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 |
559,806 |
C→G |
46.8% |
A351A (GCC→GCG) |
cmr → |
multidrug efflux system protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 559,806 | 0 | C | G | 46.8%
| 9.5
/ 106.1
| 92 | A351A (GCC→GCG) | cmr | multidrug efflux system protein |
| Reads supporting (aligned to +/- strand): ref base C (22/27); new base G (15/28); total (37/55) |
| Fisher's exact test for biased strand distribution p-value = 3.96e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.83e-01 |
GCGAATGCGGGACTGGTGCGATTAACCCTGTTTGCCAGCGATATGAGTAAAGGTACGGTTTCTGCCGCGATGGGAATGCTGCAAATGCTGATCTTTACCGTTGGTATTGAAATCAGCAAACATGCCTG > minE/559741‑559868
|
gCGAATGCGGGACTGGTGCGATTAACCCTGTTTGCCAGCGATATGAGTAAAGGTACGGTTTCTGCcgcg > 1:141593/1‑69 (MQ=255)
tGCGGGACTGGTGCGATTAACCCTGTTTGCCAGCGATATGAGTAAAGGTACGGTTTCTGCCGCGATggg < 1:2150565/69‑1 (MQ=255)
tGCGGGACTGGTGCGATTAACCCTGTTTGCCAGCGATATGAGTAAAGGTACGGTTTCTGCCGCGATggg < 1:2563931/69‑1 (MQ=255)
tGCGGGACTGGTGCGATTAACCCTGTTTGCCAGCGATATGAGTAAAGGTACGGTTTCTGCCGCGATggg < 1:1714645/69‑1 (MQ=255)
tGCGGGACTGGTGCGATTAACCCTGTTTGCCAGCGATATGAGTAAAGGTACGGTTTCTGCCGCGATggg > 1:67375/1‑69 (MQ=255)
tGCGGGACTGGTGCGATTAACCCTGTTTGCCAGCGATATGAGTAAAGGTACGGTTTCTGCCGCGATggg < 1:3174522/69‑1 (MQ=255)
tGCGGGACTGGTGCGATTAACCCTGTTTGCCAGCGATATGAGTAAAGGTACGGTTTCTGCCGCGATggg < 1:565958/69‑1 (MQ=255)
tGCGGGACTGGTGCGATTAACCCTGTTTGCCAGCGATATGAGTAAAGGTACGGTTTCTGCCGCGATggg < 1:1541347/69‑1 (MQ=255)
tGCGGGACTGGTGCGATTAACCCTGTTTGCCAGCGATATGAGTAAAGGTACGGTTTCTGCCGCGATggg < 1:3223259/69‑1 (MQ=255)
tGCGGGACTGGTCCGATTAACCCTGTTTGCCAGCGATATGAGTAAAGGTACGGTTTCTGCCGCGATggg < 1:303547/69‑1 (MQ=255)
cGGGACTGGTGCGATTAACCCTGTTTGCCAGGTATATGAGTAAAGGTACGGTTTCTGCCGCGATgtg < 1:3332341/67‑3 (MQ=255)
cGGGACTGGTGCGATTAACCCTGTTTGCCAGCGATATGAGTAAAGGTACGGTTTCTGCCGCGATggg < 1:996999/67‑1 (MQ=255)
cGGGACTGGTGCGATTAACCCTGTTTGCCAGCGATATGAGTAAAGGTACGGTTTCTGCCGCGATGGGaa < 1:1735954/69‑1 (MQ=255)
