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 |
2,736,887 |
T→C |
52.3% |
R677R (CGT→CGC) |
fusA → |
protein chain elongation factor EF‑G |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,736,887 | 0 | T | C | 52.3%
| 3.6
/ 56.7
| 67 | R677R (CGT→CGC) | fusA | protein chain elongation factor EF‑G |
| Reads supporting (aligned to +/- strand): ref base T (22/10); new base C (17/18); total (39/28) |
| Fisher's exact test for biased strand distribution p-value = 1.37e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.78e-01 |
CTGAAGTACCGCTGTCTGAAATGTTCGGATACGCAACTCAGCTGCGTTCTCTGACCAAAGGTCGTGCATCATACACTATGGAATTCCTGAAGTATGATGAAGCGCCGAGTAACGTTGCTCA > minE/2736823‑2736943
|
cTGAAGTACCGCTGTCTGAAATGTTCGGATACGCAACTCAGCTGCGTTCTCTGACCAAAGGTCGTGcat < 1:491358/69‑1 (MQ=255)
cTGAAGTACCGCTGTCTGAAATGTTCGGATACGCAACTCAGCTGCGTTCTCTGACCAAAGGTCGTGcat < 1:3030945/69‑1 (MQ=255)
cTGAAGTACCGCTGTCTGAAATGTTCGGATACGCAACTCAGCTGCGTTCTCTGACCAAAGGTCGTGcat < 1:3011515/69‑1 (MQ=255)
cTGAAGTACCGCTGTCTGAAATGTTCGGATACGCAACTCAGCTGCGTTCTCTGACCAAAGGTCGTGcat < 1:2079230/69‑1 (MQ=255)
cTGAAGTACCGCTGTCTGAAATGTTCGGATACGCAACTCAGCTGCGTTCTCTGACCAAAGGTCGTGcat < 1:2757698/69‑1 (MQ=255)
cTGAAGTACCGCTGTCTGAAATGTTCGGATACGCAACTCAGCTGCGTTCTCTGACCAAAGGTCGTGcat < 1:936856/69‑1 (MQ=255)
cTGAAGTACCGCTGTCTGAAATGTTCGGATACGCAACTCAGCTGCGTTCTCTGACCAAAGGTCGTGcat < 1:1125342/69‑1 (MQ=255)
tACCGCTGTCTGAAATGTTCGGATACGCAACTCAGCTGCGTTCTCTGACCAAAGGTCGTGCATCATac > 1:1279034/1‑68 (MQ=255)
tACCGCTGTCTGAAATGTTCGGATACGCAACTCAGCTGCGTTCTCTGACCAAAGGTCGTGCATCATac > 1:596009/1‑68 (MQ=255)
tACCGCTGTCTGAAATGTTCGGATACGCAACTCAGCTGCGTTCTCTGACCAAAGGTCGTGCATCATac > 1:3220791/1‑68 (MQ=255)
tACCGCTGTCTGAAATGTTCGGATACGCAACTCAGCTGCGTTCTCTGACCAAAGGTCGTGCATCATac > 1:1917709/1‑68 (MQ=255)
ccGCTGTCTGAAATGTTCGGATACGCAACTCAGCTGCGTTCTCTGACCAAAGGTCGTg > 1:678769/1‑58 (MQ=255)
ccGCTGTCTGAAATGTTCGGATACGCAACTCAGCTGCGTTCTCTGACCAAAGGTCGTGCATCATACACt > 1:2342617/1‑69 (MQ=255)
ccGCTGTCTGAAATGTTCGGATACGCAACTCAGCTGCGTTCTCTGACCAAAGGTCGTGCATCATACACt > 1:374751/1‑69 (MQ=255)
ccGCTGTCTGAAATGTTCGGATACGCAACTCAGCTGCGTTCTCTGACCAAAGGTCGTGCATCATACACt > 1:922527/1‑69 (MQ=255)
aTGTTCGGATATGCAACTCAGCTGCGTTCTCTGACCAAAGGTCGCGCATCATACACTATGGAATTCCt < 1:218889/68‑1 (MQ=255)
aTGTTCGGATATGCAACTCAGCTGCGTTCTCTGACCAAAGGTCGCGCATCATACACTATGGAATTCCt < 1:2809115/68‑1 (MQ=255)
aTGTTCGGATATGCAACTCAGCTGCGTTCTCTGACCAAAGGTCGCGCATCATACACTATGGAATTCCt < 1:971842/68‑1 (MQ=255)
