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 |
311,478 |
A→T |
11.3% |
A465A (GCT→GCA) |
acrB ← |
multidrug efflux system protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 311,478 | 0 | A | T | 11.3%
| 189.8
/ 15.1
| 71 | A465A (GCT→GCA) | acrB | multidrug efflux system protein |
| Reads supporting (aligned to +/- strand): ref base A (36/27); new base T (6/2); total (42/29) |
| Fisher's exact test for biased strand distribution p-value = 4.58e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.14e-01 |
CAGGATCAACGCCACCAGTACCGACAGCGCCATTGCTGAAACAATGGTAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACC > minE/311409‑311543
|
cAGGATCAACGCCACCAGTACCGACAGCGCCATTGCTGAAACAATGGTAATAGAGAACTGACGatagatag > 1:2339641/1‑71 (MQ=255)
gATCAACGCCACCAGTACCGACAGCGCCATTGCTGAAACAATGGTAATAGAGAACTGACGATAGATAGCAc > 1:2687185/1‑71 (MQ=255)
aTCAACGCCACCAGTACCGACAGCGCCATTGCTGAAACAATGGTAATAGAGAACTGACGATAGATAGCAcc < 1:907957/71‑1 (MQ=255)
cGCCACCAGTACCGACAGCGCCATTGCTGAAACAATGGTAATAGAGAACTGACGATAGATAGCACCAg > 1:1344455/1‑68 (MQ=255)
cGCCACCAGTACCGACAGCGCCATTGCTGAAACAATGGTAATAGAGAACTGACGATAGATAGCACCAg > 1:2798622/1‑68 (MQ=255)
cGCCACCAGTACCGACAGCGCCATTGCTGAAACAATGGTAATAGAGAACTGACGATAGATAGCACCAg > 1:2204283/1‑68 (MQ=255)
cGCCACCAGTACCGACAGCGCCATTGCTGAAACAATGGTAATAGAGAACTGACGATAGATAGCACCAGTAg < 1:3868617/71‑1 (MQ=255)
cGCCACCAGTACCGACAGCGCCATTGCTGAAACAATGGTAATAGAGAACTGACGATAGATAGCACCAGTAg < 1:3281954/71‑1 (MQ=255)
gCCACCAGTACCGACAGCGCCATTGCTGAAACAATGGTAATAGAGAACTGACGATAGATAGCAc > 1:1353623/1‑64 (MQ=255)
gCCACCAGTACCGACAGCGCCATTGCTGAAACAATGGTAATAGAGAACTGACGATAGATAGCACCAGTAg > 1:247677/1‑70 (MQ=255)
gCCACCAGTACCGACAGCGCCATTGCTGAAACAATGGTAATAGAGAACTGACGATAGATAGCACCAGTAg > 1:2438780/1‑70 (MQ=255)
ccaccaGTACCGACAGCGCCATTGCTGAAACAATGGTAATAGAGAACTGACGATAGATAGCACCAGTAGaa < 1:2670857/71‑1 (MQ=255)
accaGAACAGAAAGCGCCATTGCCGAAACGATGGTGATAGAGAACTGGCGATAAATTGCCCCAGTAGAAcc > 1:666546/1‑71 (MQ=12)
caGTACCGACAGCGCCATTGCTGAAACAATGGTAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGc > 1:2718405/1‑71 (MQ=255)
tACCGACAGCGCCATTGCTGAAACAATGGTAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCa > 1:117680/1‑70 (MQ=255)
aCCGACAGCGCCATTGCTGAAACAATGGTAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCa > 1:2159153/1‑69 (MQ=255)
aCCGACAGCGCCATTGCTGAAACAATGGTAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCa > 1:2570316/1‑69 (MQ=255)
ccGACAGCGCCATTGCTGAAACAATGGTAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAaag < 1:1279674/71‑1 (MQ=255)
cGACAGCGCCATTGCTGAAACAATGGTAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAaaga < 1:1799279/71‑1 (MQ=255)
cGACAGCGCCATTGCTGAAACAATGGTAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAaaga < 1:454905/71‑1 (MQ=255)
cGACAGCGCCATTGCTGAAACAATGGTAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAaaga < 1:1460748/71‑1 (MQ=255)
gACAGCGCCATTGCTGAAACAATGGTAATAGAGAACTGACGATAGATAGCACCAg > 1:546196/1‑55 (MQ=255)
gACAGCGCCATTGCTGAAACAATGGTAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAaagaa < 1:3497770/71‑1 (MQ=255)
gcgcCATTGCTGAAACAATGGTAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGc < 1:3260098/70‑1 (MQ=255)
cgcCATTGCTGAAACAATGGTAATAGAGAACTGACGATAGATAGCa > 1:2331992/1‑46 (MQ=255)
cgcCATTGCTGAAACAATGGTAATAGAGAACTGACGATAGATAGCACCAGTAGAAcc < 1:630117/57‑1 (MQ=255)
cgcCATTGCTGAAACAATGGTAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAaagaa > 1:1819940/1‑66 (MQ=255)
cgcCATTGCTGAAACAATGGTAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAaagaa > 1:2682644/1‑66 (MQ=255)
cgcCATTGCTGAAACAATGGTAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCa < 1:2867743/71‑1 (MQ=255)
gcCATTGCTGAAACAATGGTAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCAt < 1:3408709/71‑1 (MQ=255)
gcCATTGCCGAAACGATGGTGATAGAGAACTGGCGATAAATTGCCCCAGTAGAACCGCCGAAGAATGCCAt < 1:2113064/71‑1 (MQ=9)
ccATTGCTGAAACAATGGTAATAGAGAACTGACGATAGATAGCACCAGTa > 1:2686190/1‑50 (MQ=255)
cATTGCTGAAACAATGGTAATAGAGTACTGACGATAGATAGCACCAGTAGAAcc < 1:2778342/54‑1 (MQ=255)
cATTGCTGAAACAATGGTAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCg > 1:2119889/1‑71 (MQ=255)
aTTGCTGAAACAATGGTAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCgg < 1:1450810/71‑1 (MQ=255)
aTTGCTGAAACAATGGTAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCgg < 1:3003775/71‑1 (MQ=255)
ttGCTGAAACAATGGTAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCgg > 1:3866116/1‑70 (MQ=255)
ttGCTGAAACAATGGTAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCgg > 1:414223/1‑70 (MQ=255)
tGCTGAAACAATGGTAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTa > 1:3122340/1‑71 (MQ=255)
tGCCGAAACGATGGTGATAGAGAACTGGCGATAAATTGCCCCAGTAGAACCGCCGAAGAATGCCGTCggaa > 1:3936622/1‑69 (MQ=9)
gCTGAAACAATGGTAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAaag < 1:1593080/57‑1 (MQ=255)
gCTGAAACAATGGTAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAaag < 1:556139/57‑1 (MQ=255)
gCTGAAACAATGGTAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAaag < 1:2815359/57‑1 (MQ=255)
aaaCGATGGTGATAGAGAACTGGCGATAAATTGCCCCAGTAGAACCGCCGAAGAATGCCAt > 1:2092038/1‑61 (MQ=9)
aaaCAATGGTAATAGAGAACTGACGATAGATAGCACCAGTAGaa > 1:3263100/1‑44 (MQ=255)
aaaCAATGGTAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACg < 1:2689047/68‑1 (MQ=255)
aaaCAATGGTAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGaa > 1:574802/1‑70 (MQ=255)
aaaCAATGGTAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAAt < 1:3545284/71‑1 (MQ=255)
aaCGATGGTGATAGAGAACTGGCGATAAATTGCCCCAGTAGAACCGc > 1:1625577/1‑47 (MQ=12)
aCAATGGTAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAaaga > 1:2491536/1‑52 (MQ=255)
cAATGGTAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATAcc > 1:2666186/1‑71 (MQ=255)
aTGGTAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAaagaa > 1:3392439/1‑50 (MQ=255)
tGGTAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATAccgcc > 1:48657/1‑71 (MQ=255)
tAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGa > 1:3192846/1‑70 (MQ=255)
tAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGa > 1:2841052/1‑70 (MQ=255)
tAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGa > 1:702752/1‑70 (MQ=255)
aTAGAGAACTGGCGATAAATTGCCCCAGTAGAACCGCCgaa > 1:422278/1‑41 (MQ=12)
tAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTa > 1:410310/1‑54 (MQ=255)
agaACTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATa > 1:348051/1‑57 (MQ=255)
agaACTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTAcc < 1:2784490/71‑1 (MQ=255)
gaACTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCa > 1:960071/1‑71 (MQ=255)
aaCTGGCGATAAATTGCCCCAGTAGAACCGCCgaagaa > 1:2747381/1‑38 (MQ=12)
aaCTGACGATAGATAGCACCAGTAGAACCGCCAaagaa > 1:3022234/1‑38 (MQ=255)
aCTGGCGATAAATTGCCCCAGTAGAACCGCCGAAGAATGCCATCGGAATAAATACCGCTGACAGCACCAt < 1:880954/70‑1 (MQ=9)
aCTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCAt < 1:2531350/70‑1 (MQ=255)
aCTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATc < 1:3754158/71‑1 (MQ=255)
aCTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATc < 1:2104716/71‑1 (MQ=255)
aCTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCAGCGGTACGAATACCGCCGACAGTACCATc < 1:1121581/71‑1 (MQ=255)
atGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATcg > 1:1725338/2‑71 (MQ=255)
tGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATcg > 1:2672090/1‑70 (MQ=255)
tGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGAACCAt < 1:1535646/68‑1 (MQ=255)
aCGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGa > 1:1412848/1‑71 (MQ=255)
gatagataGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATa > 1:2727115/1‑71 (MQ=255)
gatagataGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATa < 1:1264754/71‑1 (MQ=255)
tagatagCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATAccgcc < 1:443508/51‑1 (MQ=255)
tagatagCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATAcc < 1:812398/71‑1 (MQ=255)
|
CAGGATCAACGCCACCAGTACCGACAGCGCCATTGCTGAAACAATGGTAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACC > minE/311409‑311543
|
| 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
