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 |
2,331,283 |
A→G |
38.9% |
intergenic (‑188/+242) |
sodA ← / ← fdhD |
superoxide dismutase, Mn/formate dehydrogenase formation protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,331,283 | 0 | A | G | 38.9%
| 22.0
/ 34.4
| 54 | intergenic (‑188/+242) | sodA/fdhD | superoxide dismutase, Mn/formate dehydrogenase formation protein |
| Reads supporting (aligned to +/- strand): ref base A (17/16); new base G (11/10); total (28/26) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.96e-01 |
GAAAATGCCCGAGATGTGAAGCAAATCAACCACTTAATGCCGTGATTGCCAGTAAATCGACAACGGCGGCAACAGGCGAAAGGTTAATCGACAGCACGATTTTTACACT > minE/2331224‑2331332
|
gAAAATGCCCAAGATGTGAAGCAAATCACCCACTTAATGCCGTGATTGCCAGTAAATCGGCAgcggcg > 1:3109226/1‑68 (MQ=38)
gAAAATGCCCAAGATGTGAAGCAAATCACCCACTTAATGCCGTGATTGCCAGTAAATCGGCAgcggcg > 1:3195261/1‑68 (MQ=38)
gAAAATGCCCAAGATGTGAAGCAAATCACCCACTTAATGCCGTGATTGCCAGTAAATCGGCAgcggcg > 1:3302624/1‑68 (MQ=38)
gAAAATGCCCAAGATGTGAAGCAAATCACCCACTTAATGCCGTGATTGCCAGTAAATCGGCAgcggcg > 1:330616/1‑68 (MQ=38)
gAAAATGCCCAAGATGTGAAGCAAATCACCCACTTAATGCCGTGATTGCCAGTAAATCGGCAgcggcg > 1:1524862/1‑68 (MQ=38)
gAAAATGCCCAAGATGTGAAGCAAATCACCCACTTAATGCCGTGATTGCCAGTAAATCGGCAgcggcg > 1:1579156/1‑68 (MQ=38)
gAAAATGCCCAAGATGTGAAGCAAATCACCCACTTAATGCCGTGATTGCCAGTAAATCGGCAgcggcg > 1:2133122/1‑68 (MQ=38)
gAAAATGCCCAAGATGTGAAGCAAATCACCCACTTAATGCCGTGATTGCCAGTAAATCGGCAgcggcg > 1:422988/1‑68 (MQ=38)
gAAAATGCCCAAGATGTGAAGCAAATCACCCACTTAATGCCGTGATTGCCAGTAAATCGGCAgcggcg > 1:2110040/1‑68 (MQ=38)
gAAAATGCCCAAGATGTGAAGCAAATCACCCACTTAATGCCGTGATTGCCAGTAAATCGGCAgcggcg > 1:1967790/1‑68 (MQ=38)
gAAAATGCCCAAGATGTGAAGCAAATCACCCACTTAATGCCGTGATTGCCAGTAAATCGGCAGcggc > 1:139477/1‑67 (MQ=38)
aaaaTGCCCGAGATGTGAAGCAAATCAACCACTTAATGCCGTGATTGCCAGTAAATCGACAACggcggc < 1:3366567/69‑1 (MQ=255)
aaaaTGCCCGAGATGTGAAGCAAATCAACCACTTAATGCCGTGATTGCCAGTAAATCGACAACggcggc < 1:2757265/69‑1 (MQ=255)
aaaaTGCCCGAGATGTGAAGCAAATCAACCACTTAATGCCGTGATTGCCAGTAAATCGACAACggcggc > 1:3323141/1‑69 (MQ=255)
aaaaTGCCCGAGATGTGAAGCAAATCAACCACTTAATGCCGTGATTGCCAGTAAATCGACAACggcggc < 1:2211711/69‑1 (MQ=255)
aaaaTGCCCGAGATGTGAAGCAAATCAACCACTTAATGCCGTGATTGCCAGTAAATCGACAACggcggc < 1:2198574/69‑1 (MQ=255)
aaaaTGCCCGAGATGTGAAGCAAATCAACCACTTAATGCCGTGATTGCCAGTAAATCGACAACggcggc < 1:1030041/69‑1 (MQ=255)
aaaaTGCCCGAGATGTGAAGCAAATCAACCACTTAATGCCGTGATTGCCAGTAAATCGACAACggcggc > 1:834821/1‑69 (MQ=255)
aaaaTGCCCGAGATGTGAAGCAAATCAACCACTTAATGCCGTGATTGCCAGTAAATCGACAACggcggc < 1:3370406/69‑1 (MQ=255)
aaaTGCCCGAGATGTGAAGCAAATCAACCACTTAATGCCGTGATTGCCAGTAAATCGACAACggcggc > 1:883383/1‑68 (MQ=255)
gaTGTGAAGCAAATCACCCACTTAATGCCGTGATTGCCAGTAAATCGGCAGCGGCGGCAACa < 1:2333701/62‑1 (MQ=255)
gaTGTGAAGCAAATCACCCACTTAATGCCGTGATTGCCAGTAAATCGGCAGCGGCGGCAACa < 1:111660/62‑1 (MQ=255)
gaTGTGAAGCAAATCACCCACTTAATGCCGTGATTGCCAGTAAATCGGCAGCGGCGGCAACa < 1:2888199/62‑1 (MQ=255)
