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 |
1,956,137 |
C→T |
42.4% |
intergenic (+80/+309) |
ygfA → / ← serA |
predicted ligase/D‑3‑phosphoglycerate dehydrogenase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,956,137 | 0 | C | T | 42.4%
| 47.4
/ 78.9
| 106 | intergenic (+80/+309) | ygfA/serA | predicted ligase/D‑3‑phosphoglycerate dehydrogenase |
| Reads supporting (aligned to +/- strand): ref base C (33/28); new base T (32/13); total (65/41) |
| Fisher's exact test for biased strand distribution p-value = 1.06e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.37e-01 |
Only 100 of 128 total aligned reads displayed.
CGCATCGCCCTGATTGACATCGTTGATTCTTTGACCTAATTTAGTGAGTAAGGGTAAGGGAGGATTGCTCCTCCCCTGAGACTGACTGTTAATAAGCGCTGAAACTTATGAGTAACAGTACAATCAGTATG > minE/1956070‑1956200
|
cGCATCGCCCTGATTGACATCGTTGATTCTTTGACCTAATTTAGTGAGTAAGGGTAAGGGAGGATTGct > 1:72019/1‑69 (MQ=255)
cGCATCGCCCTGATTGACATCGTTGATTCTTTGACCTAATTTAGTGAGTAAGGGTAAGGGAGGATTGct > 1:1392063/1‑69 (MQ=255)
gCATCGCCCTGATTGACATCGTTGATTCTTTGACCTAATTTAGTGAGTAAGGGTAAGGGAGGATTGctc < 1:527096/69‑1 (MQ=255)
gCATCGCCCTGATTGACATCGTTGATTCTTTGACCTAATTTAGTGAGTAAGGGTAAGGGAGGATTGctc < 1:2425939/69‑1 (MQ=255)
gCATCGCCCTGATTGACATCGTTGATTCTTTGACCTAATTTAGTGAGTAAGGGTAAGGGAGGATTGctc < 1:235653/69‑1 (MQ=255)
gCATCGCCCTGATTGACATCGTTGATTCTTTGACCTAATTTAGTGAGTAAGGGTAAGGGAGGATTGctc < 1:2317728/69‑1 (MQ=255)
gCATCGCCCTGATTGACATCGTTGATTCTTTGACCTAATTTAGTGAGTAAGGGTAAGGGAGGATTGctc < 1:2204266/69‑1 (MQ=255)
gCATCGCCCTGATTGACATCGTTGATTCTTTGACCTAATTTAGTGAGTAAGGGTAAGGGAGGATTGctc < 1:2151172/69‑1 (MQ=255)
gCATCGCCCTGATTGACATCGTTGATTCTTTGACCTAATTTAGTGAGTAAGGGTAAGGGAGGATTGctc < 1:2034175/69‑1 (MQ=255)
gCATCGCCCTGATTGACATCGTTGATTCTTTGACCTAATTTAGTGAGTAAGGGTAAGGGAGGATTGctc < 1:1892751/69‑1 (MQ=255)
gCATCGCCCTGATTGACATCGTTGATTCTTTGACCTAATTTAGTGAGTAAGGGTAAGGGAGGATTGctc < 1:3095605/69‑1 (MQ=255)
gCATCGCCCTGATTGACATCGTTGATTCTTTGACCTAATTTAGTGAGTAAGGGTAAGGGAGGATTGctc < 1:1593476/69‑1 (MQ=255)
gCATCGCCCTGATTGACATCGTTGATTCTTTGACCTAATTTAGTGAGTAAGGGTAAGGGAGGATTGctc < 1:3343930/69‑1 (MQ=255)
