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 |
1,484,894 |
T→C |
54.1% |
M316V (ATG→GTG) |
menF ← |
isochorismate synthase 2 |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,484,894 | 0 | T | C | 54.1%
| 5.2
/ 44.9
| 37 | M316V (ATG→GTG) | menF | isochorismate synthase 2 |
| Reads supporting (aligned to +/- strand): ref base T (6/11); new base C (9/11); total (15/22) |
| Fisher's exact test for biased strand distribution p-value = 7.38e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.55e-01 |
CTGATGTAAACAGATCACATCATCCGCTTTGTTGAGTGAAGTCCAGATACAGCGGCGAAGATGCTGCATTTTACGCAGACGCAGTACCTGCGGCGGTAAAACATCCAGCGTCTGGGTATCGGCCTGTAATCGTTGACA > minE/1484826‑1484963
|
cTGATGTAAACAGATCACATCATCCGCTTTGTTGAGTGAAGTCCAGATACAGCGGCGAAGATGCTGCActt < 1:267821/71‑1 (MQ=255)
aTGTAAACAGATCACATCATCCGCTTTGTTGAGTGAAGTCCAGATACAGCGGCGAAGATGCTGCActtt < 1:3923551/69‑1 (MQ=255)
aTGTAAACAGATCACATCATCCGCTTTGTTGAGTGAAGTCCAGATACAGCGGCGAAGATGCTGCActtt < 1:2231836/69‑1 (MQ=255)
aTGTAAACAGATCACATCATCCGCTTTGTTGAGTGAAGTCCAGATACAGCGGCGAAGATGCTGCACTTTac > 1:3678170/1‑71 (MQ=255)
tAAACAGATCACATCATCCGCTTTGTTGAGTGAAGTCCAGATACAGCGGCGAAGATGCTGCACTTTacgc < 1:2678512/70‑1 (MQ=255)
aaCAGATCACATCATCCGCTTTGTTGAGTGAAGTCCAGATACAGCGGCGAAGATGCTGCACTTTacgcaga < 1:1499191/71‑1 (MQ=255)
aCAGATCACATCATCCGCTTTGTTGAGTGAAGTCCAGATACAGCGGCGAAGATGCTGCATTTTacgcagac < 1:1212710/71‑1 (MQ=255)
cAGATCACATCATCCGCTTTGTTGAGTGAAGTCCAGATACAGCGGCGAAGATGCTGCAttt > 1:2357484/1‑61 (MQ=255)
cAGATCACATCATCCGCTTTGTTGAGTGAAGTCCAGATACAGCGGCGAAGATGCTGCATTTTacgcagacg > 1:1954848/1‑71 (MQ=255)
cAGATCACATCATCCGCTTTGTTGAGTGAAGTCCAGATACAGCGGCGAAGATGCTGCACTTTacgcagacg < 1:2262654/71‑1 (MQ=255)
cAGATCACATCATCCGCTTTGTTGAGTGAAGTCCAGATACAGCGGCGAAGATGCTGCACTTTacgcagacg < 1:1318273/71‑1 (MQ=255)
aTCACATCATCCGCTTTGTTGAGTGAAGTCCAGATACAGCGGCGAAGATGCTGCATTTTacgcagacgcag < 1:2299114/71‑1 (MQ=255)
aTCACATCATCCGCTTTGTTGAGTGAAGTCCAGATACAGCGGCGAAGATGCTGCACTTTacgcagacgcag > 1:2176289/1‑71 (MQ=255)
aTCACATCATCCGCTTTGTTGAGTGAAGTCCAGATACAGCGGCGAAGATGCTGCACTTTacgcagacgcag > 1:1770849/1‑71 (MQ=255)
aTCACATCATCCGCTTTGTTGAGTGAAGTCCAGATACAGCGGCGAAGATGCTGCACTTTacgcagacg < 1:2615989/68‑1 (MQ=255)
atcatcCGCTTTGTTGAGTGAAGTCCAGATACAGCGGCGAAGATGCTGCACTTTACGCAGACGCAGTACCt > 1:2261845/1‑71 (MQ=255)
tcatcCGCTTTGTTGAGTGAAGTCCAGATACAGCGGCGAAGATGCTGCATTTTACGCAGACGCAGTACCTg < 1:2791201/71‑1 (MQ=255)
catcCGCTTTGTTGAGTGAAGTCCAGATACAGCGGCGAAGATGCTGCATTTTacgcagacgc < 1:1479947/62‑1 (MQ=255)
