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 |
2,057,922 |
C→T |
32.2% |
T249T (ACC→ACT) |
ttdA → |
L‑tartrate dehydratase, alpha subunit |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,057,922 | 0 | C | T | 32.2%
| 55.4
/ 30.8
| 65 | T249T (ACC→ACT) | ttdA | L‑tartrate dehydratase, alpha subunit |
| Reads supporting (aligned to +/- strand): ref base C (29/15); new base T (3/18); total (32/33) |
| Fisher's exact test for biased strand distribution p-value = 1.37e-04 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.76e-01 |
CTGGAGCTACGCCTGGAAGAAGGACTCAACCGTCTGGGGATTGGTCCACAAGGGCTGACCGGCAACAGTTCAGTGATGGGCGTACATATCGAATCTGCCGCCCGCCATCCGTCAACC > minE/2057863‑2057979
|
cTGGAGCTACGCCTGGAAGAAGGACTCAACCGTCTGGGGATTGGTCCACAAGGGCTGACCGGCAACAg > 1:686729/1‑68 (MQ=255)
cTGGAGCTACACCTGGAAGAAGGACTCAACCGTCTGGGGATTGGTCCACAAGGGCTGACCGGCAACAg > 1:1817304/1‑68 (MQ=255)
gCTACGCCTGGAAGAAGGACTCAACCGTCTGGGGATTGGTCCACAAGGGCTGACCGGCAACAGTTCAGt < 1:2993972/69‑1 (MQ=255)
gCTACGCCTGGAAGAAGGACTCAACCGTCTGGGGATTGGTCCACAAGGGCTGACCGGCAACAGTTCAGt < 1:3027739/69‑1 (MQ=255)
aCGCCTGGAAGAAGGACTCAACCGTCTGGGGATTGTTCCACAAGGGCTGACCGGCAACAGTTCAGTGAt > 1:1906263/1‑69 (MQ=255)
aCGCCTGGAAGAAGGACTCAACCGTCTGGGGATTGGTCCACAAGGGCTGACCGGCAACAGTTCAGTGAt > 1:1312905/1‑69 (MQ=255)
aCGCCTGGAAGAAGGACTCAACCGTCTGGGGATTGGTCCACAAGGGCTGACCGGCAACAGTTCAGTGAt > 1:88868/1‑69 (MQ=255)
aCGCCTGGAAGAAGGACTCAACCGTCTGGGGATTGGTCCACAAGGGCTGACCGGCAACAGTTCAGTGAt > 1:2336444/1‑69 (MQ=255)
aCGCCTGGAAGAAGGACTCAACCGTCTGGGGATTGGTCCACAAGGGCTGACCGGCAACAGTTCAGTGAt > 1:81259/1‑69 (MQ=255)
aCGCCTGGAAGAAGGACTCAACCGTCTGGGGATTGGTCCACAAGGGCTGACCGGCAACAGTTCAGTGAt > 1:2083182/1‑69 (MQ=255)
aCGCCTGGAAGAAGGACTCAACCGTCTGGGGATTGGTCCACAAGGGCTGACCGGCAACAGTTCAGTGAt > 1:2070749/1‑69 (MQ=255)
aCGCCTGGAAGAAGGACTCAACCGTCTGGGGATTGGTCCACAAGGGCTGACCGGCAACAGTTCAGTGAt > 1:1123545/1‑69 (MQ=255)
aCGCCTGGAAGAAGGACTCAACCGTCTGGGGATTGGTCCACAAGGGCTGACCGGCAACAGTTCAGTGAt > 1:2043545/1‑69 (MQ=255)
cGCCTGGAAGAAGGACTCAACCGTCTGGGGATTGGTCCACAAGGGCTGACCGGCAACAGTTCAGTGAt > 1:2506833/1‑68 (MQ=255)
cGCCTGGAAGAAGGACTCAACCGTCTGGGGATTGGTCCACAAGGGCTGACCGGCAACAGTTCAGTGATg > 1:79444/1‑69 (MQ=255)
agaagGACTCAACCGTCTGGGGATTGGTCCACAAGGGCTGACCGGCAACAGTTCAGTg > 1:1401822/1‑58 (MQ=255)
agGACTCAACCGTCTGGGGATTGGTCCACAAGGGCTGACCGGCAACAGTTCa > 1:1306305/1‑52 (MQ=255)
