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 |
1,716,872 |
C→A |
17.6% |
intergenic (+130/+68) |
yphH → / ← glyA |
predicted DNA‑binding transcriptional regulator/serine hydroxymethyltransferase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,716,872 | 0 | C | A | 17.6%
| 124.8
/ 12.7
| 51 | intergenic (+130/+68) | yphH/glyA | predicted DNA‑binding transcriptional regulator/serine hydroxymethyltransferase |
| Reads supporting (aligned to +/- strand): ref base C (18/24); new base A (5/4); total (23/28) |
| Fisher's exact test for biased strand distribution p-value = 7.14e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.39e-01 |
GCCTGATGCGCTACGCTTATCAGGCCTACACGGAGATTGCAATATATTGAATTTGCAAAGTTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAACGAGCACATTGACAGCAAATCACCGTTTCGCTT > minE/1716803‑1716941
|
gCCTGATGCGCTACGCTTATCAGGCCTACACGGAGATTGCAATATATTGAATTTGCAAAGTTTTGTAGGcc > 1:318986/1‑71 (MQ=255)
gCCTGATGCGCTACGCTTATCAGGCCTACACGGAGATTGCAATATATTGAATTTGCAAAGTTTTGTAGGcc > 1:533538/1‑71 (MQ=255)
cTGATGCGCTACGCTTATCAGGCCTACACGGAGATTGCAATATATTGAATTTGCAAAGTTTTGTAGGCCgg < 1:2518958/71‑1 (MQ=255)
cTGATGCGCTACGCTTATCAGGCCTACACGGAGATTGCAATATATTGAATTTGCAAAGTTTTGTAGGCCg > 1:1166864/1‑70 (MQ=255)
tGATGCGCGATGCTTATCAGGCCTACCAGAAGATTGCAATATATTGAATTTGCACTGTTTTGTAGGCCGGa > 1:896482/1‑71 (MQ=11)
gATGCGCGATGCTTATCAGGCCTACCAGAAGATTGCAATATATTGAATTTGCACTGTTTTGTAGGCCGGa > 1:2193709/1‑70 (MQ=11)
aTGCGCTACGCTTATCAGGCCTACACGGAGATTGCAATATATTGAATTTGCAAAGTTTTGTAGGCCGGAt > 1:1539611/1‑70 (MQ=255)
aTGCGCTACGCTTATCAGGCCTACACGGAGATTGCAATATATTGAATTTGCAAAGTTTTGTAGGCCGGAt < 1:1708868/70‑1 (MQ=255)
aTGCGCTACGCTTATCAGGCCTACACGGAGATTGCAATATATTGAATTTGCAAAGTTTTGTAGGCCGGATa < 1:3098876/71‑1 (MQ=255)
aTGCGCTACGCTTATCAGGCCTACACGGAGATTGCAATATATTGAATTTGCAAAGTTTTGTAGGCCGGATa < 1:3632001/71‑1 (MQ=255)
aTGCGCGATGCTTATCAGGCCTACCAGAAGATTGCAATATATTGAATTTGCACTGTTTTGTAGGCCGGAt < 1:2435653/70‑1 (MQ=11)
tGCGCTACGCTTATCAGGCCTACAAGTGCATTGCAATCTATTGAATTTGCGATGTTTTGTAGGACGGAt > 1:83255/1‑69 (MQ=11)
cgcTACGCTTATCAGGCCTACAAGTGCATTGCAATCTATTGAATTTGCGATGTTTTGTAGGACGGATAAg < 1:920009/70‑1 (MQ=11)
gcTACGCTTATCAGGCCTACACGGAGATTGCAATATATTGAATTTGCAAAGTTTTGTAGGCCGGATAAGGc > 1:2081729/1‑71 (MQ=255)
gcTACGCTTATCAGGCCTACACGGAGATTGCAATATATTGAATTTGCAAAGTTTTGTAGGCCGGATAAGGc < 1:2621248/71‑1 (MQ=255)
gcTACGCTTATCAGGCCTACACGGAGATTGCAATATATTGAATTTGCAAAGTTTTGTAGGCCGGATAAGGc < 1:3736786/71‑1 (MQ=255)
tACGCTTATCAGGCCTACACGGAGATTGCAATATATTGAATTTGCAAAGTTTTGTAGGCCGGATAAg > 1:3572999/1‑67 (MQ=255)
gatgCTTATCAGGCCTACCAGAAGATTGCAATATATTGAATTTGCACTGTTTTGTAGGCCGGATAAGGCGt < 1:3627719/68‑1 (MQ=11)
atgCTTATCAGGCCTACCAGAAGATTGCAATATATTGAATTTGCACTGTTTTGTAGGCCGGATAAGGCGtt < 1:76576/69‑1 (MQ=11)
atgCTTATCAGGCCTACCAGAAGATTGCAATATATTGAATTTGCACTGTTTTGTAGGCCGGATAAGGCGtt < 1:3319468/69‑1 (MQ=11)
cGCTTATCAGGCCTACACGGAGATTGCAATATATTGAATTTGCAAAGTTTTGTAGGCCGGATAAGGCGtt < 1:650953/70‑1 (MQ=255)
cGCTTATCAGGCCTACACGGAGATTGCAATATATTGAATTTGCAAAGTTTTGTAGGCCGGATAAGGCGTTc < 1:3132762/71‑1 (MQ=255)
cGCTTATCAGGCCTACAAGTGCATTGCAATCTATTGAATTTGCGATGTTTTGTAGGACGGATaa > 1:2901644/1‑64 (MQ=2)
cGCTTATCAGGCCTACAAGTGCATTGCAATCTATTGAATTTGCGATGTTTTGTAGGACGGATaa > 1:1928570/1‑64 (MQ=2)
