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 |
1,112,827 |
T→C |
78.4% |
E659E (GAA→GAG) |
pps ← |
phosphoenolpyruvate synthase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,112,827 | 0 | T | C | 78.4%
| 62.3
/ 9.8
| 46 | E659E (GAA→GAG) | pps | phosphoenolpyruvate synthase |
| Reads supporting (aligned to +/- strand): ref base T (6/4); new base C (17/19); total (23/23) |
| Fisher's exact test for biased strand distribution p-value = 7.22e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.53e-01 |
GATTTTCAGCCCGTTCTCGCCACGTTTCAGCCCCTGACGCGCCAGTTCTTCAACCACCGCTTTCGCCTGATCTACGGTACGCACGAACGGGATCATGATCTCAACGTTGGTCAGT > minE/1112779‑1112893
|
gatTTTCAGCCCGTTCTCGCCACGTTTCAGCCCCTGACGCGCCAGTTCTTCAACCACCGCTTTCGCCTg < 1:3089460/69‑1 (MQ=255)
gatTTTCAGCCCGTTCTCGCCACGTTTCAGCCCCTGACGCGCCAGTTCTTCAACCACCGCTTTCGCCTg < 1:2060894/69‑1 (MQ=255)
gatTTTCAGCCCGTTCTCGCCACGTTTCAGCCCCTGACGCGCCAGTTCTTCAACCACCGCTTTCGCCTg < 1:1735074/69‑1 (MQ=255)
cccGTTCTCGCCACGTTTCAGCCCCTGACGCGCCAGTTCTTCAACCACCGCTTTCGCCTGATCTACgg < 1:3418793/68‑1 (MQ=255)
cccGTTCTCACCACGTTTCAGCCCCTGATGCGCCAGTTCCTCAACCACCGCTTTCGCCTGATCAACGGt < 1:317995/69‑1 (MQ=255)
cccGTTCTCACCACGTTTCAGCCCCTGATGCGCCAGTTCCTCAACCACCGCTTTCGCCTGATCAACGGt < 1:3227292/69‑1 (MQ=255)
cccGTTCTCACCACGTTTCAGCCCCTGATGCGCCAGTTCCTCAACCACCGCTTTCGCCTGATCAACGGt < 1:2628138/69‑1 (MQ=255)
cccGTTCTCACCACGTTTCAGCCCCTGATGCGCCAGTTCCTCAACCACCGCTTTCGCCTGATCAACGGt < 1:2288944/69‑1 (MQ=255)
cccGTTCTCACCACGTTTCAGCCCCTGATGCGCCAGTTCCTCAACCACCGCTTTCGCCTGATCAACGGt < 1:3328127/69‑1 (MQ=255)
cccGTTCTCACCACGTTTCAGCCCCTGATGCGCCAGTTCCTCAACCACCGCTTTCGCCTGATCAACGGt < 1:2737193/69‑1 (MQ=255)
cccGTTCTCACCACGTTTCAGCCCCTGATGCGCCAGTTCCTCAACCACCGCTTTCGCCTGATCAACGGt < 1:3108989/69‑1 (MQ=255)
cccGTTCTCACCACGTTTCAGCCCCTGATGCGCCAGTTCCTCAACCACCGCTTTCGCCTGATCAACGGt < 1:1925809/69‑1 (MQ=255)
cccGTTCTCACCACGTTTCAGCCCCTGATGCGCCAGTTCCTCAACCACCGCTTTCGCCTGATCAACGGt < 1:544195/69‑1 (MQ=255)
cccGTTCTCACCACGTTTCAGCCCCTGATGCGCCAGTTCCTCAACCACCGCTTTCGCCTGATCAACGGt < 1:2817975/69‑1 (MQ=255)
cccGTTCTCACCACGTTTCAGCCCCTGATGCGCCAGTTCCTCAACCACCGCTTTCGCCTGATCAACGGt < 1:1570227/69‑1 (MQ=255)
