTCt < 1:2219395/69‑1 (MQ=255)
cAAAGCCATTGCACCGTTAACCGTGCGCATTGAGTTAGCTAAACCCGGCAAAGAAGATATGCTGAGTCt < 1:2737975/69‑1 (MQ=255)
ccATTGCACCGTTAACCGTGCGCATTGAGTTAGCTAAACCCGGCAAAGAAGATATGCTGAGTCTGtttt < 1:2555601/69‑1 (MQ=255)
ccATTGCACCGTTAACCGTGCGCATTGAGTTAGCTAAACCCGGCAAAGAAGATATGCTGAGTCTGtttt < 1:1198987/69‑1 (MQ=255)
aTTGCACCGTTAACCGTGCGCATTGAGTTAGCTAAACCCGGCAAAGAAGATATGCTGAGTCTGtttt < 1:1101630/67‑1 (MQ=255)
gCACCGTTAACCGTGCGCATTGAGTTAGCTAAACCCGGCAAagaaga > 1:2803951/1‑47 (MQ=255)
|
TTTATGACCGAAGGCGTGCCGCAATTTCGTCTGGTCTACAAAGGCACCACCGTCAAAGCCATTGCACCGTTAACCGTGCGCATTGAGTTAGCTAAACCCGGCAAAGAAGATATGCTGAGTCTGTTTT > minE/1404222‑1404348
|
| 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
