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 F1 I0 R1
|
2892 |
75.3 |
5698161 |
66.1% |
3766484 |
59.5 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
1,395,393 |
G→T |
21.2% |
L33L (CTG→CTT) |
setB → |
lactose/glucose efflux system |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,395,393 | 0 | G | T | 21.2%
| 160.0
/ 23.7
| 66 | L33L (CTG→CTT) | setB | lactose/glucose efflux system |
| Reads supporting (aligned to +/- strand): ref base G (26/26); new base T (3/11); total (29/37) |
| Fisher's exact test for biased strand distribution p-value = 7.25e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.70e-01 |
CGAAATCGTTTGACCTGACCTCGACGGCGTTTTTAATCGTTGCCTTTCTCACCGGTATTGCGGGCGCTCTGCAAACCCCGACACTCAGTATTTTTCTTACCGATGAAGTACATGCCCGTCCGGCGATGGTGGGATTCTTC > minE/1395323‑1395462
|
cgAAATCGTTTGACCTGACCTCGACGGCGTTTTTAATCGTTGCCTTTCTCACCGGTATTGCGGGCGCTCTg > 1:7046/1‑71 (MQ=255)
cgAAATCGTTTGACCTGACCTCGACGGCGTTTTTAATCGTTGCCTTTCTCACCGGTATTGCGGGCGCTCTg > 1:1707370/1‑71 (MQ=255)
cgAAATCGTTTGACCTGACCTCGACGGCGTTTTTAATCGTTGCCTTTCTCACCGGTATTGCGGGCGCTCTg > 1:1719305/1‑71 (MQ=255)
gTTTGACCTGACCTCGACGGCGTTTTTAATCGTTGCCTTTCTCACCGGTATTGCGGGCGCTCTGCAAAccc > 1:2179918/1‑71 (MQ=255)
ttGACCTGACCTCGACGGCGTTTTTAATCGTTGCCTTTCTCACCGGTATTGCGGGCGCTCTGCAAAcccc > 1:1240193/1‑70 (MQ=255)
tCGGCGGCGTTTTTAATCGTTGCCTTTCTCACCGGTATTGCGGGCGCTCTGCAAAcccc < 1:5507853/59‑1 (MQ=255)
tCGACGGCGTTTTTAATCGTTGCCTTTCTCACCGGTATTGCGGGCGCTCTGCaa < 1:3094563/54‑1 (MQ=255)
ccgcGGCATTTTTACTTGTCGCCTTTCTGACGGGTATTGCGGGCTCTCTTCAGACTCCTACCCTAAGTa < 1:1912440/66‑1 (MQ=255)
ccgcGGCATTTTTACTTGTCGCCTTTCTGACGGGTATTGCGGGCGCTCTTCAGACTCCTACCCTAAGTa < 1:961379/66‑1 (MQ=255)
ccgcGGCATTTTTACTTGTCGCCTTTCTGACGGGTATTGCGGGCGCTCTTCAGACTCCTACCCTAAGTa < 1:5606809/66‑1 (MQ=255)
ccgcGGCATTTTTACTTGTCGCCTTTCTGACGGGTATTGCGGGCGCTCTTCAGACTCCTACCCTAAGTa < 1:5461045/66‑1 (MQ=255)
cGACGGCGTTTTTAATCGTTGCCTTTCTCACCGGTATTGCGGGCGCTCTGCAAAccc > 1:570409/1‑57 (MQ=255)
gACGGCGTTTATAATCGTTGCCTTTCTCACCGGTATTGCGGGCGCTCTGCAAACCCCGACACTCAGTAttt > 1:345318/1‑71 (MQ=255)
cGGCATTTTTACTTGTCGCCTTTCTGACGGGTATTGCGGGCGCTCTTCAGACTCCTACCCTAAGTAtattc < 1:1329297/71‑2 (MQ=255)
gcatttttACTTGTCGCCTTTCTGACGGGTATTGCGGGCGCTCTTCAGACTCCTACCCTAAGTATATTCCt < 1:433957/68‑1 (MQ=255)
gcatttttACTTGTCGCCTTTCTGACGGGTATTGCGGGCGCTCTTCAGACTCCTACCCTAAGTATATTCCt < 1:5433845/68‑1 (MQ=255)
gTTTTTAATCGTTGCCTTTCTCACCGGTATTGCGGGCGCTCTGCAAACCCCGACACTCAGTATTTTTCTTa > 1:3885576/1‑71 (MQ=255)
