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 F21 I0 R1
|
2169 |
63.0 |
3952800 |
76.2% |
3012033 |
62.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
1,467,905:2 |
+C |
25.9% |
intergenic (+64/+64) |
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 | 1,467,905 | 2 | . | C | 25.9%
| 158.4
/ 69.9
| 54 | intergenic (+64/+64) | ubiG/yfaL | bifunctional 3‑demethylubiquinone‑9 3‑methyltransferase and 2‑octaprenyl‑6‑hydroxy phenol methylase/adhesin |
| Reads supporting (aligned to +/- strand): ref base . (19/21); new base C (8/6); total (27/27) |
| Fisher's exact test for biased strand distribution p-value = 7.57e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.90e-01 |
TAAGTGAGGTTGATGTTTGGCCGCGCCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTAC‑AAAT‑‑‑‑G‑‑CTCC‑‑CCGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCAACCGTGCCGACTAGACAGTGATTAC > minE/1467835‑1467972
|
tAAGTGAGGTTGATGTTTGGCCGCGCCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTAC‑AAAt < 1:3314348/71‑1 (MQ=255)
tGAGGTTGATGTTTGGCCGCGCCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTAC‑AAAT‑‑‑‑G‑‑CTc < 1:1857861/71‑1 (MQ=255)
tGATGTTTGGCCGCGCCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTAC‑AAAT‑‑‑‑G‑‑CTCC‑‑CCg > 1:1061835/1‑69 (MQ=255)
gATGTTTGGCCGCGCCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTAC‑AAAT‑‑‑‑G‑‑CTCC‑‑CCGTAg > 1:1395669/1‑71 (MQ=255)
aTGTTTGGCCGCGCCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTAC‑AAAT‑‑‑‑G‑‑CTCC‑‑CCGTAg < 1:3460347/70‑1 (MQ=255)
ttGGCCGCGCCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTAC‑AAAT‑‑‑‑G‑‑CTCC‑‑CCGTAGGCCg > 1:21774/1‑70 (MQ=255)
gCCGCGCCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTAC‑AAAT‑‑‑‑G‑‑CTCC‑‑CCGTAGGCCGGATa < 1:959386/71‑1 (MQ=255)
gCCGCGCCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTAC‑AAAT‑‑‑‑G‑‑CTCC‑‑CCGTAGGCCGGATa < 1:2080018/71‑1 (MQ=255)
cgcCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTAC‑AAAT‑‑‑‑G‑‑CTCC‑‑CCGTAGGCCGGATAAGGc < 1:2404202/71‑1 (MQ=255)
ggttGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACAAAAC‑‑‑‑GCACTAC‑‑CCGTAGGTCGGATAAGGc > 1:3763323/4‑71 (MQ=2)
cAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTAC‑AAAT‑‑‑‑G‑‑CTCC‑‑CCGTAGGCCTGATAAGGCGtt < 1:105602/71‑1 (MQ=255)
aaTGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTAC‑AAAT‑‑‑‑G‑‑CTCC‑‑CCGTAGGCCGGATAAGGCGttt < 1:3945874/71‑1 (MQ=255)
aaTGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTAC‑AAAT‑‑‑‑G‑‑CTCC‑‑CCGTAGGCCGGATAAGGCGtt > 1:785002/1‑70 (MQ=255)
aTGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTAC‑AAAT‑‑‑‑G‑‑CTCC‑‑CCGTAGGCCGGATAAGGCGTTTa > 1:552824/1‑71 (MQ=255)
tGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACAAAAC‑‑‑‑GCACTAC‑‑CCGTAGGTCGGATAAGGCGt > 1:155206/1‑70 (MQ=11)
tGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTAC‑AAAT‑‑‑‑G‑‑CTCC‑‑CCGTAGGCCGGATAAGGCGTTTa < 1:3159968/70‑1 (MQ=255)
gCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTAC‑AAAT‑‑‑‑G‑‑CTCC‑‑CCGTAGGCCGGATAAGGCGTTTAcg > 1:1053630/1‑71 (MQ=255)
ccTGATGCGACGCTTGCCGCGTCTTATCAGGCCTAC‑AAAT‑‑‑‑G‑‑CTCC‑‑CCGTAGGCCGGATAAGGCGTTTAcg < 1:58221/70‑1 (MQ=255)
gATGCGACGCTTGCCGCGTCTTATCAGGCCTAC‑AAAT‑‑‑‑G‑‑CTCC‑‑CCGTAGGCCGGAt > 1:1678345/1‑55 (MQ=255)
gATGCGACGCTTGCCGCGTCTTATCAGGCCTAC‑AAAT‑‑‑‑G‑‑CTCC‑‑CCGTAGGCCGGAt > 1:2093085/1‑55 (MQ=255)
gATGCGACGCTTG‑CGCGTCTTATCAGGCCTAC‑AAATTCCCG‑‑CACCCTCCGTAGGCCGGATAAGGCGTTTAc > 1:3139993/1‑71 (MQ=0)
aTGCGACGCTTGCCGCGTCTTATCAGGCCTAC‑AAAT‑‑‑‑G‑‑CTCC‑‑CCGTAGGCCGGATAAGGCGTTTACGCCGCa > 1:3890194/1‑71 (MQ=255)
aTGCGACGCTTG‑CGCGTCTTATCAGGCCTAC‑AAATTCCCG‑‑CACCCTCCGTAGGCCGGATAAGGCGTTTAcg < 1:2865534/71‑1 (MQ=0)
aTGCGACGCTTG‑CGCGTCTTATCAGGCCTAC‑AAATTCCCG‑‑CACCCTCCGTAGGCCGGATAAGGCGTTTAcg < 1:3152114/71‑1 (MQ=0)
cGACGCTTGCCGCGTCTTATCAGGCCTAC‑AAAT‑‑‑‑G‑‑CTCC‑‑CCGTAGGCCGGATAAGGCGTTTACGCCGCATc < 1:3065057/70‑1 (MQ=255)
cGACGCTTG‑CGCGTCTTATCAGGCCTAC‑AAATTCCCG‑‑CACCCTCCGTAGGCCGGATAAGGCGTTTAcgccg < 1:1147494/71‑1 (MQ=0)
gACGCTTG‑CGCGTCTTATCAGGCCTAC‑AAATTCCCG‑‑CACCCTCCGTAGGCCGGATAAGGCGTTTAcgccg > 1:110259/1‑70 (MQ=0)
aCGCTTG‑CGCGTCTTATCAGGCCTAC‑AAATTCCCG‑‑CACCCTCCGTAGGCCGGATAAGGCGTTTACGCCGCa < 1:651183/71‑1 (MQ=0)
aCGCTTG‑CGCGTCTTATCAGGCCTAC‑AAATTCCCG‑‑CACCCTCCGTAGGCCGGATAAGGCGTTTACGCCGCa > 1:1521629/1‑71 (MQ=0)
cGCTTG‑CGCGTCTTATCAGGCCTAC‑AAATTCCCG‑‑CACCCTCCGTAGGCCGGATAAGGCGTTTACGCCGCa > 1:725712/1‑70 (MQ=0)
gCTTG‑CGCGTCTTATCAGGCCTAC‑AAATTCCCG‑‑CACCCTCCGTAGGCCGGATAAGGCGTTTACGCCGCATc > 1:2562409/1‑71 (MQ=0)
gCTTG‑CGCGTCTTATCAGGCCTAC‑AAATTCCCG‑‑CACCCTCCGTAGGCCGGATAAGGCGTTTACGCCGCATc > 1:2531117/1‑71 (MQ=0)
gCTTG‑CGCGTCTTATCAGGCCTAC‑AAATTCCCG‑‑CACCCTCCGTAGGCCGGATAAGGCGTTTACGCCGCATc > 1:3740559/1‑71 (MQ=0)
cTTGCCGCGTCTTATCTGGCCTAC‑AAAT‑‑‑‑G‑‑CTCC‑‑CCg < 1:3155041/36‑1 (MQ=255)
gCCGCGTCTTATCAGGCCTAC‑AAAT‑‑‑‑G‑‑CTCC‑‑CCGTAg > 1:3487816/1‑36 (MQ=255)
acgcgTCTTATCAGGCCTAC‑AAATTCCCG‑‑CGCCATCCGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGc < 1:2864009/70‑1 (MQ=0)
cgcgTCTTATCAGGCCTAC‑AAATTCCCG‑‑CACCCTCCGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGc > 1:1977681/1‑70 (MQ=2)