aTGTTCGGATATGCAACTCAGCTGCGTTCTCTGACCAAAGGTCGCGCATCATACACTATGGAATTCCt < 1:3123407/68‑1 (MQ=255)
aTGTTCGGATATGCAACTCAGCTGCGTTCTCTGACCAAAGGTCGCGCATCATACACTATGGAATTCCt < 1:3127243/68‑1 (MQ=255)
aTGTTCGGATATGCAACTCAGCTGCGTTCTCTGACCAAAGGTCGCGCATCATACACTATGGAATTCCt < 1:316290/68‑1 (MQ=255)
aTGTTCGGATATGCAACTCAGCTGCGTTCTCTGACCAAAGGTCGCGCATCATACACTATGGAATTCCt < 1:3256118/68‑1 (MQ=255)
aTGTTCGGATATGCAACTCAGCTGCGTTCTCTGACCAAAGGTCGCGCATCATACACTATGGAATTCCt < 1:3428245/68‑1 (MQ=255)
aTGTTCGGATATGCAACTCAGCTGCGTTCTCTGACCAAAGGTCGCGCATCATACACTATGGAATTCCt < 1:674985/68‑1 (MQ=255)
aTGTTCGGATATGCAACTCAGCTGCGTTCTCTGACCAAAGGTCGCGCATCATACACTATGGAATTCCt < 1:951062/68‑1 (MQ=255)
aTGTTCGGATATGCAACTCAGCTGCGTTCTCTGACCAAAGGTCGCGCATCATACACTATGGAATTCCt < 1:2188055/68‑1 (MQ=255)
aTGTTCGGATATGCAACTCAGCTGCGTTCTCTGACCAAAGGTCGCGCATCATACACTATGGAATTCCt < 1:1264992/68‑1 (MQ=255)
aTGTTCGGATATGCAACTCAGCTGCGTTCTCTGACCAAAGGTCGCGCATCATACACTATGGAATTCCt < 1:1263660/68‑1 (MQ=255)
aTGTTCGGATATGCAACTCAGCTGCGTTCTCTGACCAAAGGTCGCGCATCATACACTATGGAATTCCt < 1:1216421/68‑1 (MQ=255)
aTGTTCGGATATGCAACTCAGCTGCGTTCTCTGACCAAAGGTCGCGCATCATACACTATGGAATTCCt < 1:1782458/68‑1 (MQ=255)
aTGTTCGGATATGCAACTCAGCTGCGTTCTCTGACCAAAGGTCGCGCATCATACACTATGGAATTCCt < 1:1890375/68‑1 (MQ=255)
aTGTTCGGATATGCAACTCAGCTGCGTTCTCTGACCAAAGGTCGCGCATCATACACTATGGAATTCCt < 1:2039988/68‑1 (MQ=255)
aTGTTCGGATATGCAACTCAGCTGCGTTCTCTGACCAAAGGTCGCGCATCATACACTATGGAATTCCt < 1:2064938/68‑1 (MQ=255)
cGGATACGCAACTCAGCTGCGTTCTCTAACCAAAGGTCGTGCATCATACACTATGGAATTCCTGAAGt > 1:3230764/1‑68 (MQ=255)
tACGCAACTCAGCTGCGTTCTCTGACCAAAGGTCGTGCATCATACACTATGGAATTCCTGAAGTatgat < 1:1150067/69‑1 (MQ=255)
tACGCAACTCAGCTGCGTTCTCTGACCAAAGGTCGTGCATCATACACTATGGAATTCCTGAAGTatgat < 1:235154/69‑1 (MQ=255)
tACGCAACTCAGCTGCGTTCTCTGACCAAAGGTCGTGCATCATACACTATGGAATTCCTGAAGTatgat < 1:2393394/69‑1 (MQ=255)
cAGCTGCGTTCTCTGACCAAAGGTCGTGCATCATACACTATGGAATTCCTGAAGTATGATGAAGCGCCg > 1:2127703/1‑69 (MQ=255)
cAGCTGCGTTCTCTGACCAAAGGTCGTGCATCATACACTATGGAATTCCTGAAGTATGATGAAGCGCCg > 1:574787/1‑69 (MQ=255)
cAGCTGCGTTCTCTGACCAAAGGTCGTGCATCATACACTATGGAATTCCTGAAGTATGATGAAGCGCCg > 1:357373/1‑69 (MQ=255)
cAGCTGCGTTCTCTGACCAAAGGTCGTGCATCATACACTATGGAATTCCTGAAGTATGATGAAGCGCCg > 1:796408/1‑69 (MQ=255)
cAGCTGCGTTCTCTGACCAAAGGTCGTGCATCATACACTATGGAATTCCTGAAGTATGATGAAGCGCCg > 1:913480/1‑69 (MQ=255)
cAGCTGCGTTCTCTGACCAAAGGTCGTGCATCATACACTATGGAATTCCTGAAGTATGATGAAGCGCCg > 1:2098259/1‑69 (MQ=255)
