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 F8 I0 R2
|
296 |
77.6 |
4260404 |
88.1% |
3753415 |
61.2 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
1,073,671 |
C→T |
52.2% |
G50S (GGC→AGC) |
ydhQ ← |
conserved hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,073,671 | 0 | C | T | 52.2%
| ‑2.2
/ 68.4
| 46 | G50S (GGC→AGC) | ydhQ | conserved hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base C (13/9); new base T (12/12); total (25/21) |
| Fisher's exact test for biased strand distribution p-value = 5.68e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
GCGTGCCATTGTTACCGTACTGTGTGCATTTGGCGATCCCACCGGTTGCCACTTTCAACCAGCCAGCCCCCGTGACCACGGTATTTTCGGCTCTTCCGCCAGCTTCAACAATCAACTCGCCTTCAGTAAG > minE/1073608‑1073737
|
gCGTGCCATTGTTACCGTACTGTGTGCATTTGGCGATCCCACCGGTTGCCACTTTCAACCAGCCAGccccc < 1:2397636/71‑1 (MQ=255)
gTGCCATTGTTACCGTACTGTGTGCATTTGGCGATCCCACCGGTTGCCACTTTCAACCAGCCAGCCCCCGt < 1:144348/71‑1 (MQ=255)
gTTACCTTACTGTGTGCATTTGGCGATCCCACCGGTTGCCACTTTCAACCAGCCAGCCCCCGTGACCACgg > 1:543221/1‑71 (MQ=255)
gTTACCGTACTGTGTGCATTTGGCGATCCCACCGGTTGCCACTTTCAACCAGCCAGCCCCCGTGACCACgg > 1:2980144/1‑71 (MQ=255)
gTTACCGTACTGTGTGCATTTGGCGATCCCACCGGTTGCCACTTTCAACCAGCCAGCCCCCGTGACCACgg > 1:2223901/1‑71 (MQ=255)
gTTACCGTACTGTGTGCATTTGGCGATCACACCGGTTGCCACTTTCAACCAGCCAGCCCCCGTGAc > 1:725246/1‑66 (MQ=255)
tgtgCATTTGGCGATCCCACCGGTTGCCACTTTCAACCAGCTAGCCCCCGTGa > 1:3383224/1‑53 (MQ=255)
tgCATTTGGCGATCCCACCGGTTGCCACTTTCAACCAGCTAGCCCCCGTGACCACGGTATTTTCGGctct < 1:619429/70‑1 (MQ=255)
tgCATTTGGCGATCCCACCGGTTGCCACTTTCAACCAGCCAGCCCCCGTGACCACGGTATTTTCGGctct < 1:3429221/70‑1 (MQ=255)
tgCATTTGGCGATCCCACCGGTTGCCACTTTCAACCAGCCAGCCCCCGTGACCACGGTATTTTCGGctct < 1:2954292/70‑1 (MQ=255)
tgCATTTGGCGATCCCACCGGTTGCCACTTTCAACCAGCCAGCCCCCGTGACCACGGTATTTTCGGCTCtt > 1:2171572/1‑71 (MQ=255)
ggCGATCCCACCGGTTGCCACTTTCAACCAGCTAGCCCCCGTGACCACGGTATTTTCGGCTCTTCCGCCAg > 1:1809685/1‑71 (MQ=255)
ggCGATCCCACCGGTTGCCACTTTCAACCAGCTAGCCCCCGTGACCACGGTATTTTCGGCTCTTCCGCCAg > 1:255833/1‑71 (MQ=255)
aTCCCACCGGTTGCCACTTTCAACCAGCCAGCCCCCGTGACCACGGTATTTTCGGCTCTTCCGCCAGCtt > 1:206287/1‑70 (MQ=255)
aTCCCACCGGTTGCCACTTTCAACCAGCCAGCCCCCGTGACCACGGTATTTTCGGCTCTTCCGCCAGCTTc < 1:1179824/71‑1 (MQ=255)
tCCCACCGGTTGCCACTTTCAACCAGCCAGCCCCCGTGACCACGGTATTTTc < 1:2210995/52‑1 (MQ=255)
ccACCGGTTGCCACTTTCAACCAGCCAGCCCCCGTGACCACGGTATTTTCgg > 1:2189993/1‑52 (MQ=255)
aCCGGTTGGCACTTTCAACCAGCCAGCCCCCGTGACCACGGTATTTTCGGCTCTTCCGCCAGCTTca < 1:3715089/67‑1 (MQ=255)
aCCGGTTGCCACTTTCAACCAGCTAGCCCCCGTGACCACGGTATTTTCGGctct < 1:1965587/54‑1 (MQ=255)
aCCGGTTGCCACTTTCAACCAGCTAGCCCCCGTGACCACGGTATTTTCGGctct < 1:3641684/54‑1 (MQ=255)
aCCGGTTGCCACTTTCAACCAGCTAGCCCCCGTGACCACGGTATTTTCGGctct < 1:3061302/54‑1 (MQ=255)
