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 |
1,891,013 |
C→G |
48.8% |
G190G (GGG→GGC) |
gudP ← |
predicted D‑glucarate transporter |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,891,013 | 0 | C | G | 48.8%
| ‑3.3
/ 48.6
| 41 | G190G (GGG→GGC) | gudP | predicted D‑glucarate transporter |
| Reads supporting (aligned to +/- strand): ref base C (3/18); new base G (8/12); total (11/30) |
| Fisher's exact test for biased strand distribution p-value = 8.55e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.58e-01 |
TCTTATTTACCCCCGGATGTTGATTTGGCTCGTGGATGACTTTCAACCAGATAAAGCTGATGACAATCCCCAGACCGCCCATAAAGAAGAAGACGTGTGACCAGCCCACTTCATGCGTCAGCCAGCCCAT > minE/1890946‑1891075
|
tcttATTTACCCCCGGATGTTGATTTGGCTCGTGGATGACTTTCAACCAGATAAAGCTGATGACAATc > 1:3058438/1‑68 (MQ=255)
tcttATTTACCCCCGGATGTTGATTTGGCTCGTGGATGACTTTCAACCAGATAAAGCTGATGACAATc > 1:1704877/1‑68 (MQ=255)
tcttATTTACCCCCGGATGTTGATTTGGCTCGTGGATGACTTTCAACCAGATAAAGCTGATGACAATc > 1:1552494/1‑68 (MQ=255)
cttATTTACCCCCGGATGTTGATTTGGCTCGTGGATGACTTTCAACCAGATAAAGCTGATGACAATc > 1:440281/1‑67 (MQ=255)
tttGGCTCGTGGATGACTTTCAACCAGATAAAGCTGATGACAATCCCCAGACCGCCCATAaagaagaa < 1:1009383/68‑1 (MQ=255)
tttGGCTCGTGGATGACTTTCAACCAGATAAAGCTGATGACAATCCCCAGACCGCCCATAaagaagaa < 1:102877/68‑1 (MQ=255)
ttGGCTCGTGGATGACTTTCAACCAGATAAAGCTGATGACAATCCCCAGACCGCCCATAAagaagaaga < 1:62096/69‑1 (MQ=255)
ttGGCTCGTGGATGACTTTCAACCAGATAAAGCTGATGACAATCCCCAGACCGCCCATAAagaagaaga < 1:2187123/69‑1 (MQ=255)
cGTGGATGACTTTCAACCAGATAAAGCTGATGACAATCCCCAGACCGCCCATAAAGAAGAAGACGtgtg < 1:1421868/69‑1 (MQ=255)
cGTGGATGACTTTCAACCAGATAAAGCTGATGACAATCCCCAGACCGCCCATAAAGAAGAAGACGtgtg < 1:1845398/69‑1 (MQ=255)
gTGGATGACTTTCAACCAGATAAAGCTGATGACAATCCCCAGACCGCCCATAAAGAAGAAGACGtgtg < 1:3240597/68‑1 (MQ=255)
gATGAGTTTCAACCAGATAAAGCTGATGACAATGCCCAGACCGCCCATAAAGAAGAAGACGTGTGACCa < 1:557274/69‑1 (MQ=255)
gATGACTTTCAACGAGATAAAGCTGATGACAATGCCCAGACCGCCCATAAAGAAGAAGACGTGTGACCa < 1:1117007/69‑1 (MQ=255)
gATGACTTTCAACCAGATAAAGCTGATGACAATGCCCAGACCGCCCATAAAGAAGAAGACGTTTGACCa < 1:435499/69‑1 (MQ=255)
gATGACTTTCAACCAGATAAAGCTGATGACAATGCCCAGACCGCCCATAAAGAAGAAGACGTGTGACCa < 1:523452/69‑1 (MQ=255)
gATGACTTTCAACCAGATAAAGCTGATGACAATGCCCAGACCGCCCATAAAGAAGAAGACGTGTGACCa < 1:854415/69‑1 (MQ=255)
gATGACTTTCAACCAGATAAAGCTGATGACAATGCCCAGACCGCCCATAAAGAAGAAGACGTGTGACCa < 1:1013876/69‑1 (MQ=255)
gATGACTTTCAACCAGATAAAGCTGATGACAATGCCCAGACCGCCCATAAAGAAGAAGACGTGTGACCa < 1:2897193/69‑1 (MQ=255)
gATGACTTTCAACCAGATAAAGCTGATGACAATGCCCAGACCGCCCATAAAGAAGAAGACGTGTGACCa < 1:2793343/69‑1 (MQ=255)