gggACTGGTGCGATTAACCCTGTTTGCCAGCGATATGAGTAAAGGTACGGTTTCTGCCGCGATggg < 1:715963/66‑1 (MQ=255)
ggACTGGTGCGATTAACCCTGTTTGCCAGCGATATGAGTAAAGGTACGGTTTCTGCCGCGATggt < 1:3433818/65‑2 (MQ=255)
tGGTGCGATTAACCCTGTTTGCCAGCGATATGAGTAAAGGTACGGTTTCTGCCGCGATggg < 1:1260087/61‑1 (MQ=255)
ggTGCGATTAACCCTGTTTGCCAGCGATATGAGTAAAGGTACGGTTTCTGCCGCGATGGGAATGCTGCa < 1:424096/69‑1 (MQ=255)
ggTGCGATTAACCCTGTTTGCCAGCGATATGAGTAAAGGTACGGTTTCTGCCGCGATGGGAATGCTGCa < 1:582350/69‑1 (MQ=255)
ggTGCGATTAACCCTGTTTGCCAGCGATATGAGTAAAGGTACGGTTTCTGCCGCGATGGGAATGCTGCa < 1:1257728/69‑1 (MQ=255)
ggTGCGATTAACCCTGTTTGCCAGCGATATGAGTAAAGGTACGGTTTCTGCCGCGATGGGAATGCTGCa < 1:2635091/69‑1 (MQ=255)
ggTGCGATTAACCCTGTTTGCCAGCGATATGAGTAAAGGTACGGTTTCTGCCGCGATGGGAATGCTGCa < 1:1967783/69‑1 (MQ=255)
tGCGATTAACCCTGTTTGCCAGCGATATGAGTAAAGGTACGGTTTCTGCCGAGATggg < 1:3129650/58‑1 (MQ=255)
cGATTAACCCTGTTTGCCAGCGATATGAGTAAAGGTACGGTTTCTGCCGCGATGGGAATGCTGCAAATg > 1:2411998/1‑69 (MQ=255)
cGATTAACCCTGTTTGCCAGCGATATGAGTAAAGGTACGGTTTCTGCCGCGATGGGAATGCTGCAAATg > 1:2265642/1‑69 (MQ=255)
cGATTAACCCTGTTTGCCAGCGATATGAGTAAAGGTACGGTTTCTGCCGCGATGGGAATGCTGCAAATg > 1:1173901/1‑69 (MQ=255)
agATTAACCCTGTTTGCCAGCGATATGAGTAAAGGTACGGTTTCTGCcgcg > 1:3282399/2‑51 (MQ=255)
tGTTTGCCAGCGATATGAGTAAAGGTACGGTTTCTGCCGCGATGGGAATGCTGGAAATGCTGATCttt > 1:2188929/1‑68 (MQ=255)
tGTTTGCCAGCGATATGAGTAAAGGTACGGTTTCTGCCGCGATGGGAATGCTGCAAATGCTGATCttt > 1:3261027/1‑68 (MQ=255)
tGTTTGCCAGCGATATGAGTAAAGGTACGGTTTCTGCCGCGATGGGAATGCTGCAAATGCTGATCttt > 1:2860506/1‑68 (MQ=255)
tGTTTGCCAGCGATATGAGTAAAGGTACGGTTTCTGCCGCGATGGGAATGCTGCAAATGCTGATCttt > 1:1306605/1‑68 (MQ=255)
tGTTTGCCAGCGATATGAGTAAAGGTACGGTTTCTGCCGCGATGGGAATGCTGCAAATGCTGATCttt > 1:225920/1‑68 (MQ=255)
tGTTTGCCAGCGATATGAGTAAAGGTACGGTTTCTGCCGCGATGGGAATGCTGCAAATGCTGATCttt > 1:2993431/1‑68 (MQ=255)
tGTTTGCCAGCGATATGAGTAAAGGTACGGTTTCTGCCGCGATGGGAATGCTGCAAATGCTGATCttt > 1:783187/1‑68 (MQ=255)
