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 |
1,782,521 |
C→T |
38.9% |
T324T (ACC→ACT) |
yfjD → |
predicted inner membrane protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,782,521 | 0 | C | T | 38.9%
| 38.5
/ 49.2
| 77 | T324T (ACC→ACT) | yfjD | predicted inner membrane protein |
| Reads supporting (aligned to +/- strand): ref base C (10/37); new base T (4/26); total (14/63) |
| Fisher's exact test for biased strand distribution p-value = 5.47e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.03e-01 |
GCCAACACTTGCCGAAGAGGTCACGCCGCAAAACGACGGTTCGGTGATTATCGATGGCACCGCCAACGTGCGGGAAATCAACAAAGCCTTTAACTGGCATCTACCGGAAGATGATGCCCGCACGGTTA > minE/1782461‑1782588
|
gCCAACACTTGCCGAAGAGGTCACGCCGCAAAACGACGGTTCGGTGATTATCGATGGCACCGCCAACGt > 1:2419969/1‑69 (MQ=255)
gCCAACACTTGCCGAAGAGGTCACGCCGCAAAACGACGGTTCGGTGATTATCGATGGCACCGCCAACGt > 1:1791683/1‑69 (MQ=255)
gCCAACACTTGCCGAAGAGGTCACGCCGCAAAACGACGGTTCGGTGATTATCGATGGCACCGCCAACGt > 1:1134505/1‑69 (MQ=255)
gCCAACACTTGCCGAAGAGGTCACGCCGCAAAACGACGGTTCGGTGATTATCGATGGCACCGCCAACGt > 1:2130351/1‑69 (MQ=255)
gCCAACACTTGCCGAAGAGGTCACGCCGCAAAACGACGGTTCGGTGATTATCGATGGCACCGCCAACGt > 1:516266/1‑69 (MQ=255)
gCCAACACTTGCCGAAGAGGTCACGCCGCAAAACGACGGTTCGGTGATTATCGATGGCACCGCCAACGt > 1:2472204/1‑69 (MQ=255)
gCCAACACTTGCCGAAGAGGTCACGCCGCAAAACGACGGTTCGGTGATTATCGATGGCACCGCCAACGt > 1:2562557/1‑69 (MQ=255)
gCCAACACTTGCCGAAGAGGTCACGCCGCAAAACGACGGTTCGGTGATTATCGATGGCACCGCCAACGt > 1:1856485/1‑69 (MQ=255)
ggTCACGCCGCAAAACGACGGTTCGGTGATTATCGATGGCACCGCCAACGTGCGGGAAATCAACAAAGc < 1:2759397/69‑1 (MQ=255)
ggTCACGCCGCAAAACGACGGTTCGGTGATTATCGATGGCACCGCCAACGTGCGGGAAATCAACAAAGc < 1:1743851/69‑1 (MQ=255)
ggTCACGCCGCAAAACGACGGTTCGGTGATTATCGATGGCACCGCCAACGTGCGGGAAATCAACAAAGc < 1:1583389/69‑1 (MQ=255)
ggTCACGCCGCAAAACGACGGTTCGGTGATTATCGATGGCACCGCCAACGTGCGGGAAATCAACAAAGc < 1:279320/69‑1 (MQ=255)
ggTCACGCCGCAAAACGACGGTTCGGTGATTATCGATGGCACCGCCAACGTGCGGGAAATCAACAAAGc < 1:1213571/69‑1 (MQ=255)