gCATCGCCCTGATTGACATCGTTGATTCTTTGACCTAATTTAGTGAGTAAGGGTAAGGGAGGATTGctc < 1:955846/69‑1 (MQ=255)
gCATCGCCCTGATTGACATCGTTGATTCTTTGACCTAATTTAGTGAGTAAGGGTAAGGGAGGATTGctc < 1:1129459/69‑1 (MQ=255)
aTCGCCCTGATTGACATCGTTGATTCTTTGACCTAATTTAGTGAGTAAGGGTAAGGGAGGATTGctcct < 1:1855479/69‑1 (MQ=255)
aTCGCCCTGATTGACATCGTTGATTCTTTGACCTAATTTAGTGAGTAAGGGTAAGGGAGGATTGctcct < 1:767772/69‑1 (MQ=255)
aTCGCCCTGATTGACATCGTTGATTCTTTGACCTAATTTAGTGAGTAAGGGTAAGGGAGGATTGctcct < 1:2806213/69‑1 (MQ=255)
gATTGACATCGTTGATTCTTTGCCCTAATTTAGTGAGTAAGGGTAAGGGAGGATTGCTCCTCCCCTgag > 1:1979262/1‑69 (MQ=255)
gATTGACATCGTTGATTCTTTGACCTAATTTAGTGAGTAAGGGTAAGGGAGGATTGCTCCTCCCCTtag > 1:2395242/1‑69 (MQ=255)
gATTGACATCGTTGATTCTTTGACCTAATTTAGTGAGTAAGGGTAAGGGAGGATTGCTCCTCCCCTgag > 1:31703/1‑69 (MQ=255)
gATTGACATCGTTGATTCTTTGACCTAATTTAGTGAGTAAGGGTAAGGGAGGATTGCTCCTCCCCTgag > 1:3363106/1‑69 (MQ=255)
gATTGACATCGTTGATTCTTTGACCTAATTTAGTGAGTAAGGGTAAGGGAGGATTGCTCCTCCCCTgag > 1:2293049/1‑69 (MQ=255)
gATTGACATCGTTGATTCTTTGACCTAATTTAGTGAGTAAGGGTAAGGGAGGATTGCTCCTCCCCTgag > 1:2328455/1‑69 (MQ=255)
gATTGACATCGTTGATTCTTTGACCTAATTTAGTGAGTAAGGGTAAGGGAGGATTGCTCCTCCCCTgag > 1:2110176/1‑69 (MQ=255)
gATTGACATCGTTGATTCTTTGACCTAATTTAGTGAGTAAGGGTAAGGGAGGATTGCTCCTCCCCTgag > 1:255975/1‑69 (MQ=255)
gATTGACATCGTTGATTCTTTGACCTAATTTAGTGAGTAAGGGTAAGGGAGGATTGCTCCTCCCCTgag > 1:1926654/1‑69 (MQ=255)
gATTGACATCGTTGATTCTTTGACCTAATTTAGTGAGTAAGGGTAAGGGAGGATTGCTCCTCCCCTgag < 1:1176102/69‑1 (MQ=255)
gATTGACATCGTTGATTCTTTGACCTAATTTAGTGAGTAAGGGTAAGGGAGGATTGCTCCTCCCCTga > 1:3381536/1‑68 (MQ=255)
tGACATCGTTGATTCTTTGACCTAATTTAGTGAGTAAGGGTAAGGGAGGATTGCTCCTCCCCTGAgact > 1:602477/1‑69 (MQ=255)
tGACATCGTTGATTCTTTGACCTAATTTAGTGAGTAAGGGTAAGGGAGGATTGCTCCTCCCCTGAgact > 1:1737949/1‑69 (MQ=255)
tGACATCGTTGATTCTTTGACCTAATTTAGTGAGTAAGGGTAAGGGAGGATTGCTCCTCCCCTGAgact > 1:461079/1‑69 (MQ=255)
tGACATCGTTGATTCTTTGACCTAATTTAGTGAGTAAGGGTAAGGGAGGATTGCTCCTCCCCTGAgact > 1:2209050/1‑69 (MQ=255)
cATCGTTGATTCTTTGACCTAATTTAGTGAGTAAGGGTAAGGGAGGATTGCTCCTCCCCTGAgactga < 1:139158/68‑1 (MQ=255)
cATCGTTGATTCTTTGACCTAATTTAGTGAGTAAGGGTAAGGGAGGATTGCTCCTCCCCTGAgactga < 1:2319020/68‑1 (MQ=255)
