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 |
|
A6 F28 I3 R2
|
24 |
47.7 |
2431847 |
96.1% |
2337004 |
60.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
minE |
942,255 |
C→T |
R296K (AGG→AAG) |
ddpF ← |
D‑Ala‑D‑Ala transporter subunit |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 942,255 | 0 | C | T | 93.0%
| 124.1
/ 1.6
| 43 | R296K (AGG→AAG) | ddpF | D‑Ala‑D‑Ala transporter subunit |
| Reads supporting (aligned to +/- strand): ref base C (1/2); new base T (21/19); total (22/21) |
| Fisher's exact test for biased strand distribution p-value = 6.07e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.82e-01 |
GAATGCCTGATGCGTTGTTAGCATCTCTACAGCGCCCGCCAGCACCGGAGCTCACGTCCGTCCTCCCTTATTGCTAATGATTGCCGGACTTCACATCCGTGGGTTGCCAGCGGGCAACGTTCGTAGAAAAAAC > minE/942189‑942321
|
gAATGCCTGATGCGTTGTTAGCATCTCTACAGCGCCCGCCAGCACCGGAGCTCACGTCCGTCCTCCTTTAt > 1:2337385/1‑71 (MQ=255)
aaTGCCTGATGCGTTGTTAGCATCTCTACAGCGCCCGCCAGCACCGGAGCTCACGTCCGTCCTCCTTTAtt > 1:545833/1‑71 (MQ=255)
ccTGATGCGTTGTTAGCATCTCTACAGCGCCCGCCAGCACCGGAGCTGACGTCCGTCCTCCTTTATTGCTa < 1:208832/71‑1 (MQ=255)
cTGATGCGTTGTTAGCATCTCTACAGCGCCCGCCAGCACCGGAGCTCACGTCCGTCCTCCTTTATTGCTaa > 1:506914/1‑71 (MQ=255)
gATGCGTTGTTAGCATCTCTACAGCGCCCGCCAGCACCGGAGCTCACGTCCGTCCTCCTTTATTGCTAAt > 1:957568/1‑70 (MQ=255)
gATGCGTTGTTAGCATCTCTACAGCGCCCGCCAGCACCGGAGCTCACGTCCGTCCTCCCTTa < 1:272043/62‑1 (MQ=255)
cGTTGTTAGCATCTCTACAGCGCCCGCCAGCACCGGAGCTCACGTCCGTCCTCCTTTAt > 1:2393252/1‑59 (MQ=255)
cGTTGTTAGCATCTCTACAGCGCCCGCCAGCACCGGAGCTCACGTCCGTCCTCCCTTATTGCTAATGATTg > 1:1086682/1‑71 (MQ=255)
gttgttAGCATCTCTACAGCGCCCGCCAGCACCGGAGCTCACGTCCGTCCTCCTTTATTGCTAATGATTGc > 1:101278/1‑71 (MQ=255)
gttAGCATCTCTACAGCGCCCGCCAGCACCGGAGCTCACGTCCGTCCTCCTTTATTGCTAATGa > 1:2238130/1‑64 (MQ=255)
gCATCTCTACAGCGCCCGCCAGCACCGGAGCTCACGTCCGTCCTCCCTTATTGCTAATGATTGCCGGACtt < 1:2373032/71‑1 (MQ=255)
tctcTACAGCGCCCGCCAGCACCGGAGCTCACGTCCGTCCTCCTTTATTGCTAATGATTGCCGGACTTca > 1:1600572/1‑70 (MQ=255)
tctACAGCGCCCGCCAGCACCGGAGCTCACGTCCGTCCTCCTTTa > 1:536573/1‑45 (MQ=255)
tctACAGCGCCCGCCAGCACCGGAGCTCACGTCCGTCCTCCTTTATTGCTAATGATTGCCGGACTTca < 1:1632881/68‑1 (MQ=255)
tctACAGCGCCCGCCAGCACCGGAGCTCACGTCCGTCCTCCTTTATTGCTAATGATTGCCGGACTTCACAt > 1:380184/1‑71 (MQ=255)
aGCGCCCGCCAGCACCGGAGCTCACGTCCGTCCTCCTTTATTGCt < 1:1740214/45‑1 (MQ=255)
cccgccAGCACCGGAGCTCACGTCCGTCCTCCTTTATTGCTAATGATTGCCGGACTTCACATcc > 1:1941646/1‑64 (MQ=255)
gccAGCACCGGAGCTCACGTCCGTCCTCCTTTATTGCTAATGATTGCCGGACtt < 1:2168391/54‑1 (MQ=255)