ggTCACGCCGCAAAACGACGGTTCGGTGATTATCGATGGCACCGCCAACGTGCGGGAAATCAACAAAGc < 1:1078091/69‑1 (MQ=255)
gTCACGCCGCAAAACGACGGTTCGGTGATTATCGATGGCACCGCCAACGTGCGGGAAATCAACAAAGc < 1:1030002/68‑1 (MQ=255)
cACGCCGCAAAACGACGGTTCGGTGATTATTGATGGCACTGCCAAc < 1:2256603/46‑1 (MQ=39)
cACGCCGCAAAACGACGGTTCGGTGATTATTGATGGCACTGCCAAc < 1:2339948/46‑1 (MQ=39)
cACGCCGCAAAACGACGGTTCGGTGATTATTGATGGCACTGCCAAc < 1:3344368/46‑1 (MQ=39)
cACGCCGCAAAACGACGGTTCGGTGATTATTGATGGCACTGCCAAc < 1:347884/46‑1 (MQ=39)
cACGCCGCAAAACGACGGTTCGGTGATTATTGATGGCACTGCCAAc < 1:2991678/46‑1 (MQ=39)
cACGCCGCAAAACGACGGTTCGGTGATTATTGATGGCACTGCCAAc < 1:2465051/46‑1 (MQ=39)
cACGCCGCAAAACGACGGTTCGGTGATTATTGATGGCACTGCCAAc < 1:2468565/46‑1 (MQ=39)
cACGCCGCAAAACGACGGTTCGGTGATTATTGATGGCACTGCCAAc < 1:3306855/46‑1 (MQ=39)
cACGCCGCAAAACGACGGTTCGGTGATTATTGATGGCACTGCCAAc < 1:2607451/46‑1 (MQ=39)
cACGCCGCAAAACGACGGTTCGGTGATTATTGATGGCACTGCCAAc < 1:3188171/46‑1 (MQ=39)
cACGCCGCAAAACGACGGTTCGGTGATTATTGATGGCACTGCCAAc < 1:3115593/46‑1 (MQ=39)
cACGCCGCAAAACGACGGTTCGGTGATTATTGATGGCACTGCCAAc < 1:2934673/46‑1 (MQ=39)
cACGCCGCAAAACGACGGTTCGGTGATTATTGATGGCACTGCCAAc < 1:2973151/46‑1 (MQ=39)
cACGCCGCAAAACGACGGTTCGGTGATTATTGATGGCACTGCCAAc < 1:2106743/46‑1 (MQ=39)
cACGCCGCAAAACGACGGTTCGGTGATTATTGATGGCACTGCCAAc < 1:1167556/46‑1 (MQ=39)
cACGCCGCAAAACGACGGTTCGGTGATTATTGATGGCACTGCCAAc < 1:987933/46‑1 (MQ=39)
cACGCCGCAAAACGACGGTTCGGTGATTATTGATGGCACTGCCAAc < 1:1359320/46‑1 (MQ=39)
cACGCCGCAAAACGACGGTTCGGTGATTATTGATGGCACTGCCAAc < 1:923274/46‑1 (MQ=39)
cACGCCGCAAAACGACGGTTCGGTGATTATTGATGGCACTGCCAAc < 1:876772/46‑1 (MQ=39)
cACGCCGCAAAACGACGGTTCGGTGATTATTGATGGCACTGCCAAc < 1:1560564/46‑1 (MQ=39)
cACGCCGCAAAACGACGGTTCGGTGATTATTGATGGCACTGCCAAc < 1:1640703/46‑1 (MQ=39)
cACGCCGCAAAACGACGGTTCGGTGATTATTGATGGCACTGCCAAc < 1:599400/46‑1 (MQ=39)
cACGCCGCAAAACGACGGTTCGGTGATTATTGATGGCACTGCCAAc < 1:521536/46‑1 (MQ=39)
cACGCCGCAAAACGACGGTTCGGTGATTATTGATGGCACTGCCAAc < 1:508257/46‑1 (MQ=39)
cACGCCGCAAAACGACGGTTCGGTGATTATTGATGGCACTGCCAAc < 1:1960414/46‑1 (MQ=39)