atttttACTTGTCGCCTTTCTGACGGGTATTGCGGGCGCTCTTCAGACTCCTACCCTAAGTATATTCCtcg > 1:3109744/2‑69 (MQ=255)
tttttACTTGTCGCCTTTCTGACGGGTATTGCGGGCGCTCTTCa < 1:4844851/44‑1 (MQ=16)
tttttAATCGTTGCCTTTCTCACCGGTATTGCGGGCGCTCTGCAAACCCCGa < 1:4913978/52‑1 (MQ=255)
ttttAATCGTTGCCTTTCTCACCGGTATTGCGGGCGCTCTGCAAACCCCGACACTCAGTATTTTTCTTAcc > 1:5049856/1‑71 (MQ=255)
ttttAATCGTTGCCTTTCTCACCGGTATTGCGGGCGCTCTGCAAACCCCGACACTCAGTATTTTTCTTAcc > 1:2495962/1‑71 (MQ=255)
tttACTTGTCGCCTTTCTGACGGGTATTGCGGGCGCTCTTCAGACTCCTACCCtaa > 1:3363584/1‑54 (MQ=255)
tttAATCGTTGCCTTTCTCACCGGTATTGCGGGCGCTCTg > 1:4477010/1‑40 (MQ=255)
tttAATCGTTGCCTTTCTCACCGGTATTGCGGGCGCTCTGCAAACCCCGACACTCAGTATTTTTCTTAcc > 1:4926033/1‑70 (MQ=255)
ttAATCGTTGCCTTTCTCACCGGTATTGCGGGCGCTCTGCAAACCCCGACACTCAGTATTTTTCTTACCGa > 1:4581485/1‑71 (MQ=255)
aTCGTTGCCTTTCTCACCGGTATTGCGGGTGCTCTGCAAACCCCGACACTCAGTATTTTTCTTACCGATg < 1:2188262/70‑1 (MQ=255)
aTCGTTGCCTTTCTCACCGGTATTGCGGGCGCTCTGCAAACCCCGACACTCAGTATTTTTCTTACCGATGa < 1:4649244/71‑1 (MQ=255)
tCGTTGCCTTTCTCACCGGTATTGCGGGCGCTCTGCAAAcccc < 1:5166761/43‑1 (MQ=255)
tCGTTGCCTTTCTCACCGGTATTGCGGGCGCTCTGCAAAcccc < 1:4514188/43‑1 (MQ=255)
tCGTTGCCTTTCTCACCGGTATTGCGGGCGCTCTGCAAACCCCGACACTCAGTATTTTTCtt < 1:5064535/62‑1 (MQ=255)
ttGCCTTTCTCACCGGTATTGCGGGCGCTCTGCAAACCCCGACACTCAGTATTTTTCTTACCGATGAAGTa < 1:5577743/71‑1 (MQ=255)
ttGCCTTTCTCACCGGTATTGCGGGCGCTCTGCAAACCCCGACACTCAGTATTTTTCTTACCGATGAAGTa < 1:3752649/71‑1 (MQ=255)
gCCTTTCTCACCGGTATTGCGGGCGCTCTGCAAACCCCGACACTCAGTATTTTTCTTACCGATGAAGt > 1:5173362/1‑68 (MQ=255)
ccTTTCTCACCGGTATTGCGGGCGCTCTGCAAACCCCGACACTCAGTATTTTTCTTACCGATGAAGTACAt < 1:3398826/71‑1 (MQ=255)
ttCTGACGGGTATTGCGGGCGCTCTTCAGACTCCTACCCTAAGTATATTCCTCGCAGATGaa > 1:1215099/1‑62 (MQ=255)
ttCTCACCGGTATTGCGGGCGCTCTGCAAACCCCGACACTCAGTATTTTTCTTACCGATGAAGTACATGcc > 1:796732/1‑71 (MQ=255)
ttCTCACCGGTATTGCGGGCGCTCTGCAAACCCCGACACTCAGTATTTTTCTTACCGATGAAGTACATGcc > 1:4008181/1‑71 (MQ=255)
tctcACCGGTATTGCGGGCGCTCTGCAAACCCCGac > 1:1206445/1‑36 (MQ=255)
tctcACCGGTATTGCGGGCGCTCTGCAAACCCCGACACTCAGTATTTTTGTTACCGATGAAGTACATGccc > 1:2692158/1‑71 (MQ=255)
tctcACCGGTATTGCGGGCGCTCTGCAAACCCCGACACTCAGTATTTTTCTTACCGATGAAGTACATGccc > 1:1987298/1‑71 (MQ=255)
ctcACCGGTATTGCGGGCGCTCTGCAAACCCCGACACTCAGTATTTTTCTTACCGATGAAGTACATGccc > 1:557475/1‑70 (MQ=255)
aCCGGTATTGCGGGCGCTCTGCAAACCCCGACACTCAGTa < 1:2298029/40‑1 (MQ=255)
aCCGGTATTGCGGGCGCTCTGCAAACCCCGACACTCAGTATTTTTCTTACCGATGAAGTACATGCCCGTc < 1:4786186/70‑1 (MQ=255)
tATTGCGGGCGCTCTGCAAACCCCGACACTCAGTATTTTTCTTACCGATGa < 1:2040793/51‑1 (MQ=255)
