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 |
|
A8 F1 I1 R1
|
82 |
28.6 |
1225488 |
97.4% |
1193625 |
116.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
2,184,452 |
G→A |
A22V (GCC→GTC) |
thiD ← |
hydroxy‑methylpyrimidine kinase and hydroxy‑phosphomethylpyrimidine kinase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 2,184,452 | 0 | G | A | 96.3%
| 88.7
/ ‑6.2
| 27 | A22V (GCC→GTC) | thiD | hydroxy‑methylpyrimidine kinase and hydroxy‑phosphomethylpyrimidine kinase |
| Reads supporting (aligned to +/- strand): ref base G (0/0); major base A (14/12); minor base C (0/1); total (14/13) |
| Fisher's exact test for biased strand distribution p-value = 4.81e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
CGACAAAATCAGGCTCAATGCGATACACCGACTGTACGCCACGGGTATTTTGCGCCACCAGTGCAGTAATAACTGAGCAACCATAAGCGCCAAGTGCCGAGAAGGTTTTAAGATCGGCCTGAATCCCCGCACCACCACTCGGATCAGTACCGGCAATCGTCAGAGCGTTAATTCGTTTCATGCCTGCACCTCCTGCGTCAATTGCCAGAGCGCATCAAGGAAATGTGGAACAA > NC_000913/2184336‑2184568
|
cgACAAAATCAGGCTCATTTCGATACACCGTCTGTACGCCACGGGTATTTTGCGCCACCAGTGCAGTAATAACTCCGCAGCCATAAGCGTCAAGGGCCGAGAAGGTGTTAAGATCGCCCTGAAACCCCGCACCACCACt < 1:133771/139‑1 (MQ=255)
cgACAAAATCAGGCTCAATGCGATACACCGACTGTACGCCACGGGTATTTTGCGCCACCAGTGCAGTAATAACTGAGCAACCATAAGCGCCAAGTGCCGAGAAGGTTTTAAGATCGACCTGAATCCCCGcac < 2:4469/132‑1 (MQ=255)
cgACAAAATCAGGCTCAATGCGATACACCGACTGTACGCCACGGGTATTTTGCGCCACCAGTGCAGTAATAACTGAGCAACCATAAGCGCCAAGTGCCGAGAAGGTTTTAAGATCGACCTGAATCCCCGcac > 1:4469/1‑132 (MQ=255)
cgACAAAATCAGGCTCAATGCGATACACCGACTGTACGCCACGGGTATTTTGCGCCACCAGTGCAGTAATAACTGAGCAACCATAAGCGCCAAGTGCCGAGAAGGTTTTAAGATCGACCTGAATCCCCGCACCACCACt > 2:38402/1‑139 (MQ=255)
cgACAAAATCAGGCTCAATGCGATACACCGACTGTACGCCACGGGTATTTTGCGCCACCAGTGCAGTAATAACTGAGCAACCATAAGCGCCAAGTGCCGAGAAGGTTTTAAGATCGACCTGAATCCCCGCACCACCACt < 2:232388/139‑1 (MQ=255)
aCAAAATCAGGCTCAATGCGATACACCGACTGTACGCCACGGGTATTTTGCGCCACCAGTGCAGTAATAACTGAGCAACCATAAGCGCCAAGTGCCGAGAAGGTTTTAAGATCGACCTGAATCCCCGCACCACCACTCg > 2:18542/1‑139 (MQ=255)
aaTGCGATACACCGACTGTACGCCACGGGTATTTTGCGCCACCAGTGCAGTAATAACTGAGCAACCATAAGCGCCAAGTGCCGAGAAGGTTTTAAGATCGACCTGAATCCCCGCACCACCACTCGGATCAGTACCGGCa < 1:18542/139‑1 (MQ=255)
aCTGTACGCCACGGGTATTTTGCGCCACCAGTGCAGTAATAACTGAGCAACCATAAGCGCCAAGTGCCGAGAAGGTTTTAAGATCGACCTGAATCCCCGCACCACCACTCGGATCAGTACCGGCAATCGTCAGAGCGtt > 2:138322/1‑139 (MQ=255)
cGGGTATTTTGCGCCACCAGTGCAGTAATAACTGAGCAACCATAAGCGCCAAGTGCCGAGAAGGTTTTAAGATCGACCTGAATCCCCGCACCACCGCTCGGCTCAGTACCGGCAATCGTCAGAGCGTTAATTCGTTTCa < 2:407927/139‑1 (MQ=255)
cGGGTATTTTGCGCCACCAGTGCAGTAATAACTGAGCAACCATAAGCGCCAAGTGCCGAGAAGGTTTTAAGATCGACCTGAATCCCCGCACCACCACTCGGAt < 2:253590/103‑1 (MQ=255)