aCCGGTTGCCACTTTCAACCAGCCAGCCCCCGTGACCACGGTATTTTCGGCTCTTCCGCCAGCTTca < 1:589720/67‑1 (MQ=255)
aCCGGTTGCCACTTTCAACCAGCCAGCCCCCGTGACCACGGTATTTTCGGCTCTTCCGCCAGCTTca < 1:42984/67‑1 (MQ=255)
cGGTTGCCACTTTCAACCAGCTAGCCCCCGTGACCACGGTATTTTCGGCTCTTc > 1:1947282/1‑54 (MQ=255)
cGGTTGCCACTTTCAACCAGCTAGCCCCCGTGACCACGGTATTTTCGGCTCTTc > 1:1382276/1‑54 (MQ=255)
cGGTTGCCACTTTCAACCAGCTAGCCCCCGTGACCACGGTATTTTCGGCTCTTc > 1:1407200/1‑54 (MQ=255)
cGGTTGCCACTTTCAACCAGCTAGCCCCCGTGACCACGGTATTTTCGGCTCTTc > 1:178240/1‑54 (MQ=255)
cGGTTGCCACTTTCAACCAGCTAGCCCCCGTGACCACGGTATTTTCGGCTCTTc > 1:2738171/1‑54 (MQ=255)
cGGTTGCCACTTTCAACCAGCTAGCCCCCGTGACCACGGTATTTTCGGCTCTTc > 1:2405602/1‑54 (MQ=255)
ggTTGCCACTTTCAACCAGCTAGCCCCCGTGACCACGGTATTTTCGGCTCTTCCGCCAGCTTCAACAAt > 1:1253255/1‑69 (MQ=255)
cTTTCAACCAGCTAGCCCCCGTGACCACGGTATTTTCGGCTCTTCCGCCAGCTTCAACAATc < 1:2814756/62‑1 (MQ=255)
cTTTCAACCAGCTAGCCCCCGTGACCACGGTATTTTCGGCTCTTCCGCCAGCTTCAACAATc < 1:753228/62‑1 (MQ=255)
cTTTCAACCAGCTAGCCCCCGTGACCACGGTATTTTCGGCTCTTCCGCCAGCTTCAACAATc < 1:748062/62‑1 (MQ=255)
cTTTCAACCAGCTAGCCCCCGTGACCACGGTATTTTCGGCTCTTCCGCCAGCTTCAACAATc < 1:1013663/62‑1 (MQ=255)
cTTTCAACCAGCTAGCCCCCGTGACCACGGTATTTTCGGCTCTTCCGCCAGCTTCAACAATc < 1:2401714/62‑1 (MQ=255)
cTTTCAACCAGCTAGCCCCCGTGACCACGGTATTTTCGGCTCTTCCGCCAGCTTCAACAATCAACTCGCCt > 1:1408045/1‑71 (MQ=255)
cTTTCAACCAGCCAGCCCCCGTGACCACGGTATTTTCGGCTCTTCCGCCAGCTTCAACAATCAACTCGCCt > 1:1868141/1‑71 (MQ=255)
tttCAACCAGCCAGCCCCCGTGACCACGGTATTTTCGGCTCTTc > 1:3108839/1‑44 (MQ=255)
ttCAACCAGCCAGCCCCCGTGACCACGGTATTTTCGGCTCTTCCGCCAGCTTCAACAATCAACTCGCCtt > 1:2944242/1‑70 (MQ=255)
ttCAACCAGCCAGCCCCCGTGACCACGGTATTTTCGGCTCTTCCGCCAGCTTCAACAATCAACTCGCCtt > 1:3264763/1‑70 (MQ=255)
ttCAACCAGCCAGCCCCCGTGACCACGGTATTTTCGGCTCTTCCGCCAGCTTCAACAATCAACTCGCCtt > 1:320174/1‑70 (MQ=255)
tCAACCAGCTAGCCCCCGTGACCACGGTATTTTCGGCTCTTCCGCCAGCTTCAACAATCAACTCGCCtt > 1:1395487/1‑69 (MQ=255)
tCAACCAGCCAGCCCCCGTGACCACGGTATTTTCGGCTCTTCCGCCAGCTTCAACAATCAACTCGCCtt > 1:2600820/1‑69 (MQ=255)
aCCAGCTAGCCCCCGTGACCACGGTATTTTCGGCTCTTCCGCCAGCTTCAACAATCAACTCGCCTTCAGTa < 1:4209414/71‑1 (MQ=255)
aCCAGCTAGCCCCCGTGACCACGGTATTTTCGGCTCTTCCGCCAGCTTCAACAATCAACTCGCCTTCAGTa < 1:1863610/71‑1 (MQ=255)
aCCAGCTAGCCCCCGTGACCACGGTATTTTCGGCTCTTCCGCCAGCTTCAACAATCAACTCGCCTTCAGTa < 1:1915705/71‑1 (MQ=255)
ccagctagCCCCCGTGACCACGGTATTTTCGGCTCTTCCGCCAGCTTCAACAATCAACTCGCCTTCAGtt < 1:1822781/70‑2 (MQ=255)
cagctagcCCCCGTGACCACGGTATTTTCGGCTCTTCCGCCAGCTTCAACAATCAACTCGCCTTCAGTAAg > 1:347081/1‑71 (MQ=255)
|
GCGTGCCATTGTTACCGTACTGTGTGCATTTGGCGATCCCACCGGTTGCCACTTTCAACCAGCCAGCCCCCGTGACCACGGTATTTTCGGCTCTTCCGCCAGCTTCAACAATCAACTCGCCTTCAGTAAG > minE/1073608‑1073737
|
| 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