cgcgTCTTATCAGGCCTAC‑AAATTCCCG‑‑CACCATCCGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCa < 1:2418182/71‑1 (MQ=2)
gcgTCTTATCAGGCCTAC‑AAAT‑‑‑‑G‑‑CTCC‑‑CCGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCAACCGTGc < 1:400610/71‑1 (MQ=255)
tATCAGGCCTAC‑AAAT‑‑‑‑G‑‑CTCC‑‑CCGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCAACCGTGCCGAc > 1:3449640/1‑69 (MQ=255)
aTCAGGCCTAC‑AAAT‑‑‑‑G‑‑CTCC‑‑CCGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCAACCGTGCCGACTa < 1:486145/70‑1 (MQ=255)
cAGGCCTAC‑AAAT‑‑‑‑G‑‑CTCC‑‑CCGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCAACCGTGcc > 1:916471/1‑63 (MQ=255)
ggCCTAC‑AAAT‑‑‑‑G‑‑CTCC‑‑CCGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCAACCGTGCCGACTAGACAg < 1:3686530/71‑1 (MQ=255)
gCCTAC‑AAAT‑‑‑‑G‑‑CTCC‑‑CCGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCAACCGTGCCGACTAGACAGt > 1:3476971/1‑71 (MQ=255)
gCCTAC‑AAAT‑‑‑‑G‑‑CTCC‑‑CCGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCAACCGTGCCGACTAGACAGt > 1:3221245/1‑71 (MQ=255)
ccTAC‑AAAT‑‑‑‑G‑‑CTCC‑‑CCGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCAACCGTGCCGACTAGACAGTg < 1:3586403/71‑1 (MQ=255)
cTAC‑AAAT‑‑‑‑G‑‑CTCC‑‑CCGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCAACCGTGCCGACTAGACAGTGa < 1:2792831/71‑1 (MQ=255)
c‑AAAT‑‑‑‑G‑‑CTCC‑‑CCGTAGGCCGGATAAGGCGTTTAcg > 1:495872/1‑35 (MQ=255)
c‑AAAT‑‑‑‑G‑‑CTCC‑‑CCGTAGGCCGGATAAGGCGTTTACGCCGCATCCgg > 1:610608/1‑45 (MQ=255)
c‑AAAT‑‑‑‑G‑‑CTCC‑‑CCGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCAACCGTGCCGACTAGACAGTGa < 1:2453992/68‑1 (MQ=255)
c‑AAAT‑‑‑‑G‑‑CTCC‑‑CCGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCAACCGTGCCGACTAGACAGTGa < 1:2996247/68‑1 (MQ=255)
c‑AAAT‑‑‑‑G‑‑CTCC‑‑CCGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCAACCGTGCCGACTAGACAGTGAt < 1:2304244/69‑1 (MQ=255)
c‑AAAT‑‑‑‑G‑‑CTCC‑‑CCGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCAACCGTGCCGACTAGACAGTGAt < 1:1145492/69‑1 (MQ=255)
aaaT‑‑‑‑G‑‑CTCC‑‑CCGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCAACCGTGCCGACTAGACAGTGATTAc < 1:3428344/71‑1 (MQ=255)
aaaT‑‑‑‑G‑‑CTCC‑‑CCGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCAACCGTGCCGACTAGACAGTGATTAc > 1:437211/1‑71 (MQ=255)
|
TAAGTGAGGTTGATGTTTGGCCGCGCCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTAC‑AAAT‑‑‑‑G‑‑CTCC‑‑CCGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCAACCGTGCCGACTAGACAGTGATTAC > minE/1467835‑1467972
|
| 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
