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 |
1,352,188 |
C→A |
50.4% |
L180L (CTG→CTT) |
thiD ← |
bifunctional hydroxy‑methylpyrimidine kinase and hydroxy‑phosphomethylpyrimidine kinase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,352,188 | 0 | C | A | 50.4%
| 7.4
/ 80.2
| 73 | L180L (CTG→CTT) | thiD | bifunctional hydroxy‑methylpyrimidine kinase and hydroxy‑phosphomethylpyrimidine kinase |
| Reads supporting (aligned to +/- strand): ref base C (8/28); new base A (24/12); total (32/41) |
| Fisher's exact test for biased strand distribution p-value = 3.04e-04 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
CGGTGCGGTAAACCGTTGTTCACCCTCGCGGGTAAACAGCCAGTCCGGGCTTTGCTCATCATCCAGATGACCACCTTTCATTAGCACTGCGCCACAGCCCATCGCCAACAGCGATCGCCCTTGTTCCAG > minE/1352125‑1352253
|
ctgtgcggtAAACCGTTGTTCACCCTCGCGGGTAAACAGCCAGTCCGGGCTTTGCTCATCATCAAGATg < 1:956395/67‑1 (MQ=255)
ctgtgcggtAAACCGTTGTTCACCCTCGCGGGTAAACAGCCAGTCCGGGCTTTGCTCATCATCAAGATg < 1:381175/67‑1 (MQ=255)
ctgtgcggtAAACCGTTGTTCACCCTCGCGGGTAAACAGCCAGTCCGGGCTTTGCTCATCATCAAGATg < 1:255071/67‑1 (MQ=255)
ctgtgcggtAAACCGTTGTTCACCCTCGCGGGTAAACAGCCAGTCCGGGCTTTGCTCATCATCAAGATg < 1:1920456/67‑1 (MQ=255)
ctgtgcggtAAACCGTTGTTCACCCTCGCGGGTAAACAGCCAGTCCGGGCTTTGCTCATCATCAAGATg < 1:265946/67‑1 (MQ=255)
ctgtgcggtAAACCGTTGTTCACCCTCGCGGGTAAACAGCCAGTCCGGGCTTTGCTCATCATCAAGATg < 1:2890900/67‑1 (MQ=255)
ctgtgcggtAAACCGTTGTTCACCCTCGCGGGTAAACAGCCAGTCCGGGCTTTGCTCATCATCAAGATg < 1:1240939/67‑1 (MQ=255)
ctgtgcggtAAACCGTTGTTCACCCTCGCGGGTAAACAGCCAGTCCGGGCTTTGCTCATCATCAAGATg < 1:129969/67‑1 (MQ=255)
ctgtgcggtAAACCGTTGTTCACCCTCGCGGGTAAACAGCCAGTCCGGGCTTTGCTCATCATCAAGATg < 1:1316220/67‑1 (MQ=255)
ctgtgcggtAAACCGTTGTTCACCCTCGCGGGTAAACAGCCAGTCCGGGCTTTGCTCATCATCAAGATg < 1:1327681/67‑1 (MQ=255)
ctgtgcggtAAACCGTTGTTCACCCTCGCGGGTAAACAGCCAGTCCGGGCTTTGCTCATCATCAAGATg < 1:2975290/67‑1 (MQ=255)
ctgtgcggtAAACCGTTGTTCACCCTCGCGGGTAAACAGCCAGTCCGGGCTTTGCTCATCATCAAGATg < 1:1430091/67‑1 (MQ=255)
aaaCCGTTGTTCACCCTCGCGGGTAAACAGCCAGTCCGGGCTTTGCTCATCATCCAGATGACCACCttt < 1:211659/69‑1 (MQ=255)
aaaCCGTTGTTCACCCTCGCGGGTAAACAGCCAGTCCGGGCTTTGCTCATCATCCAGATGACCACCttt < 1:1664584/69‑1 (MQ=255)
aaaCCGTTGTTCACCCTCGCGGGTAAACAGCCAGTCCGGGCTTTGCTCATCATCCAGATGACCACCttt < 1:1664481/69‑1 (MQ=255)
aaaCCGTTGTTCACCCTCGCGGGTAAACAGCCAGTCCGGGCTTTGCTCATCATCCAGATGACCACCttt < 1:2998348/69‑1 (MQ=255)
aaaCCGTTGTTCACCCTCGCGGGTAAACAGCCAGTCCGGGCTTTGCTCATCATCCAGATGACCACCttt < 1:1410518/69‑1 (MQ=255)
aaaCCGTTGTTCACCCTCGCGGGTAAACAGCCAGTCCGGGCTTTGCTCATCATCCAGATGACCACCttt < 1:1226725/69‑1 (MQ=255)
