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 |
|
A6 F21 I0 R1
|
2169 |
63.0 |
3952800 |
76.2% |
3012033 |
62.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
311,562 |
C→T |
5.5% |
Q437Q (CAG→CAA) |
acrB ← |
multidrug efflux system protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 311,562 | 0 | C | T | 5.5%
| 232.0
/ 2.3
| 73 | Q437Q (CAG→CAA) | acrB | multidrug efflux system protein |
| Reads supporting (aligned to +/- strand): ref base C (34/35); new base T (2/2); total (36/37) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.94e-01 |
GCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTACGGGTAGCTTCTTTTGGCGGCAAACCTTCTTCCGCCATAACACGCTCAACGT > minE/311493‑311629
|
gCCAAAGAAGGCCATCGGTACTAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCt < 1:3610260/71‑1 (MQ=255)
gCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCt < 1:2487857/71‑1 (MQ=255)
cgaagaatGCCATCGGAATAAATACCGCTGACAGCACCATCGCGATACCCACCAGTGCGCCCTGAATTTGc > 1:2403519/3‑71 (MQ=255)
aaaGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGcc > 1:403912/1‑71 (MQ=255)
aagaagGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGccc > 1:1450726/1‑71 (MQ=255)
aagGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCAt > 1:3391678/1‑71 (MQ=255)
ggCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCg < 1:2045518/71‑1 (MQ=255)
ccATCGGAATAAATACCGCTGACAGCACCATCGCGATACCCACCAGTGCGCCCTGAATTTGCGACATCGat > 1:976105/1‑70 (MQ=255)
tCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCt < 1:1606618/57‑1 (MQ=255)
tCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTa > 1:361136/1‑71 (MQ=255)
cGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTAc > 1:905829/1‑71 (MQ=255)
cGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTAc > 1:901156/1‑71 (MQ=255)
ggTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTAc < 1:2640374/70‑1 (MQ=255)
ggTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTAc < 1:2000163/70‑1 (MQ=255)
ggTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTACg > 1:3086170/1‑71 (MQ=255)
ggTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTACg > 1:2299603/1‑71 (MQ=255)
tACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTACggg < 1:1733761/71‑1 (MQ=255)
cGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGa > 1:709963/1‑61 (MQ=255)
cGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTACggg > 1:3645596/1‑69 (MQ=255)
cGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTACGGGt < 1:611625/70‑1 (MQ=255)
tACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTACGGGTAGctt < 1:1490520/71‑1 (MQ=255)
aCCGCTGACAGCACCATCGCGATACCCACCAGTGCGCCCTGAATTTGCGACATCGAttttt < 1:3933907/61‑3 (MQ=255)
ccgccgACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTACGGGTAGcttct < 1:3703952/71‑1 (MQ=255)
ccgccgACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTACGGGTAGcttc < 1:1845213/70‑1 (MQ=255)
ccgACAGTACGATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACtt < 1:2372600/55‑1 (MQ=255)
ccgACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCt < 1:293599/42‑1 (MQ=255)
ccgACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTACGGGTAGCTTCtttt > 1:3561011/1‑71 (MQ=255)
ccgACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTACGGGTAGCTTCtttt > 1:117307/1‑71 (MQ=255)
ccgACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTACGGGTAGCTTCtttt > 1:3026723/1‑71 (MQ=255)
cgACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACtt < 1:1856760/54‑1 (MQ=255)
cgACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTACGGGTAGCTTCTTTTg < 1:1364338/71‑1 (MQ=255)
gACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTACgg > 1:209257/1‑57 (MQ=255)
gACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTACGGGTAGCTTCTTTTgg < 1:161871/71‑1 (MQ=255)
gTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGcccc > 1:307287/1‑41 (MQ=255)
gTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGa < 1:350186/46‑1 (MQ=255)
gTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGa > 1:1192713/1‑46 (MQ=255)
tACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTACGGGTAGCTTCTTTTggcggc > 1:2325397/1‑70 (MQ=255)
tACCATCGCGATACCGACAAGAGCGCCCTGAATCTGCCCCATCGACTTACGGGTAGCTTCTTTTGGCGGCa < 1:2533555/71‑1 (MQ=255)
caCCATCGCGATACCCACCAGTGCGCCCTGAATTTGCGACATCg < 1:3603010/43‑1 (MQ=19)
ccATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTACGGGTAGCTTCTTTTggcg > 1:411462/1‑66 (MQ=255)
aTCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTACGGGTAGCTTCTTTTGGCGGCAAAcc < 1:1496248/71‑1 (MQ=255)
aTCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTACGGGTAGCTTCTTTTGGCGGCAAAcc > 1:3429363/1‑71 (MQ=255)
tCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTACGGGTAGCTTCtttt < 1:1957728/59‑1 (MQ=255)
tCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTACGGGTAGCTTCTTTTGGCGGCAAACct > 1:962547/1‑71 (MQ=255)
ctcgATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTACTGGt < 1:3882380/46‑1 (MQ=25)
gcgATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTACGGGTAGCTTCTTTTGGCGGCAAACctt < 1:2469835/70‑1 (MQ=255)
gATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTACGGGTAGCTTCTTTTggc < 1:2242494/58‑1 (MQ=255)
aTACCGACCAGAGCGCCCTGAATCTGCCCCATCGACtt < 1:2647006/38‑1 (MQ=255)
aTACCGACCAGAGCGCCCTGAATCTGCCCCATCGACtt < 1:3570617/38‑1 (MQ=255)
aTACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTACGGGTAGCTTCTTTTGGCGGCAAACCttcttc < 1:3357675/71‑1 (MQ=255)
tACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTACGGGTAGCTTCTTTTGGCGGCAAAc > 1:2301690/1‑63 (MQ=255)
tACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTACGGGTAGCTTCTTTTGGCGGCAAACcttc < 1:881262/67‑1 (MQ=255)
aCCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTACGGGTAGCTTCttt > 1:395997/1‑51 (MQ=255)
cGACCAGAGCGCCCTGAATCTGCCCCATCGACTTACGGGTAGCTTCTTTTGGCGGCAAACCTTCTTCCGcc < 1:457362/71‑1 (MQ=255)
gACCAGAGCGCCCTGAATCTGCCCCATCGACTTAc > 1:3423337/1‑35 (MQ=255)
gACCAGAGCGCCCTGAATCTGCCCCATCGACTTACGGGTAGctt > 1:1352780/1‑44 (MQ=255)
aCCAGAGCGCCCTGAATCTGCCCCATCGACTTACGGGTAGCTTCTTTTGGCGGCAAACCTTCTTCCGCCa > 1:1969391/1‑70 (MQ=255)
ccAGAGCGCCCTGAATCTGCCCCATCGACTTACGGGTAGCTTCTTTTGGCGGCAAACCTTCTTCCGCCAt > 1:62895/1‑70 (MQ=255)
cAGAGCGCCCTGAATCTGCCCCATCGACTTACGGGTAGCTTCTTTTGGCGGCAAACCTTCTTCCGCCATaa > 1:3859148/1‑71 (MQ=255)
cAGAGCGCCCTGAATCTGCCCCATCGACTTACGGGTAGCTTCTTTTGGCGGCAAACCTTCTTCCGCCATa > 1:3353268/1‑70 (MQ=255)
agCGCCCTGAATCTGCCCCATCGACTTACGGGTAGCTTCTTTTGGCGGCAAACCTTCTTCCGcc < 1:3562030/64‑1 (MQ=255)
agCGCCCTGAATCTGCCCCATCGACTTACGGGTAGCTTCTTTTGGCGGCAAACCTTCTTCCGCCATAaca < 1:2813696/70‑1 (MQ=255)
gcgcCCTGAATCTGCCCCATCGACTTACGGGTAGCTTCTTTTGGCGGCAAACCTTCTTCCGCCATAac > 1:2955526/1‑68 (MQ=255)
cTGAATCTGCCCCATCGACTTACGGGTAGCTTCTTTTGGCGGCAAAcc > 1:2382027/1‑48 (MQ=255)
gAATCTGCCCCATCGACTTACGGGTAGCTTCTTTTGGCGGCAAACCTTCTTCCGCCATaa > 1:3338048/1‑60 (MQ=255)
gAATCTGCCCCATCGACTTACGGGTAGCTTCTTTTGGCGGCAAACCTTCTTCCGCCATAACACGCTCAACg > 1:2754914/1‑71 (MQ=255)
aaTCTGCCCCATCGACTTACGGGTAGCTTCTTTTGGCGGCAAAc > 1:2255476/1‑44 (MQ=255)
aaTCTGCCCCATCGACTTACGGGTAGCTTCTTTTGGCGGCAAAc > 1:3438977/1‑44 (MQ=255)
aaTCTGCCCCATCGACTTACGGGTAGCTTCTTTTGGCGGCAAACCTTCTTCCGCCATAACACGCTCAACGt < 1:3380971/71‑1 (MQ=255)
tCTGCCCCATCGACTTACGGGTAGCTTCTTTTGGCGGCAAACcttctt < 1:1294603/48‑1 (MQ=255)
tCTGCCCCATCGACTTACGGGTAGCTTCTTTTGGCGGCAAACcttctt < 1:3934355/48‑1 (MQ=255)
tCTGCCCCATCGACTTACGGGTAGCTTCTTTTGGCGGCAAACcttctt < 1:2294619/48‑1 (MQ=255)
tCTGCCCCATCGACTTACGGGTAGCTTCTTTTGGCGGCAAACcttctt < 1:2865319/48‑1 (MQ=255)
|
GCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTACGGGTAGCTTCTTTTGGCGGCAAACCTTCTTCCGCCATAACACGCTCAACGT > minE/311493‑311629
|
| 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