tGTTTGCCAGCGATATGAGTAAAGGTACGGTTTCTGCCGCGATGGGAATGCTGCAAATGCTGATCtt > 1:3396550/1‑67 (MQ=255)
tGTTTGCCAGCGATATGAGTAAAGGTACGGTTTCTGCCGCGATGGGAATGCTGCAAATGCTGATCtt > 1:2891221/1‑67 (MQ=255)
tGTTTGCCAGCGATATGAGTAAAGGTACGGTTTCTGCCGCGATGGGAATGCTGCAAATGCTGATCtt > 1:2879580/1‑67 (MQ=255)
tGTTTGCAAGCGATATGAGTAAAGGTACGGTTTCTGCCGCGATGGGAATGCTGCAAATGCTGATCtt > 1:1966056/1‑67 (MQ=255)
gCGATATGAGTAAAGGTACGGTTTCTGCGGCGATGGGGATGCTGCAAATGCTGATCTTTACCGTCGGt > 1:144186/1‑68 (MQ=255)
gCGATATGAGTAAAGGTACGGTTTCTGCGGCGATGGGGATGCTGCAAATGCTGATCTTTACCGTCGGt > 1:2264656/1‑68 (MQ=255)
gCGATATGAGTAAAGGTACGGTTTCTGCGGCGATGGGGATGCTGCAAATGCTGATCTTTACCGTCGGTa > 1:2735010/1‑69 (MQ=255)
gCGATATGAGTAAAGGTACGGTTTCTGCGGCGATGGGGATGCTGCAAATGCTGATCTTTACCGTCGGTa > 1:2039138/1‑69 (MQ=255)
gCGATATGAGTAAAGGTACGGTTTCTGCGGCGATGGGGATGCTGCAAATGCTGATCTTTACCGTCGGTa > 1:1384995/1‑69 (MQ=255)
gCGATATGAGTAAAGGTACGGTTTCTGCGGCGATGGGGATGCTGCAAATGCTGATCTTTACCGTCGGTa > 1:500124/1‑69 (MQ=255)
gCGATATGAGTAAAGGTACGGTTTCTGCGGCGATGGGGATGCTGCAAATGCTGATCTTTACCGTCGGTa > 1:3282427/1‑69 (MQ=255)
gCGATATGAGTAAAGGTACGGTTTCTGCGGCGATGGGGATGCTGCAAATGCTGATCTTTACCGTCGGTa > 1:989676/1‑69 (MQ=255)
gCGATATGAGTAAAGGTACGGTTTCTGCGGCGATGGGGATGCTGCAAATGCTGATCTTTACCGTCGGTa > 1:2108126/1‑69 (MQ=255)
gCGATATGAGTAAAGGTACGGTTTCTGCGGCGATGGGGATGCTGCAAATGCTGATCTTTACCGTCGGTa > 1:192464/1‑69 (MQ=255)
gCGATATGAGTAAAGGTACGGTTTCTGCGGCGATGGGGATGCTGCAAATGCTGATCTTTACCGTCGGTa > 1:849286/1‑69 (MQ=255)
gCGATATGAGTAAAGGTACGGTTTCTGCGGCGATGGGGATGCTGCAAATGCTGATCTTTACCGTCGGTa > 1:2226101/1‑69 (MQ=255)
gCGATATGAGTAAAGGTACGGTTTCTGCGGCGATGGGGATGCTGCAAATGCTGATCTTTACCGTCGGTa > 1:1833235/1‑69 (MQ=255)
gCGATATGAGTAAAGGTACGGTTTATGCGGCGATGGGGATGCTGCAAATGCTGATCTTTACCGTCGGTa > 1:1645494/1‑69 (MQ=255)
gCGATATGAGTAAAGGAACGGTTTCTGCGGCGATGGGGATGCTGCAAATGCTGATCTTTACCGTCGGTa > 1:3096016/1‑69 (MQ=255)
aaGGTACGGTTTCTGCGGCGATGGGGATGCTGCAAATGCTGATc < 1:2668597/44‑1 (MQ=38)