cACGCCGCAAAACGACGGTTCGGTGATTATTGATGGCACTGCCAAc < 1:420631/46‑1 (MQ=39)
cACGCCGCAAAACGACGGTTCGGTGATTATCGATGGCACCGCCAACGTGCGGGAAATCAACAAAGCCt > 1:3404278/1‑68 (MQ=255)
cAAAACGACGGTTCGGTGATTATCGATGGCACCGCCAACGTGCGGGAAATCAACAAAGCCTTTAACTgg < 1:1583813/69‑1 (MQ=255)
cAAAACGACGGTTCGGTGATTATCGATGGCACCGCCAACGTGCGGGAAATCAACAAAGCCTTTAACTgg < 1:3274276/69‑1 (MQ=255)
cAAAACGACGGTTCGGTGATTATCGATGGCACCGCCAACGTGCGGGAAATCAACAAAGCCTTTAACTgg < 1:2685458/69‑1 (MQ=255)
cAAAACGACGGTTCGGTGATTATCGATGGCACCGCCAACGTGCGGGAAATCAACAAAGCCTTTAACTgg < 1:1449384/69‑1 (MQ=255)
cAAAACGACGGTTCGGTGATTATCGATGGCACCGCCAACGTGCGGGAAATCAACAAAGCCTTTAACTgg < 1:941698/69‑1 (MQ=255)
aaaCGACGGTTCTGTGATTATCGATGGCACCGCCAACGTGCGGGAAATCAACAAAGc < 1:670005/57‑1 (MQ=255)
tCGGTGATTATCGATGGCACCGCCAACGTGCGGGAAATCAACAAAGCCTTTa > 1:3164897/1‑52 (MQ=255)
ggtggtTATTGATGGCACTGCCAACGTGCGAGAAATTAACAAAGCCTTTAACTGGCATCTACCGGAAg > 1:1053679/1‑68 (MQ=255)
ggTGATTATTGATGGCACTGCCAACGTGCGAGAAATTAACAAAGCCTTTAACTGGCATCTACCGGAAg > 1:1481354/1‑68 (MQ=255)
ggTGATTATTGATGGCACTGCCAACGTGCGAGAAATTAACAAAGCCTTTAACTGGCATCTACCGGAAg > 1:71994/1‑68 (MQ=255)
ggTGATTATTGATGGCACTGCCAACGTGCGAGAAATTAACAAAGCCTTTAACTGGCATCTACCGGAAg > 1:2405513/1‑68 (MQ=255)
tGATTATCGATGGCACCGCCAACGTGCGGGAAATCAACAAAGCCTTTAACTGGCATCTACCGGAAgat < 1:1768860/68‑1 (MQ=255)
tGATTATCGATGGCACCGCCAACGTGCGGGAAATCAACAAAGCCTTTAACTGGCATCTACCGGAAgat < 1:1184052/68‑1 (MQ=255)
tGATTATCGATGGCACCGCCAACGTGCGGGAAATCAACAAAGCCTTTAACTGGCATCTACCGGAAgat < 1:1412323/68‑1 (MQ=255)
tGATTATCGATGGCACCGCCAACGTGCGGGAAATCAACAAAGCCTTTAACTGGCATCTACCGGAAgat < 1:1530348/68‑1 (MQ=255)
tGATTATCGATGGCACCGCCAACGTGCGGGAAATCAACAAAGCCTTTAACTGGCATCTACCGGAAgat < 1:559927/68‑1 (MQ=255)
tGATTATCGATGGCACCGCCAACGTGCGGGAAATCAACAAAGCCTTTAACTGGCATCTACCGGAAgat < 1:548445/68‑1 (MQ=255)
tGATTATCGATGGCACCGCCAACGTGCGGGAAATCAACAAAGCCTTTAACTGGCATCTACCGGAAgat < 1:1807746/68‑1 (MQ=255)
tGATTATCGATGGCACCGCCAACGTGCGGGAAATCAACAAAGCCTTTAACTGGCATCTACCGGAAgat < 1:2772620/68‑1 (MQ=255)
