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 |
1,552,932 |
A→C |
31.9% |
T106T (ACT→ACG) |
dsdC ← |
DNA‑binding transcriptional dual regulator |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,552,932 | 0 | A | C | 31.9%
| 38.5
/ 32.3
| 47 | T106T (ACT→ACG) | dsdC | DNA‑binding transcriptional dual regulator |
| Reads supporting (aligned to +/- strand): ref base A (20/12); new base C (6/9); total (26/21) |
| Fisher's exact test for biased strand distribution p-value = 2.11e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
TGTAAAGTCACCTAATGCGGGCACCAACCAGCATTGGGCGATAGAGGGCCGGGAATACAGAGTTAACGTTCCCGATAACTCCTGATTTTTGATATCAAGAATTTCCTGGTTCAGGGTATCCAGCG > minE/1552872‑1552996
|
tgtAAAGTCACCTAATGCGGGCACCAACCAGCATTGGGCGATAGAGGGCCGTGAATACAGAGTTAACGt < 1:2638736/69‑1 (MQ=255)
tgtAAAGTCACCTAATGCGGGCACCAACCAGCATTGGGCGATAGAGGGCCGGGAATACAGAGTTAACGt < 1:614567/69‑1 (MQ=255)
tgtAAAGTCACCTAATGCGGGCACCAACCAGCATTGGGCGATAGAGGGCCGGGAATACAGAGTTAACGt < 1:2701503/69‑1 (MQ=255)
tgtAAAGTCACCTAATGCGGGCACCAACCAGCATTGGGCGATAGAGGGCCGGGAATACAGAGTTAACGt < 1:1507395/69‑1 (MQ=255)
tgtAAAGTCACCTAATGCGGGCACCAACCAGCATTGGGCGATAGAGGGCCGGGAATACAGAGTTAACGt < 1:1462958/69‑1 (MQ=255)
tgtAAAGGCACCTAATGCGGGCACCAACCAGCATTGGGCGATAGAGGGCCGGGAATACAGAGTTAACGt < 1:1005891/69‑1 (MQ=255)
gtAAAGTCACCTAATGCGGGCACCAACCAGCATTGGGCGATAGAGGGCCGGGAATACAGAGTTAACGt < 1:2568872/68‑1 (MQ=255)
tAAAGTCACCTAATGCGGGCACCAACCAGCATTGGGCGATAGAGGGCCGGGAATACAGAGTTAACGTTc > 1:1691634/1‑69 (MQ=255)
tCACCTAATGCGGGCACCAACCAGCATTGGGCGATAGAGGGCCGGGAATACAGAGTTAACGTTCCCGAt < 1:1630420/69‑1 (MQ=255)
tCACCTAATGCGGGCACCAACCAGCATTGGGCGATAGAGGGCCGGGAATACAGAGTTAACGTTCCCGAt < 1:1856777/69‑1 (MQ=255)
tCACCTAATGCGGGCACCAACCAGCATTGGGCGATAGAGGGCCGGGAATACAGAGTTAACGTTCCCGAt < 1:2110526/69‑1 (MQ=255)
tCACCTAATGCGGGCACCAACCAGCATTGGGCGATAGAGGGCCGGGAATACAGAGTTAACGTTCCCGAt < 1:2030389/69‑1 (MQ=255)
cGGGCACCAACCAGCATTGGGCGATAGAGGGCCGGGAATACAGCGTTAACGTTCCCGATAACTCCTGAt < 1:2890158/69‑1 (MQ=255)
cGGGCACCAACCAGCATTGGGCGATAGAGGGCCGGGAATACAGCGTTAACGTTCCCGATAACTCCTGAt < 1:3196431/69‑1 (MQ=255)
cGGGCACCAACCAGCATTGGGCGATAGAGGGCCGGGAATACAGCGTTAACGTTCCCGATAACTCCTGAt < 1:513097/69‑1 (MQ=255)
cGGGCACCAACCAGCATTGGGCGATAGAGGGCCGGGAATACAGCGTTAACGTTCCCGATAACTCCTGAt < 1:86476/69‑1 (MQ=255)
cGGGCACCAACCAGCATTGGGCGATAGAGGGCCGGGAATACAGCGTTAACGTTCCCGATAACTCCTGAt < 1:2576386/69‑1 (MQ=255)
cGGGCACCAACCAGCATTGGGCGATAGAGGGCCGGGAATACAGCGTTAACGTTCCCGATAACTCCTGAt < 1:1393424/69‑1 (MQ=255)
cGGGCACCAACCAGCATTGGGCGATAGAGGGCCGGGAATACAGCGTTAACGTTCCCGATAACTCCTGAt < 1:1556558/69‑1 (MQ=255)
gggCACCAACCAGCATTGGGCGATAGAGGGCCGGGAATACAGCGTTAACGTTCCCGATAACTCCTGAt < 1:2275083/68‑1 (MQ=255)
ggCACCAACCAGCATTGGGCGATAGAGGGCCGGGAATACAGAGTTAACGTTCCCGATAACTCCTGAttt > 1:2164752/1‑69 (MQ=255)
