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 |
1,071,798 |
C→G |
47.2% |
S217S (TCC→TCG) |
mdtK → |
multidrug efflux system transporter |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,071,798 | 0 | C | G | 47.2%
| 6.1
/ 85.3
| 72 | S217S (TCC→TCG) | mdtK | multidrug efflux system transporter |
| Reads supporting (aligned to +/- strand): ref base C (24/14); new base G (15/19); total (39/33) |
| Fisher's exact test for biased strand distribution p-value = 1.55e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.27e-01 |
GCGGCGGTGTATTGGGTCATGTTCCTTGCCATGGTTTCTTACATTAAACGCGCCCGCTCCATGCGCGATATTCGTAACGAAAAAGGCACCGCAAAACCCGATCCTGCGGTTATGAAACGA > minE/1071739‑1071858
|
gcggcgGTGTATTGGGTCATGTTCCTTGCCATGGTTTCTTACATTAAACGCGCCCGCTCCATGCGCGa < 1:966706/68‑1 (MQ=255)
gcggcgGTGTATTGGGTCATGTTCCTTGCCATGGTTTCTTACATTAAACGCGCCCGCTCCATGCGCGa < 1:2992168/68‑1 (MQ=255)
gcggcgGTGTATTGGGTCATGTTCCTTGCCATGGTTTCTTACATTAAACGCGCCCGCTCCATGCGCGa < 1:3092443/68‑1 (MQ=255)
gcggcgGTGTATTGGGTCATGTTCCTTGCCATGGTTTCTTACATTAAACGCGCCCGCTCCATGCGCGa < 1:3415127/68‑1 (MQ=255)
gcggcgGTGTATTGGGTCATGTTCCTTGCCATGGTTTCTTACATTAAACGCGCCCGCTCCATGCGCGa < 1:354469/68‑1 (MQ=255)
gcggTGTATTGGGTCATGTTCCTTGCCATGGTTTCTTACATTAAACGCGCCCGCTCCATGCGCGata < 1:1094027/67‑1 (MQ=255)
gcggTGTATTGGGTCATGTTCCTTGCCATGGTTTCTTACATTAAACGCGCCCGCTCCATGCGCGata < 1:2618462/67‑1 (MQ=255)
gcggTGTATTGGGTCATGTTCCTTGCCATGGTTTCTTACATTAAACGCGCCCGCTCCATGCGCGata < 1:3144511/67‑1 (MQ=255)
gtgtATTGGGTCATGTTCCTTGCCATGGTTTCTTACATTAAACGCGCCCGCTCCATGCGCGATATTCGt > 1:2344380/1‑69 (MQ=255)
gtgtATTGGGTCATGTTCCTTGCCATGGTTTCTTACATTAAACGCGCCCGCTCCATGCGCGATATTCGt > 1:2436884/1‑69 (MQ=255)
ttGGGTCATGTTCCTTGCCATGGTTTCTTACATTAAACGCGCCCGCTCCATGCGCGa < 1:506540/57‑1 (MQ=255)
ttGGGTCATGTTCCTTGCCATGGTTTCTTACATTAAACGCGCCCGCTCCATGCGCGATATTCGt < 1:3115788/64‑1 (MQ=255)
ttGGGTCATGTTCCTTGCCATGGTTTCTTACATTAAACGCGCCCGCTCCATGCGCGATATTCGt < 1:3112005/64‑1 (MQ=255)
ttGGGTCATGTTCCTTGCCATGGTTTCTTACATTAAACGCGCCCGCTCCATGCGCGATATTCGTaa > 1:2163082/1‑66 (MQ=255)
ttGGGTCATGTTCCTTGCCATGGTTTCTTACATTAAACGCGCCCGCTCCATGCGCGATATTCGTAAc > 1:2182866/1‑67 (MQ=255)
ttGGGTCATGTTCCTTGCCATGGTTTCTTACATTAAACGCGCCCGCTCCATGCGCGATATTCGTAACg > 1:2745860/1‑68 (MQ=255)
ttGGGTCATGTTCCTTGCCATGGTTTCTTACATTAAACGCGCCCGCTCCATGCGCGATATTCGTAACg > 1:2199325/1‑68 (MQ=255)
ttGGGTCATGTTCCTTGCCATGGTTTCTTACATTAAACGCGCCCGCTCCATGCGCGATATTCGTAACg > 1:1138851/1‑68 (MQ=255)
ttGGGTCATGTTCCTTGCCATGGTTTCTTACATTAAACGCGCCCGCTCCATGCGCGATATTCGTAACg > 1:208270/1‑68 (MQ=255)