aaGGTACGGTTTCTGCGGCGATGGGGATGCTGCAAATGCTGATc < 1:358454/44‑1 (MQ=38)
aaGGTACGGTTTCTGCGGCGATGGGGATGCTGCAAATGCTGATc < 1:3010343/44‑1 (MQ=38)
aaGGTACGGTTTCTGCGGCGATGGGGATGCTGCAAATGCTGATc < 1:584630/44‑1 (MQ=38)
aaGGTACGGTTTCTGCGGCGATGGGGATGCTGCAAATGCTGATc < 1:613982/44‑1 (MQ=38)
aaGGTACGGTTTCTGCGGCGATGGGGATGCTGCAAATGCTGATc < 1:2442078/44‑1 (MQ=38)
aaGGTACGGTTTCTGCGGCGATGGGGATGCTGCAAATGCTGATc < 1:2461550/44‑1 (MQ=38)
aaGGTACGGTTTCTGCGGCGATGGGGATGCTGCAAATGCTGATc < 1:1214162/44‑1 (MQ=38)
aaGGTACGGTTTCTGCGGCGATGGGGATGCTGCAAATGCTGATc < 1:2827355/44‑1 (MQ=38)
aaGGTACGGTTTCTGCGGCGATGGGGATGCTGCAAATGCTGATc < 1:178825/44‑1 (MQ=38)
aaGGTACGGTTTCTGCCGCGATGGGAATGCTGCAAATGCTGATCTTTACCGTTGGTATTGAAATCAGCa < 1:2928285/69‑1 (MQ=255)
aaGGTACGGTTTCTGCCGCGATGGGAATGCTGCAAATGCTGATCTTTACCGTTGGTATTGAAATCAGCa < 1:3408259/69‑1 (MQ=255)
aaGGTACGGTTTCTGCCGCGATGGGAATGCTGCAAATCCTGATCTTTACCGTTGGTATTGAAATCAGCa < 1:902227/69‑1 (MQ=255)
aGGTACGGTTTCTGCGGCGATGGGGATGCTGCAAATGCTGATc < 1:1889533/43‑1 (MQ=38)
aGGTACGGTTTCTGCGGCGATGGGGATGCTGCAAATGCTGATc < 1:1796736/43‑1 (MQ=38)
ggTACGGTTTCTGCCGCGATGGGAATGCTGCAAATGCTGATCTTTACCGTTGGTATTGAAATCAGCaaa < 1:1344951/69‑1 (MQ=255)
ggTACGGTTTCTGCCGCGATGGGAATGCTGCAAATGCTGATCTTTACCGTTGGTATTGAAATCAGCaaa < 1:2530259/69‑1 (MQ=255)
gTACGGTTTCTGCCGCGATGGGAATGCTGCAAATGCTGATCTTTACCGTTGGTATTGa > 1:764325/1‑58 (MQ=255)
gTACGGTTTCTGCCGCGATGGGAATGCTGCAAATGCTGATCTTTACCGTTGGTATTGa > 1:1097881/1‑58 (MQ=255)
gTACGGTTTCTGCCGCGATGGGAATGCTGCAAATGCTGATCTTTACCGTTGGTATTGa > 1:2201579/1‑58 (MQ=255)
gTACGGTTTCTGCCGCGATGGGAATGCTGCAAATGCTGATCTTTACCGTTGGTATTGa > 1:2959808/1‑58 (MQ=255)
gTACGGTTTCTGCCGCGATGGGAATGCTGCAAATGCTGATCTTTACCGTTGGTATTGa > 1:2877121/1‑58 (MQ=255)
tACGGTTTCTGCCGCGATGGGAATGCTGCAAATGCTGATCTTTACCGTTGGTATTGAAATc > 1:1526301/1‑61 (MQ=255)
tACGGTTTCTGCCGCGATGGGAATGCTGCAAATGCTGATCTTTACCGTTGGTATTGAAATCAGCAAACa > 1:3367192/1‑69 (MQ=255)