agGACTCAACCGTCTGGGGATTGGTCCACAAGGGCTGACCGGCAACAGTTCAGt < 1:2570271/54‑1 (MQ=255)
agGACTCAACCGTCTGGGGATTGGTCCACAAGGGCTGACCGGCAACAGTTCAGt < 1:3119595/54‑1 (MQ=255)
agGACTCAACCGTCTGGGGATTGGTCCACAAGGGCTGACCGGCAACAGTTCAGt < 1:1608447/54‑1 (MQ=255)
agGACTCAACCGTCTGGGGATTGGTCCACAAGGGCTGACCGGCAACAGTTCAGt < 1:2406906/54‑1 (MQ=255)
agGACTCAACCGTCTGGGGATTGGTCCACAAGGGCTGACCGGCAACAGTTCAGt < 1:3126094/54‑1 (MQ=255)
agGACTCAACCGTCTGGGGATTGGTCCACAAGGGCTGACCGGCAACAGTTCAGt < 1:2594243/54‑1 (MQ=255)
agGACTCAACCGTCTGGGGATTGGTCCACAAGGGCTGACCGGCAACAGTTCAGTGATGGGCGTa < 1:622608/64‑1 (MQ=255)
agGACTCAACCGTCTGGGGATTGGTCCACAAGGGCTGACCGGCAACAGTTCAGTGATGGGCGTa < 1:3079529/64‑1 (MQ=255)
agGACTCAACCGTCTGGGGATTGGTCCACAAGGGCTGACCGGCAACAGTTCAGTGATGGGCGTa < 1:725164/64‑1 (MQ=255)
agGACTCAACCGTCTGGGGATTGGTCCACAAGGGCTGACCGGCAACAGTTCAGTGATGGGCGTACata > 1:2587907/1‑68 (MQ=255)
agGACTCAACCGTCTGGGGATTGGTCCACAAGGGCTGACCGGCAACAGTTCAGTGATGGGCGTACata > 1:2030258/1‑68 (MQ=255)
agGACTCAACCGTCTGGGGATTGGTCCACAAGGGCTGACCGGCAACAGTTCAGTGATGGGCGTACata > 1:2255448/1‑68 (MQ=255)
agGACTCAACCGTCTGGGGATTGGTCCACAAGGGCTGACCGGCAACAGTTCAGTGATGGGCGTACata > 1:1043503/1‑68 (MQ=255)
agGACTCAACCGTCTGGGGATTGGTCCACAAGGGCTGACCGGCAACAGTTCAGTGATGGGCGTACa < 1:469689/66‑1 (MQ=255)
agGACTCAACCGTCTGGGGATTGGTCCACAAGGGCTGACCGGCAACAGTTCAGTGATGGGCGTACa < 1:1390057/66‑1 (MQ=255)
agGACTCAACCGTCTGGGGATTGCTCCACAAGGGCTGACCGGCAACAGTTCAGt < 1:3282851/54‑1 (MQ=255)
agGACCCAACCGTCTGGGGATTGGTCCACAAGGGCTGACCGGCAACAGTTCAGt < 1:3399436/54‑1 (MQ=255)
tGGGGATTGGTCCACAAGGGCTGACCGGCAACAGTTCAGTGATGGGCGTACATATCGAATCTgccgcc > 1:1198852/1‑68 (MQ=255)
tGGGGATTGGTCCACAAGGGCTGACCGGCAACAGTTCAGTGATGGGCGTACATATCGAATCTGccgccc > 1:3318407/1‑69 (MQ=255)
tGGGGATTGGTCCACAAGGGCTGACCGGCAACAGTTCAGTGATGGGCGTACATATCGAATCTGccgccc > 1:3379849/1‑69 (MQ=255)
tGGGGATTGGTCCACAAGGGCTGACCGGCAACAGTTCAGTGATGGGCGTACATATCGAATCTGccgccc > 1:95821/1‑69 (MQ=255)
tGGGGATTGGTCCACAAGGGCTGACCGGCAACAGTTCAGTGATGGGCGTACATATCGAATCTGccgccc > 1:3038221/1‑69 (MQ=255)
tGGGGATTGGTCCACAAGGGCTGACCGGCAACAGTTCAGTGATGGGCGTACATATCGAATCTGccgccc > 1:2449759/1‑69 (MQ=255)
tGGGGATTGGTCCACAAGGGCTGACCGGCAACAGTTCAGTGATGGGCGTACATATCGAATCTGccgccc > 1:1645533/1‑69 (MQ=255)
tGGGGATTGGTCCACAAGGGCTGACCGGCAACAGTTCAGTGATGGGCGTACATATCGAATCTGccgccc > 1:1902571/1‑69 (MQ=255)
tGGGGATTGGTCCACAAGGGCTGACCGGCAACAGTTCAGTGATGGGCGTACATATCGAATCTGccgccc > 1:2970442/1‑69 (MQ=255)