ttGGGTCATGTTCCTTGCCATGGTTTCTTACATTAAACGCGCCCGCTCCATGCGCGATATTCGTAACg > 1:3098497/1‑68 (MQ=255)
ttGGGTCATGTTCCTTGCCATGGTTTCTTACATTAAACGCGCCCGCTCCATGCGCGATATTCGTAACg > 1:458499/1‑68 (MQ=255)
ttGGGTCATGTTCCTTGCCATGGTTTCTTACATTAAACGCGCCCGCTCCATGCGCGATATTCGTAACg > 1:1723555/1‑68 (MQ=255)
ttGGGTCATGTTCCTTGCCATGGTTTCTTACATTAAACGCGCCCGCTCCATGCGCGATATTCGTAACg > 1:3326735/1‑68 (MQ=255)
ttGGGTCATGTTCCTTGCCATGGTTTCTTACATTAAACGCGCCCGCTCCATGCGCGATATTCGTAACg > 1:548302/1‑68 (MQ=255)
ttGGGTCATGTTCCTTGCCATGGTTTCTTACATTAAACGCGCCCGCTCCATGCGCGATATTCGTAACg > 1:315451/1‑68 (MQ=255)
ttGGGTCATGTTCCTTGCCATGGTTTCTTACATTAAACGCGCCCGCTCCATGCGCGATATTCGTAACg > 1:1632869/1‑68 (MQ=255)
gggTCATGTTCCTTGCCATGGTTTCTTACATTAAACGCGCCCGCTCCATGCGCGATATTCGTAACGa > 1:790820/1‑67 (MQ=255)
gTCATGTTCCTTGCCATGGTTTCTTACATTAAACGCGCCCGCTCCATGCGCGa < 1:1798038/53‑1 (MQ=255)
gTTCCTTGCCATGGTTTCTTACATTAAACGCGCCCGCTCCATGCGCGATATTCGTAACGAAAAAGGCAc > 1:2528317/1‑69 (MQ=255)
gTTCCTTGCCATGGTTTCTTACATTAAACGCGCCCGCTCCATGCGCGATATTCGTAACGAAAAAGGCAc > 1:1923343/1‑69 (MQ=255)
gTTCCTTGCCATGGTTTCTTACATTAAACGCGCCCGCTCCATGCGCGATATTCGTAACGAAAAAGGCAc > 1:312478/1‑69 (MQ=255)
gTTCCTTGCCATGGTTTCTTACATTAAACGCGCCCGCTCCATGCGCGATATTCGTAACGAAAAAGGCAc > 1:3168687/1‑69 (MQ=255)
gTTCCTTGCCATGGTTTCTTACATTAAACGCGCCCGCTCCATGCGCGATATTCGTAACGAAAAAGGCAc > 1:152900/1‑69 (MQ=255)
tGCCATGGTTTCTAAGATTAAACGCGCCCGCTCCATGCGCGATATTCGt < 1:1095755/49‑1 (MQ=255)
tGGTTTCTTACATTAAACGCGCCCGCTCCATGCGCGATATTCGTAACGAAAAAGGCACCGCAAAACCCg > 1:1312472/1‑69 (MQ=255)
ttttCTTACATTAAACGCGCCCGCTCGATGCGCGATATTCGTAACGAAAAAGGCACCGCGAAGCCCGAt < 1:2634566/68‑1 (MQ=255)
gTTTCTTACATTAAACGCGCCCGCTCGATGCGCGATATTCGTAACGAAAAAGGCACCGCGAATCCCGAt < 1:438685/69‑1 (MQ=255)
gTTTCTTACATTAAACGCGCCCGCTCGATGCGCGATATTCGTAACGAAAAAGGCACCGCGAAGCCCGAt < 1:1103953/69‑1 (MQ=255)
gTTTCTTACATTAAACGCGCCCGCTCGATGCGCGATATTCGTAACGAAAAAGGCACCGCGAAGCCCGAt < 1:900123/69‑1 (MQ=255)
gTTTCTTACATTAAACGCGCCCGCTCGATGCGCGATATTCGTAACGAAAAAGGCACCGCGAAGCCCGAt < 1:169490/69‑1 (MQ=255)
gTTTCTTACATTAAACGCGCCCGCTCGATGCGCGATATTCGTAACGAAAAAGGCACCGCGAAGCCCGAt < 1:2494882/69‑1 (MQ=255)
tttCTTACATTAAACGCGCCCGCTCGATGCGCGATATTCGTAACGAAAAAGGCACCGCGAAGCCCGAt < 1:492933/68‑1 (MQ=255)
cATTAAACGCGCCCGCTCGATGCGCGATATTCGTAACGAAAAAGGCACCGCGAAGCCCg < 1:371985/59‑1 (MQ=38)
cATTAAACGCGCCCGCTCGATGCGCGATATTCGTAACGAAAAAGGCACCGCGAAGCCCg < 1:2606583/59‑1 (MQ=38)
cATTAAACGCGCCCGCTCGATGCGCGATATTCGTAACGAAAAAGGCACCGCGAAGCCCg < 1:927878/59‑1 (MQ=38)