cccGTTCTCACCACGTTTCAGCCCCTGATGCGCCAGTTCCTCAACCACCGCTTTCGCCTGATCAACGGt < 1:2820836/69‑1 (MQ=255)
cccGTTCTCACCACGTTTCAGCCCCTGATGCGCCAGTTCCTCAACCACCGCTTTCGCCTGATCAACGGt < 1:2916267/69‑1 (MQ=255)
cccGTTCTCACCACGTTTCAGCCCCTGATGCGCCAGTTCCTCAACCACCGCTTTCGCCTGATCAACGGt < 1:1291284/69‑1 (MQ=255)
cccGTTCTCACCACGTTTCAGCCCCTGATGCGCCAGTTCCTCAACCACCGCTTTCGCCTGATCAACGGt < 1:929303/69‑1 (MQ=255)
cccGTTCTCACCACGTTTCAGCCCCTGATGCGCCAGTTCCTCAACCACCGCTTTCGCCTGATCAACGGt < 1:1034492/69‑1 (MQ=255)
cccGTTCTCACCACGTTTCAGCCCCTGATGCGCCAGTTCCTCAACCACCGCTTTCGCCTGATCAACCGt < 1:3163005/69‑1 (MQ=255)
ccGTTCTCACCACGTTTCAGCCCCTGATGCGCCAGTTCCTCAACCACCGCTTTCGCCTGATCAACGGt < 1:493064/68‑1 (MQ=255)
ccGTTCTCACCACGTTTCAGCCCCTGATGCGCCAGTTCCTCAACCACCGCTTTCGCCTGATCAACGGt < 1:188708/68‑1 (MQ=255)
ctcGCCACGTTTCAGCCCCTGACGCGCCAGTTCTTCAACCACCGCTTTCGCCTGATCTACGGTACGCa > 1:2785149/1‑68 (MQ=255)
ctcGCCACGTTTCAGCCCCTGACGCGCCAGTTCTTCAACCACCGCTTTCGCCTGATCTACGGTACGCa > 1:2248657/1‑68 (MQ=255)
ctcGCCACGTTTCAGCCCCTGACGCGCCAGTTCTTCAACCACCGCTTTCGCCTGATCTACGGTACGCa > 1:3197036/1‑68 (MQ=255)
ctcGCCACGTTTCAGCCCCTGACGCGCCAGTTCTTCAACCACCGCTTTCGCCTGATCTACGGTACGCa > 1:3227671/1‑68 (MQ=255)
ctcGCCACGTTTCAGCCCCTGACGCGCCAGTTCTTCAACCACCGCTTTCGCCTGATCTACGGTACGCa > 1:731676/1‑68 (MQ=255)
ctcGCCACGTTTCAGCCCCTGACGCGCCAGTTCTTCAACCACCGCTTTCGCCTGATCTACGGTACGCa > 1:1453614/1‑68 (MQ=255)
gTTTCAGCCCCTGATGCGCCAGTTCCTCAACCACCGCTTTCg > 1:2743188/1‑42 (MQ=37)
gTTTCAGCCCCTGATGCGCCAGTTCCTCAACCACCGCTTTCGCCTGATCAACGGTACGCACGAACggg > 1:1147270/1‑68 (MQ=255)
gTTTCAGCCCCTGATGCGCCAGTTCCTCAACCACCGCTTTCGCCTGATCAACGGTACGCACGAACggg > 1:340276/1‑68 (MQ=255)
gTTTCAGCCCCTGATGCGCCAGTTCCTCAACCACCGCTTTCGCCTGATCAACGGTACGCACGAACggg > 1:340341/1‑68 (MQ=255)
gTTTCAGCCCCTGATGCGCCAGTTCCTCAACCACCGCTTTCGCCTGATCAACGGTACGCACGAACggg > 1:774937/1‑68 (MQ=255)
gTTTCAGCCCCTGATGCGCCAGTTCCTCAACCACCGCTTTCGCCTGATCAACGGTACGCACGAACggg > 1:824543/1‑68 (MQ=255)
gTTTCAGCCCCTGATGCGCCAGTTCCTCAACCACCGCTTTCGCCTGATCAACGGTACGCACGAACggg > 1:3049002/1‑68 (MQ=255)
gTTTCAGCCCCTGATGCGCCAGTTCCTCAACCACCGCTTTCGCCTGATCAACGGTACGCACGAACggg > 1:2742419/1‑68 (MQ=255)
gTTTCAGCCCCTGATGCGCCAGTTCCTCAACCACCGCTTTCGCCTGATCAACGGTACGCACGAACggg > 1:2728363/1‑68 (MQ=255)