cAGCTGCGTTCTCTGACCAAAGGTCGTGAATCATACACTATGGAATTCCTGAAGTATGATGAAGCGCCg > 1:1863939/1‑69 (MQ=255)
ctctGACCAAAGGTCGTGCATCATACACTATGGAATTCCTGAAg > 1:2717313/1‑44 (MQ=255)
ctctGACCAAAGGTCGTGCATCATACACTATGGAATTCCTGAAg > 1:257060/1‑44 (MQ=255)
ctctGACCAAAGGTCGTGCATCATACACTATGGAATTCCTGAAg > 1:2354252/1‑44 (MQ=255)
ctctGACCAAAGGTCGTGCATCATACACTATGGAATTCCTGAAGTATGATGAAGCGCCGAGTAACGt > 1:1289831/1‑67 (MQ=255)
ctctGACCAAAGGTCGTGCATCATACACTATGGAATTCCTGAAGTATGATGAAGCGCCGAGTAACGTTg > 1:470328/1‑69 (MQ=255)
ctctGACCAAAGGTCGTGCATCATACACTATGGAATTACTGAAGTATGATGAAGCGCCGAGTAACGTTg > 1:2052989/1‑69 (MQ=255)
gACCAAAGGTCGCGCATCATACACTATGGAATTCCTGAAGTATGATGAAGCGCCGAGTAAc > 1:781303/1‑61 (MQ=255)
gACCAAAGGTCGCGCATCATACACTATGGAATTCCTGAAGTATGATGAAGCGCCGAGTAACGTTGCTCa > 1:12208/1‑69 (MQ=255)
gACCAAAGGTCGCGCATCATACACTATGGAATTCCTGAAGTATGATGAAGCGCCGAGTAACGTTGCTCa > 1:69639/1‑69 (MQ=255)
gACCAAAGGTCGCGCATCATACACTATGGAATTCCTGAAGTATGATGAAGCGCCGAGTAACGTTGCTCa > 1:1012744/1‑69 (MQ=255)
gACCAAAGGTCGCGCATCATACACTATGGAATTCCTGAAGTATGATGAAGCGCCGAGTAACGTTGCTCa > 1:1324203/1‑69 (MQ=255)
gACCAAAGGTCGCGCATCATACACTATGGAATTCCTGAAGTATGATGAAGCGCCGAGTAACGTTGCTCa > 1:453674/1‑69 (MQ=255)
gACCAAAGGTCGCGCATCATACACTATGGAATTCCTGAAGTATGATGAAGCGCCGAGTAACGTTGCTCa > 1:419890/1‑69 (MQ=255)
gACCAAAGGTCGCGCATCATACACTATGGAATTCCTGAAGTATGATGAAGCGCCGAGTAACGTTGCTCa > 1:37624/1‑69 (MQ=255)
gACCAAAGGTCGCGCATCATACACTATGGAATTCCTGAAGTATGATGAAGCGCCGAGTAACGTTGCTCa > 1:1609719/1‑69 (MQ=255)
gACCAAAGGTCGCGCATCATACACTATGGAATTCCTGAAGTATGATGAAGCGCCGAGTAACGTTGCTCa > 1:1669607/1‑69 (MQ=255)
gACCAAAGGTCGCGCATCATACACTATGGAATTCCTGAAGTATGATGAAGCGCCGAGTAACGTTGCTCa > 1:1770420/1‑69 (MQ=255)
gACCAAAGGTCGCGCATCATACACTATGGAATTCCTGAAGTATGATGAAGCGCCGAGTAACGTTGCTCa > 1:2945023/1‑69 (MQ=255)
gACCAAAGGTCGCGCATCATACACTATGGAATTCCTGAAGTATGATGAAGCGCCGAGTAACGTTGCTCa > 1:2892791/1‑69 (MQ=255)
gACCAAAGGTCGCGCATCATACACTATGGAATTCCTGAAGTATGATGAAGCGCCGAGTAACGTTGCTCa > 1:2075095/1‑69 (MQ=255)
gACCAAAGGTCGCGCATCATACACTATGGAATTCCTGAAGTATGATGAAGCGCCGAGTAACGTTGCTCa > 1:2613146/1‑69 (MQ=255)
gACCAAAGGTCGCGCATCATACACTATGGAATTCCTGAAGTATGATGAAGCGCCGAGTAACGTTGCTCa > 1:2101623/1‑69 (MQ=255)
gACCAAAGGTCGCGCATCATACACTATGGAATTCCTGAAGTATGATGAAGCGCCGAGTAACGTTGCTCa > 1:2256460/1‑69 (MQ=255)
|
CTGAAGTACCGCTGTCTGAAATGTTCGGATACGCAACTCAGCTGCGTTCTCTGACCAAAGGTCGTGCATCATACACTATGGAATTCCTGAAGTATGATGAAGCGCCGAGTAACGTTGCTCA > minE/2736823‑2736943
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