tGATTATCGATGGCACCGCCAACGTGCGGGAAATCAACAAAGCCTTTAACTGGCATCTACCGGAAgat < 1:2608647/68‑1 (MQ=255)
tGATTATCGATGGCACCGCCAACGTGCGGGAAATCAACAAAGCCTTTAACTGGCATCTACCGGAAgat < 1:2514554/68‑1 (MQ=255)
tGATTATCGATGGCACCGCCAACGTGCGGGAAATCAACAAAGCCTTTAACTGGCATCTACCGGAAgat < 1:2296053/68‑1 (MQ=255)
tGATTATCGATGGCACCGCCAACGTGCGGGAAATCAACAAAGCCTTTAACTGGCATCTACCGGAAgat < 1:2157272/68‑1 (MQ=255)
gATGGCACCGCCAACGTGCGGGAAATCAACAAAGCCTTTAACTGGCATCTACCGGAAGATGATGCCCg < 1:640157/68‑1 (MQ=255)
gATGGCACCGCCAACGTGCGGGAAATCAACAAAGCCTTTAACTGGCATCTACCGGAAGATGATGCCCg < 1:2821176/68‑1 (MQ=255)
gATGGCACCGCCAACGTGCGGGAAATCAACAAAGCCTTTAACTGGCATCTACCGGAAGATGATGCCCg < 1:869143/68‑1 (MQ=255)
gATGGCACCGCCAACGTGCGGGAAATCAACAAAGCCTTTAACTGGCATCTACCGGAAGATGATGCCCg < 1:693811/68‑1 (MQ=255)
gATGGCACCGCCAACGTGCGGGAAATCAACAAAGCCTTTAACTGGCATCTACCGGAAGATGATGCCCg < 1:1738813/68‑1 (MQ=255)
gATGGCACCGCCAACGTGCGGGAAATCAACAAAGCCTTTAACTGGCATCTACCGGAAGATGATGCCCg < 1:2330987/68‑1 (MQ=255)
gATGGCACCGCCAACGTGCGGGAAATCAACAAAGCCTTTAACTGGCATCTACCGGAAGATGATGCCCg < 1:2991394/68‑1 (MQ=255)
gATGGCACCGCCAACGTGCGGGAAATCAACAAAGCCTTTAACTGGCATCTACCGGAAGATGATGCCCg < 1:3675/68‑1 (MQ=255)
gATGGCACCGCCAACGTGCGGGAAATCAACAAAGCCTTTAACTGGCATCTACCGGAAGATGATGCCCg < 1:510742/68‑1 (MQ=255)
gATGGCACCGCCAACGTGCGGGAAATCAACAAAGCCTTTAACTGGCATCTACCGGAAGATGATGCCCg < 1:456863/68‑1 (MQ=255)
aCCGCCAACGTGCGGGAAATCAACAAAGCCTTTAACTGGCATCTACCGGAAGATGATGCCCGCACGGtt < 1:662228/69‑1 (MQ=255)
aCCGCCAACGTGCGGGAAATCAACAAAGCCTTTAACTGGCATCTACCGGAAGATGATGCCCGCACGGtt < 1:1838095/69‑1 (MQ=255)
ccGCCAACGTGCGGGAAATCAACAAAGCCTTTAACTGGCATCTACCGGAAgat < 1:1752667/53‑1 (MQ=255)
ccGCCAACGTGCGGGAAATCAACAAAGCCTTTAACTGGCATCTACCGGAAGATGATGCCCGCACGGTTa < 1:2910228/69‑1 (MQ=255)
ccGCCAACGTGCGGGAAATCAACAAAGCCTTTAACTGGCATCTACCGGAAGATGATGCCCGCACGGTTa < 1:64532/69‑1 (MQ=255)
|
GCCAACACTTGCCGAAGAGGTCACGCCGCAAAACGACGGTTCGGTGATTATCGATGGCACCGCCAACGTGCGGGAAATCAACAAAGCCTTTAACTGGCATCTACCGGAAGATGATGCCCGCACGGTTA > minE/1782461‑1782588
|
| 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