cATTAAACGCGCCCGCTCGATGCGCGATATTCGTAACGAAAAAGGCACCGCGAAGCCCg < 1:1107394/59‑1 (MQ=38)
cATTAAACGCGCCCGCTCGATGCGCGATATTCGTAACGAAAAAGGCACCGCGAAGCCCg < 1:1178269/59‑1 (MQ=38)
cATTAAACGCGCCCGCTCGATGCGCGATATTCGTAACGAAAAAGGCACCGCGAAGCCCg < 1:1331224/59‑1 (MQ=38)
cATTAAACGCGCCCGCTCGATGCGCGATATTCGTAACGAAAAAGGCACCGCGAAGCCCg < 1:3372982/59‑1 (MQ=38)
cATTAAACGCGCCCGCTCGATGCGCGATATTCGTAACGAAAAAGGCACCGCGAAGCCCg < 1:3246860/59‑1 (MQ=38)
cATTAAACGCGCCCGCTCGATGCGCGATATTCGTAACGAAAAAGGCACCGCGAAGCCCg < 1:1634031/59‑1 (MQ=38)
cATTAAACGCGCCCGCTCGATGCGCGATATTCGTAACGAAAAAGGCACCGCGAAGCCCg < 1:1780806/59‑1 (MQ=38)
cATTAAACGCGCCCGCTCGATGCGCGATATTCGTAACGAAAAAGGCACCGCGAAGCCCg < 1:1609348/59‑1 (MQ=38)
aTTAAACGCGCCCGCTCGATGCGCGATATTCGTAACGAAAAAGGCACCGCGAAGCCCg < 1:2239959/58‑1 (MQ=38)
tAAACGCGCCCGCTCGATGCGCGATATTCGTAACGAAAAAGGCACCGCgaag > 1:1172495/1‑51 (MQ=38)
tAAACGCGCCCGCTCGATGCGCGATATTCGTAACGAAAAAGGCACCGCgaag > 1:306600/1‑51 (MQ=38)
tAAACGCGCCCGCTCGATGCGCGATATTCGTAACGAAAAAGGCACCGCgaag > 1:2155317/1‑51 (MQ=38)
tAAACGCGCCCGCTCGATGCGCGATATTCGTAACGAAAAAGGCACCGCgaag > 1:2733879/1‑51 (MQ=38)
tAAACGCGCCCGCTCGATGCGCGATATTCGTAACGAAAAAGGCACCGCgaag > 1:898264/1‑51 (MQ=38)
tAAACGCGCCCGCTCGATGCGCGATATTCGTAACGAAAAAGGCACCGCgaag > 1:2064647/1‑51 (MQ=38)
tAAACGCGCCCGCTCGATGCGCGATATTCGTAACGAAAAAGGCACCGCgaag > 1:641629/1‑51 (MQ=38)
tAAACGCGCCCGCTCGATGCGCGATATTCGTAACGAAAAAGGCACCGCgaag > 1:1149615/1‑51 (MQ=38)
tAAACGCGCCCGCTCGATGCGCGATATTCGTAACGAAAAAGGCACCGCgaag > 1:1850529/1‑51 (MQ=38)
tAAACGCGCCCGCTCGATGCGCGATATTCGTAACGAAAAAGGCACCGCgaag > 1:394073/1‑51 (MQ=38)
tAAACGCGCCCGCTCGATGCGCGATATTCGTAACGAAAAAGGCACCGCgaag > 1:3043954/1‑51 (MQ=38)
tAAACGCGCCCGCTCGATGCGCGATATTCGTAACGAAAAAGGCACCGCgaag > 1:2869420/1‑51 (MQ=38)
tAAACGCGCCCGCTCGATGCGCGATATTCGTAACGAAAAAGGCACCGCgaag > 1:350549/1‑51 (MQ=38)
tAAACGCGCCCGCTCGATGCGCGATATTCGTAACGAAAAAGGCACCGCgaag > 1:1644834/1‑51 (MQ=38)
tAAACGCGCCCGCTCGATGCGCGATATTCGTAACGAAAAAGGCACCGCgaag > 1:1470554/1‑51 (MQ=38)
aCGCGCCCGCTCCATGCGCGATATTCGTAACGAAAAAGGCACCGCAAAACCCGATCCTGCGGTTATGa < 1:563197/68‑1 (MQ=255)
cccGCTCCATGCGCGATATTCGTAACGAAAAAGGCACCGCAAAACCCGATCCTGCGGTTATGAAACGa > 1:630092/1‑68 (MQ=255)
cccGCTCCATGCGCGATATTCGTAACGAAAAAGGCACCGCAAAACCCGATCCTGCGGTTATGAAACGa > 1:667816/1‑68 (MQ=255)
|
GCGGCGGTGTATTGGGTCATGTTCCTTGCCATGGTTTCTTACATTAAACGCGCCCGCTCCATGCGCGATATTCGTAACGAAAAAGGCACCGCAAAACCCGATCCTGCGGTTATGAAACGA > minE/1071739‑1071858
|
| 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