ttgttCACCCTCGCGGGTAAACAGCCAGTCCGGGCTTTGCTCATCATCCAGATGACCACCTTTCATTAg < 1:2983372/69‑1 (MQ=255)
ttgttCACCCTCGCGGGTAAACAGCCAGTCCGGGCTTTGCTCATCATCCAGATGACCACCTTTCATTAg < 1:3038996/69‑1 (MQ=255)
ttgttCACCCTCGCGGGTAAACAGCCAGTCCGGGCTTTGCTCATCATCCAGATGACCACCTTTCATTAg < 1:2735576/69‑1 (MQ=255)
ttgttCACCCTCGCGGGTAAACAGCCAGTCCGGGCTTTGCTCATCATCCAGATGACCACCTTTCATTAg < 1:3299959/69‑1 (MQ=255)
ttgttCACCCTCGCGGGTAAACAGCCAGTCCGGGCTTTGCTCATCATCCAGATGACCACCTTTCATTAg < 1:103979/69‑1 (MQ=255)
ttgttCACCCTCGCGGGTAAACAGCCAGTCCGGGCTTTGCTCATCATCCAGATGACCACCTTTCATTAg < 1:3322702/69‑1 (MQ=255)
ttgttCACCCTCGCGGGTAAACAGCCAGTCCGGGCTTTGCTCATCATCCAGATGACCACCTTTCATTAg < 1:3341823/69‑1 (MQ=255)
ttgttCACCCTCGCGGGTAAACAGCCAGTCCGGGCTTTGCTCATCATCCAGATGACCACCTTTCATTAg < 1:2543807/69‑1 (MQ=255)
ttgttCACCCTCGCGGGTAAACAGCCAGTCCGGGCTTTGCTCATCATCCAGATGACCACCTTTCATTAg < 1:2562622/69‑1 (MQ=255)
ttgttCACCCTCGCGGGTAAACAGCCAGTCCGGGCTTTGCTCATCATCCAGATGACCACCTTTCATTAg < 1:1745975/69‑1 (MQ=255)
ttgttCACCCTCGCGGGTAAACAGCCAGTCCGGGCTTTGCTCATCATCCAGATGACCACCTTTCATTAg < 1:181011/69‑1 (MQ=255)
ttgttCACCCTCGCGGGTAAACAGCCAGTCCGGGCTTTGCTCATCATCCAGATGACCACCTTTCATTAg < 1:2038955/69‑1 (MQ=255)
tAAACAGCCAGTCCGGGCTTTGCTCATCATCGAGATGACCACCTTTCATTAg < 1:2398989/52‑1 (MQ=255)
tAAACAGCCAGTCCGGGCTTTGCTCATCATCCAGATGACCACCTTTCATTAg < 1:1710435/52‑1 (MQ=255)
tAAACAGCCAGTCCGGGCTTTGCTCATCATCCAGATGACCACCTTTCATTAg < 1:1170053/52‑1 (MQ=255)
tAAACAGCCAGTCCGGGCTTTGCTCATCATCCAGATGACCACCTTTCATTAg < 1:2114218/52‑1 (MQ=255)
tAAACAGCCAGTCCGGGCTTTGCTCATCATCCAGATGACCACCTTTCATTAg < 1:239904/52‑1 (MQ=255)
tAAACAGCCAGTCCGGGCTTTGCTCATCATCCAGATGACCACCTTTCATTAg < 1:2366410/52‑1 (MQ=255)
tAAACAGCCAGTCCGGGCTTTGCTCATCATACAGATGACCACCTTTCATTAg < 1:2800107/52‑1 (MQ=255)
aaaCAGCCAGTCCGGGCTTTGCTCATCATCCAGATGACCACCTTTCATTAg < 1:2751719/51‑1 (MQ=255)
aGCCAGTCCGGGCTTTGCTCATCATCCAGATGACCACCTTTCATTAg < 1:2403671/47‑1 (MQ=255)
cGGGCTTTGCTCATCATCCAGATGACCACCTTTCAt < 1:2445991/36‑1 (MQ=255)
cGGGCTTTGCTCATCATCCAGATGACCACCTTTCATTAGCACTGCGCCACAGCCCATCGCCAAc > 1:8390/1‑64 (MQ=255)
cGGGCTTTGCTCATCATCCAGATGACCACCTTTCATTAGCACTGCGCCACAGCCCATCGCCAAc > 1:1178367/1‑64 (MQ=255)
cGGGCTTTGCTCATCATCCAGATGACCACCTTTCATTAGCACTGCGCCACAGCCCATCGCCAAc > 1:2628207/1‑64 (MQ=255)
cGGGCTTTGCTCATCATCCAGATGACCACCTTTCATTAGCACTGCGCCACAGCCCATCGCCAAc > 1:2275221/1‑64 (MQ=255)
cGGGCTTTGCTCATCATCCAGATGACCACCTTTCATTAGCACTGCGCCACAGCCCATCGCCAAc > 1:1837944/1‑64 (MQ=255)
cGGGCTTTGCTCATCATCCAGATGACCACCTTTCATTAGCACTGCGCCACAGCCCATCGCCAAc > 1:1375438/1‑64 (MQ=255)