cATCGTTGATTCTTTGACCTAATTTAGTGAGTAAGGGTAAGGGAGGATTGCTCCTCCCCTGAgactga < 1:845511/68‑1 (MQ=255)
cATCGTTGATTCTTTGACCTAATTTAGTGAGTAAGGGTAAGGGAGGATTGCTCCTCCCCTGAgactga < 1:1373058/68‑1 (MQ=255)
cGTTGATTCTTTGACCTAATTTAGTGAGTAAGGGTAAGGGAGGATTGCTCCTCCCCTGAGACTGACTGt < 1:919930/69‑1 (MQ=255)
cGTTGATTCTTTGACCTAATTTAGTGAGTAAGGGTAAGGGAGGATTGCTCCTCCCCTGAGACTGACTGt < 1:461285/69‑1 (MQ=255)
cGTTGATTCTTTGACCTAATTTAGTGAGTAAGGGTAAGGGAGGATTGCTCCTCCCCTGAGACTGACTGt < 1:2910423/69‑1 (MQ=255)
tGACCTAATTTAGTGAGTAAGGGTAAGGGAGGATTGCTCCTCCCCTGAGACTGACTGt < 1:979755/58‑1 (MQ=255)
aaTTTAGTGAGTAAGGGTAAGGGAGGATTGTTCCTCCCCTGTGACTGACTGTTAATAAGCTGGGAAACt < 1:636111/69‑1 (MQ=21)
aaTTTAGTGAGTAAGGGTAAGGGAGGATTGTTCCTCCCCTGTGACTGACTGTTAATAAGCTGGGAAACt < 1:2988063/69‑1 (MQ=21)
aaTTTAGTGAGTAAGGGTAAGGGAGGATTGTTCCTCCCCTGTGACTGACTGTTAATAAGCTGGGAAACt < 1:1947979/69‑1 (MQ=21)
aaTTTAGTGAGTAAGGGTAAGGGAGGATTGTTCCTCCCCTGTGACTGACTGTTAATAAGCTGGGAAACt < 1:3041282/69‑1 (MQ=21)
aaTTTAGTGAGTAAGGGTAAGGGAGGATTGTTCCTCCCCTGTGACTGACTGTTAATAAGCTGGGAAACt < 1:1263475/69‑1 (MQ=21)
aaTTTAGTGAGTAAGGGTAAGGGAGGATTGTTCCTCCCCTGTGACTGACTGTTAATAAGCTGGGAAACt < 1:3154489/69‑1 (MQ=21)
aaTTTAGTGAGTAAGGGTAAGGGAGGATTGTTCCTCCCCTGTGACTGACTGTTAATAAGCTGGGAAACt < 1:2732735/69‑1 (MQ=21)
aaTTTAGTGAGTAAGGGTAAGGGAGGATTGTTCCTCCCCTGTGACTGACTGTTAATAAGCTGGGAAACt < 1:753942/69‑1 (MQ=21)
aaTTTAGTGAGTAAGGGTAAGGGAGGATTGTTCCTCCCCTGTGACTGACTGTTAATAAGCTGGGAAACt < 1:1471151/69‑1 (MQ=21)
aaTTTAGTGAGTAAGGGTAAGGGAGGATTGCTCCTCCCCTGAGACTGACTGTTAATAAGCGCTGAAACt < 1:918779/69‑1 (MQ=255)
ttAGTGAGTAAGGGTAAGGGAGGATTGTTCCTCCCCTGTGACTGACTGTtaataa > 1:224935/1‑55 (MQ=39)
ttAGTGAGTAAGGGTAAGGGAGGATTGTTCCTCCCCTGTGACTGACTGTTAATAAGCTGGGAAACtt > 1:2844873/1‑67 (MQ=21)
ttAGTGAGTAAGGGTAAGGGAGGATTGTTCCTCCCCTGTGACTGACTGTTAATAAGCTGGGAAACtt > 1:2854725/1‑67 (MQ=21)
ttAGTGAGTAAGGGTAAGGGAGGATTGTTCCTCCCCTGTGACTGACTGTTAATAAGCTGGGAAACtt > 1:64374/1‑67 (MQ=21)
ttAGTGAGTAAGGGTAAGGGAGGATTGTTCCTCCCCTGTGACTGACTGTTAATAAGCTGGGAAACtt > 1:528746/1‑67 (MQ=21)
ttAGTGAGTAAGGGTAAGGGAGGATTGTTCCTCCCCTGTGACTGACTGTTAATAAGCTGGGAAACtt > 1:256654/1‑67 (MQ=21)