aCGGTTTCTGCCGCGATGGGAAGGCTGCAAATGCTGATCTTTACCGTTGGTATTGAAATCAGCAAACAt < 1:2762531/69‑1 (MQ=255)
ttCTGCGGCGATGGGGATGCTGCAAATGCTGATCTTTACCGTCGGTATTGAAATCAGCAAACATGCCTg < 1:205025/69‑1 (MQ=39)
ttCTGCGGCGATGGGGATGCTGCAAATGCTGATCTTTACCGTCGGTATTGAAATCAGCAAACATGCCTg < 1:2077308/69‑1 (MQ=39)
ttCTGCGGCGATGGGGATGCTGCAAATGCTGATCTTTACCGTCGGTATTGAAATCAGCAAACATGCCTg < 1:907064/69‑1 (MQ=39)
ttCTGCGGCGATGGGGATGCTGCAAATGCTGATCTTTACCGTCGGTATTGAAATCAGCAAACATGCCTg < 1:2289678/69‑1 (MQ=39)
ttCTGCGGCGATGGGGATGCTGCAAATGCTGATCTTTACCGTCGGTATTGAAATCAGCAAACATGCCTg < 1:724569/69‑1 (MQ=39)
ttCTGCGGCGATGGGGATGCTGCAAATGCTGATCTTTACCGTCGGTATTGAAATCAGCAAACATGCCTg < 1:717454/69‑1 (MQ=39)
ttCTGCGGCGATGGGGATGCTGCAAATGCTGATCTTTACCGTCGGTATTGAAATCAGCAAACATGCCTg < 1:2844028/69‑1 (MQ=39)
ttCTGCGGCGATGGGGATGCTGCAAATGCTGATCTTTACCGTCGGTATTGAAATCAGCAAACATGCCTg < 1:2999204/69‑1 (MQ=39)
ttCTGCGGCGATGGGGATGCTGCAAATGCTGATCTTTACCGTCGGTATTGAAATCAGCAAACATGCCTg < 1:1765040/69‑1 (MQ=39)
ttCTGCGGCGATGGGGATGCTGCAAATGCTGATCTTTACCGTCGGTATTGAAATCAGCAAACATGCCTg < 1:43417/69‑1 (MQ=39)
ttCTGCGGCGATGGGGATGCTGCAAATGCTGATCTTTACCGTCGGTATTGAAATCAGCAAACATGCCTg < 1:424454/69‑1 (MQ=39)
ttCTGCGGCGATGGGGATGCTGCAAATGCTGATCTTTACCGTCGGTATTGAAATCAGCAAACATGCCTg < 1:3311067/69‑1 (MQ=39)
ttCTGCGGCGATGGGGATGCTGCAAATGCTGATCTTTACCGTCGGTATTGAAATCAGCAAACATGCCTg < 1:144238/69‑1 (MQ=39)
ttCTGCGGCGATGGGGATGCTGCAAATGCTGATCTTTACCGTCGGTATTGAAATCAGCAAACATGCCTg < 1:1444577/69‑1 (MQ=39)
tCTGCGGCGATGGGGATGCTGCAAATGCTGATCTTTACCGTCGGTATTGAAATCAGCAAACATGCCTg < 1:3253842/68‑1 (MQ=39)
tCTGCGGCGATGGGGATGCTGCAAATGCTGATCTTTACCGTCGGTATTGAAATCAGCAAACATGCCTg < 1:2146368/68‑1 (MQ=39)
tCTGCCGCGATGGGAATGCTGCAAATGCTGATCTTTACCGGTGGTATTGAAATCAGCAAACAt < 1:1639229/63‑1 (MQ=255)
|
GCGAATGCGGGACTGGTGCGATTAACCCTGTTTGCCAGCGATATGAGTAAAGGTACGGTTTCTGCCGCGATGGGAATGCTGCAAATGCTGATCTTTACCGTTGGTATTGAAATCAGCAAACATGCCTG > minE/559741‑559868
|
| 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
