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 |
|
A2 F1 I0 R1
|
4577 |
57.4 |
3436498 |
77.7% |
2670158 |
63.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
1,489,413 |
T→G |
100% |
G540G (GGA→GGC) |
nuoL ← |
NADH:ubiquinone oxidoreductase, membrane subunit L |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,489,413 | 0 | T | G | 88.3%
| 73.2
/ 1.2
| 34 | G540G (GGA→GGC) | nuoL | NADH:ubiquinone oxidoreductase, membrane subunit L |
| Reads supporting (aligned to +/- strand): ref base T (2/2); new base G (21/9); total (23/11) |
| Fisher's exact test for biased strand distribution p-value = 5.80e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.81e-01 |
| Rejected as polymorphism: E-value score below prediction cutoff. |
CAGGCAATACCCAGGAACGGCTTGACGAACACTTTGTCATACAGCCAGTCAAATCCCCAGGCGTTGTACCACCAGGTGCCCAGCAGACGGCCCGGCGCACTGTTGGCGATGGAGGTC > minE/1489360‑1489476
|
cAGGCAATACCCAGGAACGGCTTGACGAACACTTTGTCGTAGAGCCAGTCAAAGCCCCAGGCGTTGTac < 1:2736385/69‑1 (MQ=255)
cAGGCAATACCCAGGAACGGCTTGACGAACACTTTGTCGTACAGCCAGTCAAAGCCCCAGGCGTTGTac < 1:945168/69‑1 (MQ=255)
cAGGCAATACCCAGGAACGGCTTGACGAACACTTTGTCGTACAGCCAGTCAAAGCCCCAGGCGTTGTac < 1:1254922/69‑1 (MQ=255)
cAGGCAATACCCAGGAACGGCTTGACGAACACTTTGTCGTACAGCCAGTCAAAGCCCCAGGCGTTGTac < 1:1276519/69‑1 (MQ=255)
cAGGCAATACCCAGGAACGGCTTGACGAACACTTTGTCGTACAGCCAGTCAAAGCCCCAGGCGTTGTac < 1:826679/69‑1 (MQ=255)
cAGGCAATACCCAGGAACGGCTTGACGAACACTTTGTCGTACAGCCAGTCAAAGCCCCAGGCGTTGTac < 1:23020/69‑1 (MQ=255)
cAGGCAATACCCAGGAACGGCTTGACGAACACTTTGTCGTACAGCCAGTCAAAGCCCCAGGCGTTGTac < 1:2051408/69‑1 (MQ=255)
cAGGCAATACCCAGGAACGGCTTGACGAACACTTTGTCGTACAGCCAGTCAAAGCCCCAGGCGTTGTac < 1:3402798/69‑1 (MQ=255)
aaCACTTTGTCGTACAGCCAGTCAAAGCCCCAGGCGTTGTac < 1:3324798/42‑1 (MQ=37)
cacTTTGTCATACAGCCAGTCAAATCCCCAGGCGTTGTACCACCAGGTGCCCAGCAGACGGCCCGgcgc < 1:174886/69‑1 (MQ=255)
aTACAGCCAGTCAAATCCCCAGGCGTTGTACCACCAGGTGCCCAGCAGACGGCCCGGCGCACTGTTGGc < 1:538903/69‑1 (MQ=255)
aGTCAAAGCCCCAGGCGTTGTACCACCAGGTACCCAGCAGACGGc > 1:3344054/1‑45 (MQ=38)
aGTCAAAGCCCCAGGCGTTGTACCACCAGGTACCCAGCAGACGGCCCGgcg > 1:1820847/1‑51 (MQ=38)
aGTCAAAGCCCCAGGCGTTGTACCACCAGGTACCCAGCAGACGGCCCGGCGCACTGTTGGCGATGGAg > 1:1247887/1‑68 (MQ=255)