gATGACTTTCAACCAGATAAAGCTGATGACAATGCCCAGACCGCCCATAAAGAAGAAGACGTGTGACCa < 1:2724284/69‑1 (MQ=255)
gATGACTTTCAACCAGATAAAGCTGATGACAATGCCCAGACCGCCCATAAAGAAGAAGACGTGTGACCa < 1:1022307/69‑1 (MQ=255)
gATGACTTTCAACCAGATAAAGCTGATGACAATGCCCAGACCGCCCATAAAGAAGAAGACGTGTGACCa < 1:2031156/69‑1 (MQ=255)
gATGACTTTCAACCAGATAAAGCTGATGACAATGCCCAGACCGCCCATAAAGAAGAAGACGTGTGACCa < 1:1817124/69‑1 (MQ=255)
caTGACTTTCAACCAGATAAAGCTGATGACAATCACCAGACCGCCCATAAAGAAGAAGACGTGTGACCa > 1:2252597/2‑69 (MQ=255)
gACTTTCAACCAGATAAAGCTGATGACAATGCCCAGACCGc > 1:3232942/1‑41 (MQ=255)
gACTTTCAACCAGATAAAGCTGATGACAATGCCCAGACCGc > 1:1075274/1‑41 (MQ=255)
gACTTTCAACCAGATAAAGCTGATGACAATGCCCAGACCGc > 1:1290484/1‑41 (MQ=255)
gACTTTCAACCAGATAAAGCTGATGACAATGCCCAGACCGc > 1:1548651/1‑41 (MQ=255)
gACTTTCAACCAGATAAAGCTGATGACAATGCCCAGACCGc > 1:1749472/1‑41 (MQ=255)
gACTTTCAACCAGATAAAGCTGATGACAATGCCCAGACCGc > 1:2984137/1‑41 (MQ=255)
gACTTTCAACCAGATAAAGCTGATGACAATGCCCAGACCGc > 1:1827106/1‑41 (MQ=255)
gACTTTCAACCAGATAAAGCTGATGACAATGCCCAGACCGc > 1:2769517/1‑41 (MQ=255)
aaCCAGATAAAGCTGATGACAATCCCCAGACCGCCCATAAAGAAGAAGACGTGTGACCAGCCCACtt < 1:2807955/67‑1 (MQ=255)
aaCCAGATAAAGCTGATGACAATCCCCAGACCGCCCATAAAGAAGAAGACGTGTGACCAGCCCACtt < 1:2430998/67‑1 (MQ=255)
cAGATAAAGCTGATGACAATCCCCAGACCGCCCATAAAGAAGAAGACGTGTGACCAGCCCACTTCATGc > 1:3270850/1‑69 (MQ=255)
cAGATAAAGCTGATGACAATCCCCAGACCGCCCATAAAGAAGAAGACGTGTGACCAGCCCACTTCATGc > 1:2316168/1‑69 (MQ=255)
aaGCTGATGACAATCCCCAGACCGCCCATAAAGAAGAAGACGTGTGACCAGCCCACTTCATGCGTcagc < 1:2931854/69‑1 (MQ=255)
aaGCTGATGACAATCCCCAGACCGCCCATAAAGAAGAAGACGTGTGACCAGCCCACTTCATGCGTcagc < 1:3321614/69‑1 (MQ=255)
aaGCTGATGACAATCCCCAGACCGCCCATAAAGAAGAAGACGTGTGACCAGCCCACTTCATGCGTcagc < 1:3399359/69‑1 (MQ=255)
aaGCTGATGACAATCCCCAGACCGCCCATAAAGAAGAAGACGTGTGACCAGCCCACTTCATGCGTcagc < 1:2213381/69‑1 (MQ=255)
aaGCTGATGACAATCCCCAGACCGCCCATAAAGAAGAAGACGTGTGACCAGCCCACTTCATGCGTcagc < 1:487622/69‑1 (MQ=255)
aaGCTGATGACAATCCCCAGACCGCCCATAAAGAAGAAGACGTGTGACCAGCCCACTTCATGCGTcagc < 1:748118/69‑1 (MQ=255)
aaGCTGATGACAATCCCCAGACCGCCCATAAAGAAGAAGACGTGTGACCAGCCCACTTCATGCGTcagc < 1:2257770/69‑1 (MQ=255)
gaCAATCCCCAGACCGCCCATAAAGAAGAAGACGTGTGACCAGCCCACTTCATGCGTCAGCCAGCCCAt < 1:1624076/69‑1 (MQ=255)
aCAATCCCCAGACCGCCCATAAAGAAGAAGACGTGTGACCAGCCCACTTCATGCGTCAGCCAGCCCAt < 1:1373675/68‑1 (MQ=255)
|
TCTTATTTACCCCCGGATGTTGATTTGGCTCGTGGATGACTTTCAACCAGATAAAGCTGATGACAATCCCCAGACCGCCCATAAAGAAGAAGACGTGTGACCAGCCCACTTCATGCGTCAGCCAGCCCAT > minE/1890946‑1891075
|
| 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