ttAGTGAGTAAGGGTAAGGGAGGATTGTTCCTCCCCTGTGACTGACTGTTAATAAGCTGGGAAACtt > 1:112858/1‑67 (MQ=21)
ttAGTGAGTAAGGGTAAGGGAGGATTGTTCCTCCCCTGTGACTGACTGTTAATAAGCTGGGAAACtt > 1:1211094/1‑67 (MQ=21)
ttAGTGAGTAAGGGTAAGGGAGGATTGTTCCTCCCCTGTGACTGACTGTTAATAAGCTGGGAAACtt > 1:124112/1‑67 (MQ=21)
ttAGTGAGTAAGGGTAAGGGAGGATTGTTCCTCCCCTGTGACTGACTGTTAATAAGCTGGGAAACtt > 1:1271572/1‑67 (MQ=21)
ttAGTGAGTAAGGGTAAGGGAGGATTGTTCCTCCCCTGTGACTGACTGTTAATAAGCTGGGAAACtt > 1:152641/1‑67 (MQ=21)
ttAGTGAGTAAGGGTAAGGGAGGATTGTTCCTCCCCTGTGACTGACTGTTAATAAGCTGGGAAACtt > 1:1812320/1‑67 (MQ=21)
ttAGTGAGTAAGGGTAAGGGAGGATTGTTCCTCCCCTGTGACTGACTGTTAATAAGCTGGGAAACtt > 1:850626/1‑67 (MQ=21)
ttAGTGAGTAAGGGTAAGGGAGGATTGTTCCTCCCCTGTGACTGACTGTTAATAAGCTGGGAAACtt > 1:2392232/1‑67 (MQ=21)
ttAGTGAGTAAGGGTAAGGGAGGATTGTTCCTCCCCTGTGACTGACTGTTAATAAGCTGGGAAACtt > 1:2556405/1‑67 (MQ=21)
ttAGTGAGTAAGGGTAAGGGAGGATTGTTCCTCCCCTGTGACTGACTGTTAATAAGCTGGGAAACtt > 1:2453531/1‑67 (MQ=21)
ttAGTGAGTAAGGGTAAGGGAGGATTGTTCCTCCCCTGTGACTGACTGTTAATAAGCTGGGAAACtt > 1:2532201/1‑67 (MQ=21)
ttAGTGAGTAAGGGTAAGGGAGGATTGTTCCTCCCCTGTGACTGACTGTTAATAAGCTCGGAAACtt > 1:982191/1‑67 (MQ=25)
ttAGTGAGTAAGGGTAAGGGAGGATTGCTCCTCCCCTGAGACTGACTGTTAATAAGCGCTGAAACtt < 1:2223254/67‑1 (MQ=255)
ttAGTGAGTAAGGGTAAGGGAGGATTGCTCCTCCCCTGAGACTGACTGTTAATAAGCGCTGAAACtt < 1:539630/67‑1 (MQ=255)
ttAGTGAGTAAGGGTAAGGGAGGATTGCTCCTCCCCTGAGACTGACTGTTAATAAGCGCTGAAACtt < 1:1110299/67‑1 (MQ=255)
ttAGTGAGTAAGGGTAAGGCAGGATTGTTCCTCCCCTGTgactg > 1:1389105/1‑44 (MQ=255)
gAGTAAGGGTAAGGGAGGATTGCTCCTCCCCTGAGACTGACTGTTAATAAGCGCTGAAACTTATGAGt < 1:3259641/68‑1 (MQ=255)
gAGTAAGGGTAAGGGAGGATTGCTCCTCCCCTGAGACTGACTGTTAATAAGCGCTGAAACTTATGAGt < 1:659361/68‑1 (MQ=255)
gAGTAAGGGTAAGGGAGGATTGCTCCTCCCCTGAGACTGACTGTTAATAAGCGCTGAAACTTATGAGt < 1:469255/68‑1 (MQ=255)
gAGTAAGGGTAAGGGAGGATTGCTCCTCCCCTGAGACTGACTGTTAATAAGCGCTGAAACTTATGAGt < 1:2118400/68‑1 (MQ=255)
aGTAAGGGTAAGGGAGGATTGCTCCTCCCCTGAGACTGACTGTTAATAAGCGCTGAAACTTATGAGt < 1:882660/67‑1 (MQ=255)
ggaggaTTGCTCCTCCCCTGAGACTGACTGTTAATAAGCGCTGAAACTTATGAGTAACAGTACAATCAg > 1:9255/1‑69 (MQ=255)
ggaggaTTGCTCCTCCCCTGAGACTGACTGTTAATAAGCGCTGAAACTTATGAGTAACAGTACAATCAg > 1:534675/1‑69 (MQ=255)