gaTGTGAAGCAAATCACCCACTTAATGCCGTGATTGCCAGTAAATCGGCAGCGGCGGCAACa < 1:1174839/62‑1 (MQ=255)
gaTGTGAAGCAAATCACCCACTTAATGCCGTGATTGCCAGTAAATCGGCAGCGGCGGCAACa < 1:3302953/62‑1 (MQ=255)
gaTGTGAAGCAAATCACCCACTTAATGCCGTGATTGCCAGTAAATCGGCAGCGGCGGCAACa < 1:2378630/62‑1 (MQ=255)
gaTGTGAAGCAAATCACCCACTTAATGCCGTGATTGCCAGTAAATCGGCAGCGGCGGCAACa < 1:720533/62‑1 (MQ=255)
gaTGTGAAGCAAATCACCCACTTAATGCCGTGATTGCCAGTAAATCGGCAGCGGCGGCAACa < 1:333034/62‑1 (MQ=255)
gaTGTGAAGCAAATCACCCACTTAATGCCGTGATTGCCAGTAAATCGGCAGCGGCGGCAACa < 1:1707818/62‑1 (MQ=255)
tgAAGCAAATCAACCACTTAATGCCGTGATTGCCAGTAAATCGACAACGGCGGCAACAGGCGAAAGGtt > 1:1263073/1‑69 (MQ=255)
tgAAGCAAATCAACCACTTAATGCCGTGATTGCCAGTAAATCGACAACGGCGGCAACAGGCGAAAGGtt > 1:1122582/1‑69 (MQ=255)
tgAAGCAAATCAACCACTTAATGCCGTGATTGCCAGTAAATCGACAACGGCGGCAACAGGCGAAAGGtt > 1:346864/1‑69 (MQ=255)
tgAAGCAAATCAACCACTTAATGCCGTGATTGCCAGTAAATCGACAACGGCGGCAACAGGCGAAAGGtt > 1:3015227/1‑69 (MQ=255)
tgAAGCAAATCAACCACTTAATGCCGTGATTGCCAGTAAATCGACAACGGCGGCAACAGGCGAAAGGtt > 1:3131200/1‑69 (MQ=255)
aaGCAAATCAACCACTTAATGCCGTGATTGCCAGTAAATCGACAACGGCGGCAACAGGCGAAAGGTTaa > 1:992138/1‑69 (MQ=255)
aaGCAAATCAACCACTTAATGCCGTGATTGCCAGTAAATCGACAACGGCGGCAACAGGCGAAAGGTTaa > 1:216525/1‑69 (MQ=255)
gCAAATCAACCACTTAATGCCGTGATTGCCAGTAAATCGACAACGGCGGCAACAGGCGAAAGGTTAATc < 1:907481/69‑1 (MQ=255)
gCAAATCAACCACTTAATGCCGTGATTGCCAGTAAATCGACAACGGCGGCAACAGGCGAAAGGTTAATc < 1:1233972/69‑1 (MQ=255)
gCAAATCAACCACTTAATGCCGTGATTGCCAGTAAATCGACAACGGCGGCAACAGGCGAAAGGTTAATc < 1:2315303/69‑1 (MQ=255)
cAAATCAACCACTTAATGCCGTGATTGCCAGTAAATCGACAACGGCGGCAACAGGCGAAAGGTTAATc < 1:667084/68‑1 (MQ=255)
cAACCACTTAATGCCGTGATTGGCAGTAAATCGACAACggcggc > 1:3031554/1‑44 (MQ=255)
cAACCACTTAATGCCGTGATTGCCAGTAAATCGACAACggcggc > 1:1391333/1‑44 (MQ=255)
cAACCACTTAATGCCGTGATTGCCAGTAAATCGACAACggcggc > 1:1807393/1‑44 (MQ=255)
cAACCACTTAATGCCGTGATTGCCAGTAAATCGACAACggcggc > 1:1956778/1‑44 (MQ=255)
aCTTAATGCCGTGATTGCCAGTAAATCGGCAGCGGCGGCAACa < 1:3142784/43‑1 (MQ=38)
aaTGCCGTGATTGCCAGTAAATCGACAACGGCGGCa > 1:1848767/1‑36 (MQ=255)
aaTGCCGTGATTGCCAGTAAATCGACAACGGCGGCAACAGGCGAAAGGTTAATc > 1:376034/1‑54 (MQ=255)
aaTGCCGTGATTGCCAGTAAATCGACAACGGCGGCAACAGGCGAAAGGTTAATc < 1:2309473/54‑1 (MQ=255)
aaTGCCGTGATTGCCAGTAAATCGACAACGGCGGCAACAGGCGAAAGGTTAATc > 1:28010/1‑54 (MQ=255)
gTGATTGCCAGTAAATCGACAACGGCGGCAACAGGCGAAAGGTTAATCGACAGCACGATTTTTACACt < 1:204255/68‑1 (MQ=255)
gTGATTGCCAGTAAATCGACAACGGCGGCAACAGGCGAAAGGTTAATCGACAGCACGATTTTTACACt < 1:1695171/68‑1 (MQ=255)
gTGATTGCCAGTAAATCGACAACGGCGGCAACAGGCGAAAGGTTAATCGACAGCACGATTTTTACACt < 1:258551/68‑1 (MQ=255)
gTGATTGCCAGTAAATCGACAACGGCGGCAACAGGCGAAAGGTTAATCGACAGCACGATTTTTACACt < 1:2814266/68‑1 (MQ=255)
gTGATTGCCAGTAAATCGACAACGGCGGCAACAGGCGAAAGGTTAATCGACAGCACGATTTTTACACt < 1:1225501/68‑1 (MQ=255)
|
GAAAATGCCCGAGATGTGAAGCAAATCAACCACTTAATGCCGTGATTGCCAGTAAATCGACAACGGCGGCAACAGGCGAAAGGTTAATCGACAGCACGATTTTTACACT > minE/2331224‑2331332
|
| 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