aGTCAAAGCCCCAGGCGTTGTACCACCAGGTACCCAGCAGACGGCCCGGCGCACTGTTGGCGATGGAg > 1:3416153/1‑68 (MQ=255)
aGTCAAAGCCCCAGGCGTTGTACCACCAGGTACCCAGCAGACGGCCCGGCGCACTGTTGGCGATGGAg > 1:3295895/1‑68 (MQ=255)
aGTCAAAGCCCCAGGCGTTGTACCACCAGGTACCCAGCAGACGGCCCGGCGCACTGTTGGCGATGGAg > 1:695312/1‑68 (MQ=255)
aGTCAAAGCCCCAGGCGTTGTACCACCAGGTACCCAGCAGACGGCCCGGCGCACTGTTGGCGATGGAg > 1:3276397/1‑68 (MQ=255)
aGTCAAAGCCCCAGGCGTTGTACCACCAGGTACCCAGCAGACGGCCCGGCGCACTGTTGGCGATGGAg > 1:752909/1‑68 (MQ=255)
aGTCAAAGCCCCAGGCGTTGTACCACCAGGTACCCAGCAGACGGCCCGGCGCACTGTTGGCGATGGAg > 1:3132777/1‑68 (MQ=255)
aGTCAAAGCCCCAGGCGTTGTACCACCAGGTACCCAGCAGACGGCCCGGCGCACTGTTGGCGATGGAg > 1:293778/1‑68 (MQ=255)
aGTCAAAGCCCCAGGCGTTGTACCACCAGGTACCCAGCAGACGGCCCGGCGCACTGTTGGCGATGGAg > 1:281163/1‑68 (MQ=255)
aGTCAAAGCCCCAGGCGTTGTACCACCAGGTACCCAGCAGACGGCCCGGCGCACTGTTGGCGATGGAg > 1:2740836/1‑68 (MQ=255)
aGTCAAAGCCCCAGGCGTTGTACCACCAGGTACCCAGCAGACGGCCCGGCGCACTGTTGGCGATGGAg > 1:2157803/1‑68 (MQ=255)
aGTCAAAGCCCCAGGCGTTGTACCACCAGGTACCCAGCAGACGGCCCGGCGCACTGTTGGCGATGGAg > 1:2068864/1‑68 (MQ=255)
aGTCAAAGCCCCAGGCGTTGTACCACCAGGTACCCAGCAGACGGCCCGGCGCACTGTTGGCGATGGAg > 1:1996342/1‑68 (MQ=255)
aGTCAAAGCCCCAGGCGTTGTACCACCAGGTACCCAGCAGACGGCCCGGCGCACTGTTGGCGATGGAg > 1:1946992/1‑68 (MQ=255)
aGTCAAAGCCCCAGGCGTTGTACCACCAGGTACCCAGCAGACGGCCCGGCGCACTGTTGGCGATGGAg > 1:1691628/1‑68 (MQ=255)
aGTCAAAGCCCCAGGCGTTGTACCACCAGGTACCCAGCAGACGGCCCGGCGCACTGTTGGCGATGGAg > 1:1599201/1‑68 (MQ=255)
aGTCAAAGCCCCAGGCGTTGTACCACCAGGTACCCAGCAGACGGCCCGGCGCACTGTTGGCGATGGAg > 1:1524786/1‑68 (MQ=255)
aGTCAAAGCCCCAGGCGTTGTACCACCAGGTACCCAGCAGACGGCCCGGCGCACTGTTGGCGATGGAg > 1:1070969/1‑68 (MQ=255)
aGTCAAAGCCCCAGGCGTTGTACCACAAGGTACCCAGCAGACGGCCCGGCGCACTGTTGGCGATGGAg > 1:2439203/1‑68 (MQ=255)
cAACTCCCCAGGCGTTGTACCACCAGGTGCCCAGCAGACGGCCCGGCGCACTGTTGGCGATGGAGGTc > 1:1786059/1‑68 (MQ=255)
cAAATCCCCAGGCGTTGTACCACCAGGTGCCCAGCAGACGGCCCGGCGCACTGTTGGCGATGGAGGTc > 1:1619654/1‑68 (MQ=255)
|
CAGGCAATACCCAGGAACGGCTTGACGAACACTTTGTCATACAGCCAGTCAAATCCCCAGGCGTTGTACCACCAGGTGCCCAGCAGACGGCCCGGCGCACTGTTGGCGATGGAGGTC > minE/1489360‑1489476
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