ggaggaTTGCTCCTCCCCTGAGACTGACTGTTAATAAGCGCTGAAACTTATGAGTAACAGTACAATCAg > 1:2527023/1‑69 (MQ=255)
ggaggaTTGCTCCTCCCCTGAGACTGACTGTTAATAAGCGCTGAAACTTATGAGTAACAGTACAATCAg > 1:397651/1‑69 (MQ=255)
ggaggaTTGCTCCTCCCCTGAGACTGACTGTTAATAAGCGCTGAAACTTATGAGTAACAGTACAATCAg > 1:3024078/1‑69 (MQ=255)
ggaggaTTGCTCCTCCCCTGAGACTGACTGTTAATAAGCGCTGAAACTTATGAGTAACAGTACAATCAg > 1:1226073/1‑69 (MQ=255)
ggaggaTTGCTCCTCCCCTGAGACTGACTGTTAATAAGCGCTGAAACTTATGAGTAACAGTACAATCAg > 1:1474023/1‑69 (MQ=255)
ggaggaTTGCTCCTCCCCTGAGACTGACTGTTAATAAGCGCTGAAACTTATGAGTAACAGTACAATCAg > 1:2387928/1‑69 (MQ=255)
aggaTTGTTCCTCCCCTGTGACTGACTGTTAATAAGCTGGGAAACTTATGAGTAACAGTACAATCAGt > 1:3367122/1‑68 (MQ=18)
aggaTTGTTCCTCCCCTGTGACTGACTGTTAATAAGCTGGGAAACTTATGAGTAACAGTACAATCAGt > 1:1220807/1‑68 (MQ=18)
aggaTTGTTCCTCCCCTGTGACTGACTGTTAATAAGCTGGGAAACTTATGAGTAACAGTACAATCAGt > 1:1414714/1‑68 (MQ=18)
aggaTTGTTCCTCCCCTGTGACTGACTGTTAATAAGCTGGGAAACTTATGAGTAACAGTACAATCAGt > 1:910071/1‑68 (MQ=18)
aggaTTGTTCCTCCCCTGTGACTGACTGTTAATAAGCTGGGAAACTTATGAGTAACAGTACAATCAGt > 1:1868031/1‑68 (MQ=18)
aggaTTGTTCCTCCCCTGTGACTGACTGTTAATAAGCTGGGAAACTTATGAGTAACAGTACAATCAGt > 1:2291836/1‑68 (MQ=18)
aggaTTGTTCCTCCCCTGTGACTGACTGTTAATAAGCTGGGAAACTTATGAGTAACAGTACAATCAGt > 1:2454470/1‑68 (MQ=18)
aggaTTGTTCCTCCCCTGTGACTGACTGTTAATAAGCTGGGAAACTTATGAGTAACAGTACAATCAGt > 1:2965056/1‑68 (MQ=18)
gaTTGCTCCTCCCCTGAGACTGACTGTTAATAAGCGCTGAAACTTATGAGTAACAGTACAATCAGTatg < 1:2941549/69‑1 (MQ=255)
gaTTGCTCCTCCCCTGAGACTGACTGTTAATAAGCGCTGAAACTTATGAGTAACAGTACAATCAGTatg < 1:1123261/69‑1 (MQ=255)
gCTCCTCCCCTGAGACTGACTGTTAATAAGCGCTGAAACTTATGAGTAACAGTAc > 1:1801411/1‑55 (MQ=255)
gCTCCTCCCCTGAGACTGACTGTTAATAAGCGCTGAAACTTATGAGTAACAGTAc > 1:1561351/1‑55 (MQ=255)
gCTCCTCCCCTGAGACTGACTGTTAATAAGCGCTGAAACTTATGAGTAACAGTAc > 1:2641591/1‑55 (MQ=255)
gCTCCTCCCCTGAGACTGACTGTTAATAAGCGCTGAAACTTATGAGTAACAGTAc > 1:2676539/1‑55 (MQ=255)
|
CGCATCGCCCTGATTGACATCGTTGATTCTTTGACCTAATTTAGTGAGTAAGGGTAAGGGAGGATTGCTCCTCCCCTGAGACTGACTGTTAATAAGCGCTGAAACTTATGAGTAACAGTACAATCAGTATG > minE/1956070‑1956200
|
| 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