cGGGCTTTGCTCATCATCCAGATGACCACCTTTCATTAGCACTGCGCCACAGCCCATCGCCAAc > 1:3418746/1‑64 (MQ=255)
cGGGCTTTGCTCATCATCCAGATGACCACCTTTCATTAGCACTGCGCCACAGCCCATCGCCAAc > 1:115422/1‑64 (MQ=255)
gCTCATCATCAAGATGCCCACCTTTCATTAGCACTGCGCCACAGCCCATCGCCAACAGc > 1:2822309/1‑59 (MQ=255)
gCTCATCATCAAGATGACCACCTTTCATTAGCACTGCGCCACAGCCCATCGCCAACAg > 1:3104730/1‑58 (MQ=255)
gCTCATCATCAAGATGACCACCTTTCATTAGCACTGCGCCACAGCCCATCGCCAACAGc > 1:414201/1‑59 (MQ=255)
gCTCATCATCAAGATGACCACCTTTCATTAGCACTGCGCCACAGCCCATCGCCAACAGc > 1:1197495/1‑59 (MQ=255)
gCTCATCATCAAGATGACCACCTTTCATTAGCACTGCGCCACAGCCCATCGCCAACAGc > 1:3434398/1‑59 (MQ=255)
gCTCATCATCAAGATGACCACCTTTCATTAGCACTGCGCCACAGCCCATCGCCAACAGc > 1:2936435/1‑59 (MQ=255)
gCTCATCATCAAGATGACCACCTTTCATTAGCACTGCGCCACAGCCCATCGCCAACAGc > 1:542716/1‑59 (MQ=255)
gCTCATCATCAAGATGACCACCTTTCATTAGCACTGCGCCACAGCCCATCGCCAACAGc > 1:636513/1‑59 (MQ=255)
gCTCATCATCAAGATGACCACCTTTCATTAGCACTGCGCCACAGCCCATCGCCAACAGc > 1:640514/1‑59 (MQ=255)
gCTCATCATCAAGATGACCACCTTTCATTAGCACTGCGCCACAGCCCATCGCCAACAGc > 1:667301/1‑59 (MQ=255)
gCTCATCATCAAGATGACCACCTTTCATTAGCACTGCGCCACAGCCCATCGCCAACAGc > 1:1080702/1‑59 (MQ=255)
gCTCATCATCAAGATGACCACCTTTCATTAGCACTGCGCCACAGCCCATCGCCAACAGc > 1:3182203/1‑59 (MQ=255)
gCTCATCATCAAGATGACCACCTTTCATTAGCACTGCGCCACAGCCCATCGCCAACAGc > 1:3167638/1‑59 (MQ=255)
gCTCATCATCAAGATGACCACCTTTCATTAGCACTGCGCCACAGCCCATCGCCAACAGc > 1:3135979/1‑59 (MQ=255)
gCTCATCATCAAGATGACCACCTTTCATTAGCACTGCGCCACAGCCCATCGCCAACAGc > 1:3074242/1‑59 (MQ=255)
gCTCATCATCAAGATGACCACCTTTCATTAGCACTGCGCCACAGCCCATCGCCAACAGc > 1:141449/1‑59 (MQ=255)
gCTCATCATCAAGATGACCACCTTTCATTAGCACTGCGCCACAGCCCATCGCCAACAGc > 1:2740735/1‑59 (MQ=255)
gCTCATCATCAAGATGACCACCTTTCATTAGCACTGCGCCACAGCCCATCGCCAACAGc > 1:27029/1‑59 (MQ=255)
gCTCATCATCAAGATGACCACCTTTCATTAGCACTGCGCCACAGCCCATCGCCAACAGc > 1:2668880/1‑59 (MQ=255)
gCTCATCATCAAGATGACCACCTTTCATTAGCACTGCGCCACAGCCCATCGCCAACAGc > 1:2653891/1‑59 (MQ=255)
gCTCATCATCAAGATGACCACCTTTCATTAGCACTGCGCCACAGCCCATCGCCAACAGc > 1:259672/1‑59 (MQ=255)
gCTCATCATCAAGATGACCACCTTTCATTAGCACTGCGCCACAGCCCATCGCCAACAGc > 1:1874677/1‑59 (MQ=255)
gCTCATCATCAAGATGACCACCTTTCATTAGCACTGCGCCACAGCCCATCGCCAACAGc > 1:231898/1‑59 (MQ=255)
gCTCATCATCAAGATGACCACCTTTCATTAGCACTGCCCCACAGCCCATCGCCAACAGc > 1:1572627/1‑59 (MQ=255)
atcCAGATGACCACCTTTCATTAGCACTGCGCCACAGCCCATCGCCAACAGCGATCGCCCTTGTTCCAg < 1:2662286/69‑1 (MQ=255)
|
CGGTGCGGTAAACCGTTGTTCACCCTCGCGGGTAAACAGCCAGTCCGGGCTTTGCTCATCATCCAGATGACCACCTTTCATTAGCACTGCGCCACAGCCCATCGCCAACAGCGATCGCCCTTGTTCCAG > minE/1352125‑1352253
|
| 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