ggCACCAACCAGCATTGGGCGATAGAGGGCCGGGAATACAGAGTTAACGTTCCCGATAACTCCTGAttt > 1:1417471/1‑69 (MQ=255)
gCACCAACCAGCATTGGGCGATAGAGGGCCGGGAATACAGCGTTAACGTTCCCGATAACTCCTGAt < 1:1893151/66‑1 (MQ=255)
gggCGATAGAGGGCCGGGAATACAGAGTTAACGTTCCCGATAACTCCTGATTTTTGATATCAAGAAttt > 1:1011544/1‑69 (MQ=255)
gggCGATAGAGGGCCGGGAATACAGAGTTAACGTTCCCGATAACTCCTGATTTTTGATATCAAGAAttt > 1:3198595/1‑69 (MQ=255)
gggCGATAGAGGGCCGGGAATACAGAGTTAACGTTCCCGATAACTCCTGATTTTTGATATCAAGAAttt > 1:3109428/1‑69 (MQ=255)
gggCGATAGAGGGCCGGGAATACAGAGTTAACGTTCCCGATAACTCCTGATTTTTGATATCAAGAAttt > 1:2569901/1‑69 (MQ=255)
gggCGATAGAGGGCCGGGAATACAGAGTTAACGTGCCCGATAACTCCTGATTTTTGATATCAAGAAttt > 1:726565/1‑69 (MQ=255)
cGGGAATACAGAGTTAACGTTCCCGATAACTCCTGATTTTTGATATCAAGAATTTCCTGGTTCAGGGTa < 1:2889070/69‑1 (MQ=255)
aTACAGCGTTAACGTTCCCGATAACTCCTGATTTTTGATATCCAGAATTTCCTGATTCAGGGTATCCa > 1:2232318/1‑68 (MQ=255)
aTACAGCGTTAACGTTCCCGATAACTCCTGATTTTTGATATCCAGAATTTCCTGATTCAGGGTATCCa > 1:2020303/1‑68 (MQ=255)
aTACAGCGTTAACGTTCCCGATAACTCCTGATTTTTGATATCCAGAATTTCCTGATTCAGGGTATCCa > 1:672746/1‑68 (MQ=255)
aTACAGCGTTAACGTTCCCGATAACTCCTGATTTTTGATATCCAGAATTTCCTGATTCAGGGTATCCa > 1:545566/1‑68 (MQ=255)
aTACAGCGTTAACGTTCCCGATAACTCCTGATTTTTGATATCCAGAATTTCCTGATTCAGGGTATCCa > 1:154222/1‑68 (MQ=255)
aTACAGCGTTAACGTTCCCGATAACTCCTGAATTTTGATATCCAGAATTTCCTgat > 1:2768461/1‑54 (MQ=255)
cAGAGTTAACGTTCCCGATAACTCCTGATTTTTGATATCAAGAAt > 1:2668482/1‑45 (MQ=255)
cAGAGTTAACGTTCCCGATAACTCCTGATTTTTGATATCAAGAATTTCCTGGTTCAGGGTATCCAGcg > 1:2905196/1‑68 (MQ=255)
cAGAGTTAACGTTCCCGATAACTCCTGATTTTTGATATCAAGAATTTCCTGGTTCAGGGTATCCAGcg > 1:1722480/1‑68 (MQ=255)
cAGAGTTAACGTTCCCGATAACTCCTGATTTTTGATATCAAGAATTTCCTGGTTCAGGGTATCCAGcg > 1:2632796/1‑68 (MQ=255)
cAGAGTTAACGTTCCCGATAACTCCTGATTTTTGATATCAAGAATTTCCTGGTTCAGGGTATCCAGcg > 1:2091261/1‑68 (MQ=255)
cAGAGTTAACGTTCCCGATAACTCCTGATTTTTGATATCAAGAATTTCCTGGTTCAGGGTATCCAGcg > 1:3363581/1‑68 (MQ=255)
cAGAGTTAACGTTCCCGATAACTCCTGATTTTTGATATCAAGAATTTCCTGGTTCAGGGTATCCAGcg > 1:3411809/1‑68 (MQ=255)
cAGAGTTAACGTTCCCGATAACTCCTGATTTTTGATATCAAGAATTTCCTGGTTCAGGGTATCCAGcg > 1:1310683/1‑68 (MQ=255)
cAGAGTTAACGTTCCCGATAACTCCTGATTTTTGATATCAAGAATTTCCTGGTTCAGGGTATCCAGcg > 1:593937/1‑68 (MQ=255)
cAGAGTTAACGTTCCCGATAACTCCTGATTTTTGATATCAAGAATTTCCTGGTTCAGGGTATCCAGcg > 1:1547579/1‑68 (MQ=255)
cAGAGTTAACGTTCCCGATAACTCCTGATTTTTGATATCAAGAATTTCCTGGTTCAGGGTATCCAGc > 1:3192225/1‑67 (MQ=255)
cAGAGTTAACGTTCCCGATAACTCCTGATTTTTGATATCAAGAATTTCCTGGTTCAGGGTATCCAGc > 1:1236816/1‑67 (MQ=255)
|
TGTAAAGTCACCTAATGCGGGCACCAACCAGCATTGGGCGATAGAGGGCCGGGAATACAGAGTTAACGTTCCCGATAACTCCTGATTTTTGATATCAAGAATTTCCTGGTTCAGGGTATCCAGCG > minE/1552872‑1552996
|
| 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