cGGGTATTTTGCGCCACCAGTGCAGTAATAACTGAGCAACCATAAGCGCCAAGTGCCGAGAAGGTTTTAAGATCGACCTGAATCCCCGCACCACCACTCGGAt > 1:253590/1‑103 (MQ=255)
gggTATTTTGCGCCACCAGTGCAGTAATAACTGAGCAACCATAAGCGCCAAGTGCCGAGAAGGTTTTAAGATCGACCTGAATCCCCGCACCACCACt > 2:118405/1‑97 (MQ=255)
gggTATTTTGCGCCACCAGTGCAGTAATAACTGAGCAACCATAAGCGCCAAGTGCCGAGAAGGTTTTAAGATCGACCTGAATCCCCGCACCACCACt < 1:118405/97‑1 (MQ=255)
tATTTTGCGCCACCAGTGCAGTAATAACTGAGCAACCATAAGCGCCAAGTGCCGAGAAGGTTTTAAGATCGACCTGAATCCCCGCACCACCACTCGGATCAGTACCGGCAATCGTCAGAGCGTTAATTCGTTTCATGcc < 1:38402/139‑1 (MQ=255)
ccaGTGCAGTAATAACTGAGCAACCATAAGCGCCAAGTGCCGAGAAGGTTTTAAGATCGACCTGAATCCCCGCACCACCACTCGGATCAGTACCGGCAATCGTCAGAGCGTTAATTCGTTTCATGCCTGCACCTCCTGc > 2:253538/1‑139 (MQ=255)
aCTGAGCAACCATAAGCGCCAAGTGCCGAGAAGGTTTTAAGATCGACCTGAATCCCCGCACCACCACTCGGATCAGTACCGGCAATCGTCAGAGCGTTAATTCGTTTCATGCCTGCACCTCCTGCGTCAATTGCCagag > 2:253743/1‑139 (MQ=255)
aCTGAGCAACCATAAGCGCCAAGTGCCGAGAAGGTTTTAAGATCGACCTGAATCCCCGCACCACCACTCGGATCAGTACCGGCAATCGTCAGAGCGTTAATTCGTTTCATGCCTGCACCTCCTGCGTCAATTGCCagag < 2:524512/139‑1 (MQ=255)
aCTGAGCAACCATAAGCGCCAAGTGCCGAGAAGGTTTTAAGATCGACCTGAATCCCCGCACCACCACTCGGATCAGTACCGGCAATCGTCAGAGCGTTAATTCGTTTCATGCCTGCACCTCCTGCGTCAATTGCCagag > 2:53169/1‑139 (MQ=255)
aGCAACCATAAGCGCCAAGTGCCGAGAAGGTTTTAAGATCGACCTGAATCCCCGCACCACCACTCGGATCAGTACCGGCAATCGTCAGAGCGTTAATTCGTTTCATGCCTGCACCTCCTGCGTCAATTGCCAGAGCGCa > 1:385278/1‑139 (MQ=255)
cgcCAAGTGCCGAGAAGGTTTTAAGATCGACCTGAATCCCCGCACCACCACTCGGATCAGTACCGGCAATCGTCAGAGCGTTAATTCGTTTCATGCCTGCACCTCCTGCGTCAATTGCCAGAGCGCAt < 1:448297/128‑1 (MQ=255)
cgcCAAGTGCCGAGAAGGTTTTAAGATCGACCTGAATCCCCGCACCACCACTCGGATCAGTACCGGCAATCGTCAGAGCGTTAATTCGTTTCATGCCTGCACCTCCTGCGTCAATTGCCAGAGCGCAt > 2:448297/1‑128 (MQ=255)
cAAGTGCCGAGAAGGTTTTAAGATCGACCTGAATCCCCGcac > 2:147030/1‑42 (MQ=255)
cAAGTGCCGAGAAGGTTTTAAGATCGACCTGAATCCCCGcac < 1:147030/42‑1 (MQ=255)
cAAGTGCCGAGAAGGTTTTAAGATCGACCTGAATCCCCGCACCACCACTCGGATCAGTACCGGCAATCGTCAGAGCGTTAATTCGTTTCATGCCTGCAc > 1:69103/1‑99 (MQ=255)
cAAGTGCCGAGAAGGTTTTAAGATCGACCTGAATCCCCGCACCACCACTCGGATCAGTACCGGCAATCGTCAGAGCGTTAATTCGTTTCATGCCTGCAc < 2:69103/99‑1 (MQ=255)
cAAGTGCCGAGAAGGTTTTAAGATCGACCTGAATCCCCGCACCACCACTCGGATCAGTACCGGCAATCGTCAGAGCGTTAATTCGTTTCATGCCTGCACCTCCTGCGTCAATTGCCAGAGCGCATCAAGGAAATGTGGa > 2:38854/1‑139 (MQ=255)
tGCCGAGAAGGTTTTAAGATCGACCTGAATCCCCGCACCACCACTCGGATCAGTACCGGCAATCGTCAGAGCGTTAATTCGTTTCATGCCTGCACCTCCTGCGTCAATTGCCAGAGCGCATCAAGGAAATGTGGAACaa < 2:385278/139‑1 (MQ=255)
|
CGACAAAATCAGGCTCAATGCGATACACCGACTGTACGCCACGGGTATTTTGCGCCACCAGTGCAGTAATAACTGAGCAACCATAAGCGCCAAGTGCCGAGAAGGTTTTAAGATCGGCCTGAATCCCCGCACCACCACTCGGATCAGTACCGGCAATCGTCAGAGCGTTAATTCGTTTCATGCCTGCACCTCCTGCGTCAATTGCCAGAGCGCATCAAGGAAATGTGGAACAA > NC_000913/2184336‑2184568
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