cGCTTATCAGGCCTACAAGTGCATTGCAATCTATTGAATTTGCGATGTTTTGTAGGACGGATAAGGCgc < 1:152775/69‑2 (MQ=11)
cGCTTATCAGGCCTACAAGTGCATTGCAATCTATTGAATTTGCGATGTTTTGTAGGACGGATAAGGCGCTc > 1:1089706/1‑71 (MQ=2)
ttATCAGGCCTACAAGTGCATTGCAATCTATTGAATTTGCGATGTTTTGTAGGACGGATAAGGCGCTcgcg > 1:3753857/1‑71 (MQ=2)
aTCAGGCCTACAAGTGCATTGCAATCTATTGAATTTGCGATGTTTTGTAGGACGGATAAGGCgct < 1:1792260/65‑3 (MQ=2)
aGGCCTACCAGAAGATTGCAATATATTGAATTTGCACTGTTTTGTAGGCCGGATAAGGCGt > 1:2792880/1‑61 (MQ=11)
ggAGATTGCAATATATTGAATTTGCAAAGTTTTGTAGGCCGGATAAGGCGTTCACGCCGCAt > 1:2561440/1‑62 (MQ=255)
ggAGATTGCAATATATTGAATTTGCAAAGTTTTGTAGGCCGGATAAGGCGTTCACGCCGCAt > 1:3395276/1‑62 (MQ=255)
aagaTTGCAATATATTGAATTTGCACTGTTTTGTAGGCCg < 1:2694764/39‑1 (MQ=11)
agaTTGCAATATATTGAATTTGCACTGTTTTGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCATGaac < 1:1855622/71‑1 (MQ=11)
gaTTGCAATATATTGAATTTGCAAAGTTTTGTAGGCCGGATAAGGCGTTCAcg > 1:2952213/1‑53 (MQ=255)
caTTGCAATCTATTGAATTTGCGATGTTTTGTAGGACGGATAAGGCGCTCGCGCCGCATCCGGCATCaaca < 1:1112107/70‑1 (MQ=11)
ttGCAATATATTGAATTTGCACTGTTTTGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCATGaacaat > 1:345471/1‑70 (MQ=11)
atatTGAATTTGCAAAGTTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAACGAGcaca > 1:2907564/1‑71 (MQ=255)
atatTGAATTTGCAAAGTTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAACGAGcaca > 1:736985/1‑71 (MQ=255)
tatTGAATTTGCAAAGTTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAACGAGcaca < 1:2241551/70‑1 (MQ=255)
atTGAATTTGCAAAGTTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAACGAGCACAt < 1:3313617/70‑1 (MQ=255)
ttGAATTTGCAAAGTTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAACGAGCACAtt < 1:376076/70‑1 (MQ=255)
gAATTTGCAAAGTTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAACGAGCACAtt > 1:235304/1‑68 (MQ=255)
gAATTTGCAAAGTTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAACGAGCACATTGa < 1:3779635/70‑1 (MQ=255)
ttGCAAAGTTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAACGAGCACATTGACa > 1:2126778/1‑68 (MQ=255)
cAAAGTTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAACGAGCACATTGACAGCaaa < 1:2845940/70‑1 (MQ=255)
aaaGTTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAACGAGCACATTg < 1:588361/61‑1 (MQ=255)
aGTTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAACGAGCACATTGACAGCAAATCAc < 1:2498404/71‑1 (MQ=255)
aGTTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAACGAGCACATTGACAGCAAATCAc > 1:692247/1‑71 (MQ=255)
gTTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGa > 1:3546272/1‑43 (MQ=32)
ttGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAACGAGCACATTGACAGCAAATCACCGt < 1:1687430/70‑1 (MQ=255)
ttGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAACGAGCACATTAACAGCAAATCACCGtt > 1:3374656/1‑71 (MQ=255)
gCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAACGAGCACATTGACAGCAAATCACCGTTTCGCtt < 1:745625/71‑1 (MQ=255)
gCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAACGAGCACATTGACAGCAAATCACCGTTTCGCtt < 1:2897407/71‑1 (MQ=255)
|
GCCTGATGCGCTACGCTTATCAGGCCTACACGGAGATTGCAATATATTGAATTTGCAAAGTTTTGTAGGCCGGATAAGGCGTTCACGCCGCATCCGGCATGAACAACGAGCACATTGACAGCAAATCACCGTTTCGCTT > minE/1716803‑1716941
|
| 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