gccAGCACCGGAGCTCACGTCCGTCCTCCTTTATTGCTAATGATTGCCGGACtt < 1:1416977/54‑1 (MQ=255)
gccAGCACCGGAGCTCACGTCCGTCCTCCTTTATTGCTAATGATTGCCGGACTTCACATCCGTGGGTTGc > 1:650864/1‑70 (MQ=255)
ccAGCACCGGAGCTCACGTCCGTCCTCCTTTATTGCTAATGATTGCCGGa < 1:1171938/50‑1 (MQ=255)
ccAGCACCGGAGCTCACGTCCGTCCTCCTTTATTGCTAATGATTGCCGGACTTCACATCCGTGGGTTGc > 1:1049504/1‑69 (MQ=255)
cAGCACCGGAGCTCACGTCCGTCCTCCTTTATTGCTAATGATTGCCGGACTTCACATCCGTGGGTTGCCAg < 1:332275/71‑1 (MQ=255)
cAGCACCGGAGCTCACGTCCGTCCTCCTTTATTGCTAATGATTGCCGGACTTCACATCCGTGGGTTGCCAg < 1:605279/71‑1 (MQ=255)
cAGCACCGGAGCTCACGTCCGTCCTCCTTTATTGCTAATGATTGCCGGACTTCACATCCGTGGGTTGCCAg < 1:2186043/71‑1 (MQ=255)
cACCGGAGCTCACGTCCGTCCTCCTTTATTGCTAATGATTGCCGGACTTCACATCCGTGGGTTGCCAGCgg > 1:2068053/1‑71 (MQ=255)
ccGGAGCTCACGTCCGTCCTCCTTTATTGCTAATGATTGCCGGACTTCACATCCGTGGGTTGCCAGCGGGc < 1:266581/71‑1 (MQ=255)
cGGAGCTCACGTCCGTCCTCCTTTATTGCTAATGATTGCCGGACTTCACATCCGTGGGTTGCCAGCGGGc < 1:1212654/70‑1 (MQ=255)
ggAGCTCACGTCCGTGCTCCTTTATTGCTAATGATTGCCGGACTTCACATCCGTGGGTTGCCCGCGGGCa > 1:1093260/1‑70 (MQ=255)
ggAGCTCACGTCCGTCCTCCTTTATTGCTAATGAt > 1:1724370/1‑35 (MQ=255)
aGCTCACGTCCGTCCTCCTTTATTGCTAATGATTGCCGGACTTCACATCCGTGGGTTGCCAGCGGGCAACg < 1:552609/71‑1 (MQ=255)
aGCTCACGTCCGTCCTCCTTTATTGCTAATGATTGCCGGACTTCACATCCGTGGGTTGCCAGCGGGCAACg < 1:2008761/71‑1 (MQ=255)
gCTCACGTCCGTCCTCCTTTATTGCTAATGATTGCCGGACTTCACATCCGTGGGTTGCCAGCGGGCAACGt < 1:728528/71‑1 (MQ=255)
tCACGTCCGTCCTCCTTTATTGCTAATGATTGCCGGACTTCACATCCGTGGGTTGCCAGc < 1:938392/60‑1 (MQ=255)
cACGTCCGTCCTCCTTTATTGCTAATGATTGCCGGACTTCACATCCGTGGGTTGCCAGCGGGCAACGTTCg > 1:1712626/1‑71 (MQ=255)
cgtccgtcCTCCTTTATTGCTAATGATTGCCGGACTTCACATCCGTGGGTTGCCAGCGGGCAACGTTCg > 1:515556/1‑69 (MQ=255)
cgtccgtcCTCCTTTATTGCTAATGATTGCCGGACTTCACATCCGTGGGTTGCCAGCGGGCAACGTTCg > 1:2381104/1‑69 (MQ=255)
gtccgtccTCCTTTATTGCTAATGATTGCCGGACTTCAAATCCgtgtgt > 1:186149/1‑49 (MQ=255)
ccgtccTCCTTTATTGCTAATGATTGCCGTACTTCACATcc < 1:32664/41‑1 (MQ=38)
ccgtccTCCTTTATTGCTAATGATTGCCGGACTTCACATcc < 1:376230/41‑1 (MQ=255)
cgtccTCCTTTATTGCTAATGATTGCCGGACTTCACATCCGTGGGTTGCCAGCGGGCAACGTTCGTAGaaa < 1:633242/71‑1 (MQ=255)
ctccTTTATTGCTAATGATTGCCGGACTTCACATCCGTGGGTTGCCAGCGGGCAACGTTCGTAGaaaaaa > 1:528390/1‑70 (MQ=255)
ctccTTTATTGCTAATGATTGCCGGACTTCACATCCGTGGGTTGCCAGCGGGCAACGTTCGTAGAAAAAAc < 1:828361/71‑1 (MQ=255)
|
GAATGCCTGATGCGTTGTTAGCATCTCTACAGCGCCCGCCAGCACCGGAGCTCACGTCCGTCCTCCCTTATTGCTAATGATTGCCGGACTTCACATCCGTGGGTTGCCAGCGGGCAACGTTCGTAGAAAAAAC > minE/942189‑942321
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
