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 F1 I0 R1
|
2892 |
75.3 |
5698161 |
66.1% |
3766484 |
59.5 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
1,467,882 |
Δ1 bp |
28.6% |
intergenic (+41/+87) |
ubiG → / ← yfaL |
bifunctional 3‑demethylubiquinone‑9 3‑methyltransferase and 2‑octaprenyl‑6‑hydroxy phenol methylase/adhesin |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,467,882 | 0 | C | . | 28.6%
| 112.9
/ 43.5
| 49 | intergenic (+41/+87) | ubiG/yfaL | bifunctional 3‑demethylubiquinone‑9 3‑methyltransferase and 2‑octaprenyl‑6‑hydroxy phenol methylase/adhesin |
| Reads supporting (aligned to +/- strand): ref base C (18/16); new base . (7/7); total (26/23) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.57e-01 |
AACTATATGCTGCACACGCAGAATAAGTGAGGTTGATGTTTGGCCGCGCCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACAAAT‑‑‑‑GCTCC‑‑CCGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGC > minE/1467812‑1467946
|
aaCTATATGCTGCACACGCAGAATAAGTGAGGTTGATGTTTGGCCGCGCCAATGCCTGATGCGACGCTTGc > 1:1855911/1‑71 (MQ=255)
tatGCTGCACACGCAGAATAAGTGAGGTTGATGTTTGGCCGCGCCAATGCCTGATGCGACGCTTGCcgc < 1:1572228/69‑1 (MQ=255)
tatGCTGCACACGCAGAATAAGTGAGGTTGATGTTTGGCCGCGCCAATGCCTGATGCGACGCTTGCCGCGt > 1:3275972/1‑71 (MQ=255)
tgctgcACACGCAGAATAAGTGAGGTTGATGTTTGGCCGCGCCAATGCCTGATGCGACGCTTGCCGCGTCt < 1:4200223/71‑1 (MQ=255)
acacGCAGAATAAGTGAGGTTGATGTTTGGCCGCGCCAATTCCTGATGCGACGCTTGCCGCGTCTTATCAg < 1:1863481/71‑1 (MQ=255)
acacGCAGAATAAGTGAGGTTGATGTTTGGCCGCGCCAATGCCTGATGCGACGCTTGCCGCGTCTTAt > 1:4636442/1‑68 (MQ=255)
acacGCAGAATAAGTGAGGTTGATGTTTGGCCGCGCCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAg < 1:2071342/71‑1 (MQ=255)
gAATAAGTGAGGTTGATGTTTGGCCGCGCCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTAc > 1:72546/1‑70 (MQ=255)
aTAAGTGAGGTTGATGTTTGGCCGCGCCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACaa > 1:3396830/1‑70 (MQ=255)
tAAGTGAGGTTGATGTTTGGCCGCGCCAATGCCTGATGCGACGCTTGCCGCGTCTTa < 1:135197/57‑1 (MQ=255)
tAAGTGAGGTTGATGTTTGGCCGCGCCAATGCCTGATGCGACGCTTGCCGCGTCTTa < 1:2119619/57‑1 (MQ=255)
gTGAGGTTGATGTTTGGCCGCGCCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACAAAT‑‑‑‑GCt < 1:1940781/71‑1 (MQ=255)
gAGGTTGATGTTTGGCCGCGCCAATGCCTGATGCGACGCTTGCCGCGTCTTAt > 1:1451398/1‑53 (MQ=255)
gTTGATGTTTGGCCGCGCCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACAAAT‑‑‑‑GCTcc‑‑cc < 1:843942/70‑1 (MQ=255)
tGATGTTTGGCCGCGCCAATGCCTGATGCGACGCTTGGCGCGTCt > 1:2197221/1‑45 (MQ=255)
tGATGTTTGGCCGCGCCAATGCCTGATGCGACGCTTGCCGCGTCt > 1:1664298/1‑45 (MQ=255)
tGATGTTTGGCCGCGCCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACAAAT‑‑‑‑GCTCC‑‑CCGt > 1:2447871/1‑70 (MQ=255)
tGTTTGGCCGCGCCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACAAAT‑‑‑‑GCTCC‑‑CCGTAGGc < 1:2023096/71‑1 (MQ=255)
tGTTTGGCCGCGCCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACAAAT‑‑‑‑GCTCC‑‑CCGTAGGc > 1:3144410/1‑71 (MQ=255)
tGGCCGCGCCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACAAAT‑‑‑‑GCTCC‑‑CCGTAGGCCGGa > 1:3473915/1‑71 (MQ=255)
cgcgCCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACAAAT‑‑‑‑GCTCC‑‑CCGTAGGCCGGATAAg < 1:468940/71‑1 (MQ=255)
cgcgCCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACAAAT‑‑‑‑GCTCC‑‑CCGTAGGCCGGATAAg < 1:3733454/71‑1 (MQ=255)
cgcCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACAAAT‑‑‑‑GCTCC‑‑CCGTAGGCCGGATAAGGc < 1:150269/71‑1 (MQ=255)
ccAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACAAAT‑‑‑‑GCTCC‑‑CCGTAGGCCGGATAAGGCGt > 1:5322616/1‑71 (MQ=255)
ccAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACAAAT‑‑‑‑GCTCC‑‑CCGTAGGCCGGATAAGGCGt > 1:1534616/1‑71 (MQ=255)
cAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACAAAT‑‑‑‑GCTCC‑‑CCGTAGGCCGGATAAGGCGtt < 1:1838129/71‑1 (MQ=255)
cAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACAAAT‑‑‑‑GCTCC‑‑CCGTAGGCCGGATAAGGCGtt < 1:647468/71‑1 (MQ=255)
aaTGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACAAAT‑‑‑‑GCTCC‑‑CCGTAGGCCGGATAAGGCGtt > 1:125423/1‑70 (MQ=255)
ccTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACAAAT‑‑‑‑GCTCC‑‑CCGt > 1:5569488/1‑49 (MQ=255)
tGATGCGACGCTTGCCGCGTCTTATCAGGCCTACAAAT‑‑‑‑GCTCC‑‑CCg < 1:2097987/46‑1 (MQ=255)
aTGCGACGCTTGCCGCGTCTTATCAGGCCTACAAAT‑‑‑‑GCTCC‑‑CCGTAGGCCGGATAAGGCGTTTACGCCGCa > 1:2453231/1‑71 (MQ=255)
aTGCGACGCTTG‑CGCGTCTTATCAGGCCTACAAATTCCCGCACCCTCCGTAGGCCGGATAAGGCGTTTAcg < 1:5374231/71‑1 (MQ=0)
aTGCGACGCTTG‑CGCGTCTTATCAGGCCTACAAATTCCCGCACCCTCCGTAGGCCGGATAAGGCGTTTAcg > 1:4890722/1‑71 (MQ=0)
aTGCGACGCTTG‑CGCGTCTTATCAGGCCTACAAATTCCCGCACCCTCCGTAGGCCGGATAAGGCGTTTAcg > 1:4963371/1‑71 (MQ=0)
aTGCGACGCTTG‑CGCGTCTTATCAGGCCTACAAATTCCCGCACCCTCCGTAGGCCGGATAAGGCGTTTAc < 1:4719260/70‑1 (MQ=0)
tGCGACGCTTGCCGCGTCTTATCAGGCCTACAAAT‑‑‑‑GCTCC‑‑CCg > 1:37603/1‑43 (MQ=255)
tGCGACGCTTGCCGCGTCTTATCAGGCCTACAAAT‑‑‑‑GCTCC‑‑CCg > 1:1700515/1‑43 (MQ=255)
tGCGACGCTTGCCGCGTCTTATCAGGCCTACAAAT‑‑‑‑GCTCC‑‑CCGTAGGCCGGATAAGGCGTTTACGCCGCa < 1:4427823/70‑1 (MQ=255)
tGCGACGCTTG‑CGCGTCTTATCAGGCCTACAAATTCCCGCACCCTCCGTAGGCCGGATAAGGCGTTTAcgc > 1:1345902/1‑71 (MQ=0)
gCGACGCTTG‑CGCGTCTTATCAGGCCTACAAATTCCCGCACCATCCGTAGGCCGGATAAGGCGTTTAcgcc > 1:29656/1‑71 (MQ=0)
gCGACGCTTG‑CGCGTCTTATCAGGCCTACAAATTCCCGCACCATCCGTAGGCCGGATAAGGCGTTTAcgcc > 1:4485858/1‑71 (MQ=0)
cGACGCTTG‑CGCGTCTTATCAGGCCTACAAATTCCCGCACCATCCGTAGGCCGGATAAGGCGTTTAcgcc < 1:4567717/70‑1 (MQ=0)
aCGCTTGCCGCGTCTTATCAGGCCTACAAAT‑‑‑‑GCTCC‑‑CCGTAGGCCGGATAAGGCGTTTACGCCGCATCCgg > 1:1858644/1‑71 (MQ=255)
aCGCTTG‑CGCGTCTTATCAGGCCTACAAATTCCCGCACCCTCCGTAGGCCGGATAAGGCGTTTACGCCGCa < 1:3533806/71‑1 (MQ=0)
aCGCTTG‑CGCGTCTTATCAGGCCTACAAATTCCCGCACCCTCCGTAGGCCGGATAAGGCGTTTACGCCGCa > 1:1204526/1‑71 (MQ=0)
aCGCTTG‑CGCGTCTTATCAGGCCTACAAATTCCCGCACCCTCCGTAGGCCGGATAAGGCGTTTACGCCGCa > 1:3608400/1‑71 (MQ=0)
cGCTTG‑CGCGTCTTATCAGGCCTACAAATTCCCGCACCCTCCGTAGGCCGGATAAGGCGTTTACGCCGCAt < 1:5289091/71‑1 (MQ=0)
cGCTTG‑CGCGTCTTATCAGGCCTACAAATTCCCGCACCCTCCGTAGGCCGGATAAGGCGTTTACGCCGCAt < 1:4720923/71‑1 (MQ=0)
gCTTGCCGCGTCTTATCAGGCCTACAAAT‑‑‑‑GCTCC‑‑CCGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGc > 1:3375370/1‑70 (MQ=255)
gCTTG‑CGCGTCTTATCAGGCCTACAAATTCCCGCACCATCCGTAGGCCGGATAAGGCGTTTACGCCGCATc < 1:445947/71‑1 (MQ=0)
|
AACTATATGCTGCACACGCAGAATAAGTGAGGTTGATGTTTGGCCGCGCCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACAAAT‑‑‑‑GCTCC‑‑CCGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGC > minE/1467812‑1467946
|
| 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