atcCGCTTTGTTGAGTGAAGTCCAGATACAGCGGCGAATATGCTGCATTTTACGCAGACGCAGTACCTgcg < 1:3799074/71‑1 (MQ=255)
atcCGCTTTGTTGAGTGAAGTCCAGATACAGCGGCGAAGATGCTGCATTTTACGCAGACGCAGTACCTgcg < 1:193237/71‑1 (MQ=255)
ttgttgAGTGAAGTCCAGATACAGCGGCGAAGATGCTGCACTTTACGCAGAAGCAGTACCTGCGGCGGTa > 1:2486156/1‑70 (MQ=255)
ttgAGTGAAGTCCAGATACAGCGGCGAAGATGCTGCATTTTACGCAGACGCAGTACCTGCGGCGGTAAAAc < 1:3303441/71‑1 (MQ=255)
tgAGTGAAGTCCAGATACAGCGGCGAAGATGCTGCATTTTACGCAGACGCAGTACCTGCGGCGGTAAAACa > 1:253792/1‑71 (MQ=255)
gAGTGAAGTCCAGATACAGCGGCGAAGATGCTGCATTTTACGCAGACGCAGTACCTgcg > 1:191262/1‑59 (MQ=255)
gAGTGAAGTCCAGATACAGCGGCGAAGATGCTGCATTTTACGCAGACGCAGTACCTGCGGCGGTAAAACAt > 1:3193498/1‑71 (MQ=255)
gAGTGAAGTCCAGATACAGCGGCGAAGATGCTGCATTTTACGCAGAAGCAGTACCTGCGGCGGTAAAACAt > 1:2956127/1‑71 (MQ=255)
aGTGAAGTCCAGATACAGCGGCGAAGATGCTGCATTTTACGCAGACGCAGTACCTGCGGCGGTAAAACATc < 1:1698877/71‑1 (MQ=255)
aaGTCCAGATACAGCGGCGAAGATTCTGCACTTTACGCAGACGCAGTACCTgcggc < 1:3179676/56‑1 (MQ=255)
aaGTCCAGATACAGCGGCGAAGATGCTGCATTTTACGCAGACGCAGTACCTGCGGCGGTAAAACATCCAGc < 1:2388129/71‑1 (MQ=255)
tCCAGATACAGCGGCGAAGATGCTGCATTTTACGCAGACGCAGTACCt < 1:3777752/48‑1 (MQ=255)
cAGATACAGCGGCGAAGATGCTGCACTTTACGCAGACGCAGTACCTGCGGCGGTAAAACATCCAGCGTCt < 1:84632/70‑1 (MQ=255)
cAGATACAGCGGCGAAGATGCTGCACTTTACGCAGACGCAGTACCTGCGGCGGTAAAACATCCAGCGTCTg > 1:2362768/1‑71 (MQ=255)
aGCGGCGAAGATGCTGCACTTTACGCAGACGCAGTACCTGCGGCGGTAAAACATCCAGCGTCTGGGTATCg < 1:2128403/71‑1 (MQ=255)
aGCGGCGAAGATGCTGCACTTTACGCAGACGCAGTACCTGCGGCGGTAAAACATCCAGCGTCTGGGTATCg < 1:550595/71‑1 (MQ=255)
cggcgAAGATGCTGCACTTTACGCAGACGCAGTACCTGCGGCGGTaaaa > 1:2339887/1‑49 (MQ=255)
cggcgAAGATGCTGCACTTTACGCAGACGCAGTACCTGCGGCGGTAAAACATCCAGCGTCTGGGTATCGGc < 1:2399439/71‑1 (MQ=255)
cggcgAAGATGCTGCACTTTACGCAGACGCAGTACCTGCGGCGGTAAAACATCCAGCGTCTGGGTATCGGc < 1:2394736/71‑1 (MQ=255)
gcgAAGATGCTGCACTTTACGCAGACGCAGTACCTGCGGCGGTAAAACATCCa > 1:1645907/1‑53 (MQ=255)
tgcACTTTACGCAGACGCAGTACCTGCGGCGGTAAAACATCCAGCGTCTgg > 1:1257045/1‑51 (MQ=255)
cATTTTACGCAGACGCAGTACCTGCGGCGGTAAAACATCCAGCGTCTGGGTATCGGCCTGTAATCGTTGa > 1:2584339/1‑70 (MQ=255)
aTTTTAAGCAGACGCAGTACCTGCGGCGGTAAAACATCCAGCGTCTGGGTATCGGCCTGTAATCGTTGACa < 1:3252505/71‑1 (MQ=255)
|
CTGATGTAAACAGATCACATCATCCGCTTTGTTGAGTGAAGTCCAGATACAGCGGCGAAGATGCTGCATTTTACGCAGACGCAGTACCTGCGGCGGTAAAACATCCAGCGTCTGGGTATCGGCCTGTAATCGTTGACA > minE/1484826‑1484963
|
| 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