tGGGGAATGGTCCACAAGGGCTGACCGGCAACAGTTCAGTGATGGGCGTACATATCGAATCTGccgccc > 1:441496/1‑69 (MQ=255)
tGGTCCACAAGGGCTGACTGGCAACAGTTCAGTGATGGGCGTGCATATCGAATCTGCCGCTCGCCATcc > 1:445190/1‑69 (MQ=255)
tGGTCCACAAGGGCTGACTGGCAACAGTTCAGTGATGGGCGTGCATATCGAATCTGCCGCTCGCCATcc > 1:1068570/1‑69 (MQ=255)
tGGTCCACAAGGGCTGACTGG‑AACAGTTCAGTGATGGGCGTGCATATCGAATCTGCCGCTCGCCATcc > 1:2082076/1‑68 (MQ=255)
caAGGGCTGACTGGCAACAGTTCAGTGATGGGCGTGCATATCGAATCTGCCGCTCGCCATCCGTCAAcc < 1:602792/69‑1 (MQ=255)
caAGGGCTGACTGGCAACAGTTCAGTGATGGGCGTGCATATCGAATCTGCCGCTCGCCATCCGTCAAcc < 1:2733263/69‑1 (MQ=255)
caAGGGCTGACTGGCAACAGTTCAGTGATGGGCGTGCATATCGAATCTGCCGCTCGCCATCCGTCAAcc < 1:1329164/69‑1 (MQ=255)
caAGGGCTGACTGGCAACAGTTCAGTGATGGGCGTGCATATCGAATCTGCCGCTCGCCATCCGTCAAcc < 1:1484657/69‑1 (MQ=255)
caAGGGCTGACTGGCAACAGTTCAGTGATGGGCGTGCATATCGAATCTGCCGCTCGCCATCCGTCAAcc < 1:802147/69‑1 (MQ=255)
caAGGGCTGACTGGCAACAGTTCAGTGATGGGCGTGCATATCGAATCTGCCGCTCGCCATCCGTCAAcc < 1:1516947/69‑1 (MQ=255)
caAGGGCTGACTGGCAACAGTTCAGTGATGGGCGTGCATATCGAATCTGCCGCTCGCCATCCGTCAAcc < 1:756073/69‑1 (MQ=255)
caAGGGCTGACTGGCAACAGTTCAGTGATGGGCGTGCATATCGAATCTGCCGCTCGCCATCCGTCAAcc < 1:3107909/69‑1 (MQ=255)
caAGGGCTGACTGGCAACAGTTCAGTGATGGGCGTGCATATCGAATCTGCCGCTCGCCATCCGTCAAcc < 1:1744864/69‑1 (MQ=255)
caAGGGCTGACTGGCAACAGTTCAGTGATGGGCGTGCATATCGAATCTGCCGCTCGCCATCCGTCAAcc < 1:2439877/69‑1 (MQ=255)
caAGGGCTGACTGGCAACAGTTCAGTGATGGGCGTGCATATCGAATCTGCCGCTCGCCATCCGTCAAcc < 1:3211413/69‑1 (MQ=255)
caAGGGCTGACTGGCAACAGTTCAGTGATGGGCGTGCATATCGAATCTGCCGCTCGCCATCCGTCAAcc < 1:546725/69‑1 (MQ=255)
caAGGGCTGACTGGCAACAGTTCAGTGATGGGCGTGCATATCGAATCTGCCGCTCGCCATCCGTCAAcc < 1:2395462/69‑1 (MQ=255)
caAGGGCTGACTGGCAACAGTTCAGTGATGGGCGTGCATATCGAATCTGCCGCTCGCCATCCGTCAAcc < 1:3159477/69‑1 (MQ=255)
caAGGGCTGACTGGCAACAGTTCAGTGATGGGCGTGCATATCGAATCTGCCGCTCGCCATCCGTCAAcc < 1:1968877/69‑1 (MQ=255)
caAGGGCTGACTGGCAACAGTTCAGTGATGGGCGTGCATATCGAATCTGCCGCTCGCCATCCGTCAAcc < 1:2051014/69‑1 (MQ=255)
caAGGGCTGACTGGCAACAGTTCAGTGATGGGCGTGCATATCGAATCTGCCGCTCGCCATCCGTCAAcc < 1:2126044/69‑1 (MQ=255)
cTGACTGGCAACAGTTCAGTGATGGGCGTGCATATCGAATCTGCCGCTCGCCATCCGTCAAcc < 1:1964533/63‑1 (MQ=255)
|
CTGGAGCTACGCCTGGAAGAAGGACTCAACCGTCTGGGGATTGGTCCACAAGGGCTGACCGGCAACAGTTCAGTGATGGGCGTACATATCGAATCTGCCGCCCGCCATCCGTCAACC > minE/2057863‑2057979
|
| 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