gTTTCAGCCCCTGATGCGCCAGTTCCTCAACCACCGCTTTCGCCTGATCAACGGTACGCACGAACggg > 1:272334/1‑68 (MQ=255)
gTTTCAGCCCCTGATGCGCCAGTTCCTCAACCACCGCTTTCGCCTGATCAACGGTACGCACGAACggg > 1:3013331/1‑68 (MQ=255)
gTTTCAGCCCCTGATGCGCCAGTTCCTCAACCACCGCTTTCGCCTGATCAACGGTACGCACGAACggg > 1:1233903/1‑68 (MQ=255)
gTTTCAGCCCCTGATGCGCCAGTTCCTCAACCACCGCTTTCGCCTGATCAACGGTACGCACGAACggg > 1:1543061/1‑68 (MQ=255)
gTTTCAGCCCCTGATGCGCCAGTTCCTCAACCACCGCTTTCGCCTGATCAACGGTACGCACGAACggg > 1:179038/1‑68 (MQ=255)
gTTTCAGCCCCTGATGCGCCAGTTCCTCAACCACCGCTTTCGCCTGATCAACGGTACGCACGAACggg > 1:1879779/1‑68 (MQ=255)
gTTTCAGCCCCTGATGCGCCAGTTCCTCAACCACCGCTTTCGCCTGATCAACGGTACGCACGAACggg > 1:1874741/1‑68 (MQ=255)
gTTTCAGCCCCTGATACGCCAGTTCCTCAACCACCGCTTTCGCCTGATCAACGGTACGCACGAACggg > 1:1614958/1‑68 (MQ=255)
tcttcAACCACCGCTTTCGCCTGATCTACGGTACGCAc > 1:2634094/1‑38 (MQ=255)
tcttcAACCACCGCTTTCGCCTGATCTACGGTACGCACGAACGGGATCATGATCTCAACGTTGGTCAGt > 1:2679807/1‑69 (MQ=255)
tcttcAACCACCGCTTTCGCCTGATCTACGGTACGCACGAACGGGATCATGATCTCAACGTTGGTCAGt > 1:1448764/1‑69 (MQ=255)
cttcAACCACCGCTTTCGCCTGATCTACGGTACGCACGAACGGGATCATGATGTCAACGTTGGTCAGt > 1:2844170/1‑68 (MQ=255)
cttcAACCACCGCTTTCGCCTGATCTACGGTACGCACGAACGGGATCATGATCTCAACGTTGGTCAg > 1:954172/1‑67 (MQ=255)
cttcAACCACCGCTTTCGCCTGATCTACGGTACGCACGAACGGGATCATGATCTCAACGTTGGTCAGt > 1:2147378/1‑68 (MQ=255)
cttcAACCACCGCTTTCGCCTGATCTACGGTACGCACGAACGGGATCATGATCTCAACGTTGGTCAGt > 1:1740035/1‑68 (MQ=255)
cttcAACCACCGCTTTCGCCTGATCTACGGTACGCACGAACGGGATCATGATCTCAACGTTGGTCAGt > 1:3381236/1‑68 (MQ=255)
cttcAACCACCGCTTTCGCCTGATCTACGGTACGCACGAACGGGATCATGATCTCAACGTTGGTCAGt > 1:2267364/1‑68 (MQ=255)
cttcAACCACCGCTTTCGCCTGATCTACGGTACGCACGAACGGGATCATGATCTCAACGTTGGTCAGt > 1:3297703/1‑68 (MQ=255)
cttcAACCACCGCTTTCGCCTGATCTACGGTACGCACGAACGGGATCATGATCTCAACGTTGGTCAGt > 1:3243025/1‑68 (MQ=255)
cttcAACCACCGCTTTCGCCTGATCTACGGTACGCACGAACGGGATCATGATCTCAACGTTGGTCAGt > 1:2565099/1‑68 (MQ=255)
|
GATTTTCAGCCCGTTCTCGCCACGTTTCAGCCCCTGACGCGCCAGTTCTTCAACCACCGCTTTCGCCTGATCTACGGTACGCACGAACGGGATCATGATCTCAACGTTGGTCAGT > minE/1112779‑1112893
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