tATTGCGGGCGCTCTGCAAACCCCGACACTCAGTATTTTTCTTACCGATGa < 1:5633364/51‑1 (MQ=255)
aTTGCGGGCGCTCTTCAGACTCCTACCCTAAGTATATTCCTCGCAGATGAACTGAAAGCCCGTcctat < 1:5156775/68‑4 (MQ=255)
aTTGCGGGCGCTCTTCAGACTCCTACCCTAAGTATATTCCTCGCAGATGAACTGAAAGCCCGTcctat < 1:4691839/68‑4 (MQ=255)
aTTGCGGGCGCTCTTCAGACTCCTACCCTAAGTATATTCCTCGCAGATGAACTGAAAGCCCGTcctat < 1:1824549/68‑4 (MQ=255)
ttGCGGGCGCTCTGCAAACCCCGACACTCAGTAttt < 1:1616264/36‑1 (MQ=255)
ttGCGGGCGCTCTGCAAACCCCGACACTCAGTATTTTTCTTACCGATGAAg < 1:4564215/51‑1 (MQ=255)
ttGCGGGCGCTCTGCAAACCCCGACACTCAGTATTTTTCTTACCGATGAAGTACATGCCCGTCCGGCGAtg < 1:3216434/71‑1 (MQ=255)
ttGCGGGCGCTCTGCAAACCCCGACACTCAGTATTTTTCTTACCGATGAAGTACATGCCCGTCCGGCGAtg < 1:4153850/71‑1 (MQ=255)
ttGCGGGCGCTCTGCAAACCCCGACACTCAGTATTTTTCTTA‑CGATGAAGTAc > 1:261351/1‑53 (MQ=255)
gCGGGCGCTCTGCAAACCCCGACACTCAGTATTTTTCTTa > 1:4262473/1‑40 (MQ=255)
gCGGGCGCTCTGCAAACCCCGACACTCAGTATTTTTCTTa > 1:3901986/1‑40 (MQ=255)
gCGGGCGCTCTGCAAACCCCGACACTCAGTATTTTTCTTACCGATGAAGTACATGCCCGTCCGGCGAtggt > 1:4023571/1‑71 (MQ=255)
cGGGCGCTCTGCAAACCCCGACACTCAGTATTTTTCTTACCGATGAAGTACATGCCCGTCCGGCGAtggtg > 1:4463386/1‑71 (MQ=255)
gggCGCTCTGCAAACCCCGACACTCAGTATTTTTCTTACCGATGAAGTACATGCCCGTCCGGCGAtggtgg < 1:2389281/71‑1 (MQ=255)
cgcTCTGCAAACCCCGACACTCAGTATTTTTCTTACCGATGAAGTACATGCCCGTCCGGCGATGGTGGGAt > 1:5515954/1‑71 (MQ=255)
ctGCAAACCCCGACACTCAGTATTTTTCTTACCGATg < 1:2538815/37‑1 (MQ=255)
ctGCAAACCCCGACACTCAGTATTTTTCTTACCGATg < 1:3362466/37‑1 (MQ=255)
ctGCAAACCCCGACACTCAGTATTTTTCTTACCGATg < 1:4276862/37‑1 (MQ=255)
ctGCAAACCCCGACACTCAGTATTTTTCTTACCGATGAAGTACATGcc > 1:4824744/1‑48 (MQ=255)
ctGCAAACCCCGACACTCAGTATTTTTCTTACCGATGAAGTACATGCCCGTCCGGCGAtgg < 1:2533110/61‑1 (MQ=255)
ctGCAAACCCCGACACTCAGTATTTTTCTTACCGATGAAGTACATGCCCGTCCGGCGAtgg < 1:5537199/61‑1 (MQ=255)
tGCAAACCCCGACACTCAGTATTTTTCTTACCGATGAAGTACATGCCCGTCCGGCGATGGTGGGAttcttc > 1:2153550/1‑71 (MQ=255)
tGCAAACCCCGACACTCAGTATTTTTCTTACCGATGAAGTACATGCCCGTCCGGCGATGGTGGGAttcttc > 1:5036779/1‑71 (MQ=255)
tGCAAACCCCGACACTCAGTATTTTTCTTACCGATGAAGTACATGCCCGTCCGGCGATGGTGGGAttcttc > 1:459481/1‑71 (MQ=255)
tGCAAACCCCGACACTCAGTATTTTTCTTACCGATGAAGTACATGCCCGTCCGGCGATGGTGGGAttct < 1:5132943/69‑1 (MQ=255)
gCAAACCCCGACACTCAGTATTTTTCTTACCGATGAAGTACATGCCCGTCCGGCGATGGTGGGAtt > 1:2390881/1‑66 (MQ=255)
|
CGAAATCGTTTGACCTGACCTCGACGGCGTTTTTAATCGTTGCCTTTCTCACCGGTATTGCGGGCGCTCTGCAAACCCCGACACTCAGTATTTTTCTTACCGATGAAGTACATGCCCGTCCGGCGATGGTGGGATTCTTC > minE/1395323‑1395462
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
