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 |
834,548 |
A→G |
34.5% |
A1002A (GCA→GCG) |
narG → |
nitrate reductase 1, alpha subunit |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 834,548 | 0 | A | G | 34.5%
| 55.9
/ 51.0
| 58 | A1002A (GCA→GCG) | narG | nitrate reductase 1, alpha subunit |
| Reads supporting (aligned to +/- strand): ref base A (21/17); new base G (12/8); total (33/25) |
| Fisher's exact test for biased strand distribution p-value = 7.86e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.90e-01 |
CGGTCGTGACCATACGCATCTGGCGCTGAATAAAGAAGACGAGAAGATCCGCTTCCGCGATATTCAGGCACAGCCGCGCAAAATTATCTCCAGCCCGACCTGGTCTGGTCTGGAAGATGAACACGTTTCTTACAACGCCG > minE/834479‑834618
|
cGGTCGTGACCATACGCATCTGGCGCTGAATAAAGAAGACGAGAAGATCCGCTTCCGCGATATTCAGGcac < 1:708986/71‑1 (MQ=255)
gTCGTGACCATACGCATCTGGCGCTGAATAAAGAAGACGAGAAGATCCGCTTCCGCGATATTCAGGCACAg < 1:3711096/71‑1 (MQ=255)
cGTGACCATACGCATCTGGCGCTGAATAAAGAAGACGAGAAGATCCGCTTCCGCGATATTCAGGCACAGcc > 1:1505855/1‑71 (MQ=255)
gaacATACCCATCTGGCGCTGCACAAAGAGGACGAGAAGATTCGCTTTCGCGATATTCAGGCGCAGCcgcg > 1:2012385/4‑71 (MQ=255)
aCCATACGCATCTGGCGCTGAATAAAGAAGACGAGAAGATCCGCTTCCGCGATATTCAGGCACAGCcgcg > 1:3373149/1‑70 (MQ=255)
aTACGCATCTGGCGCTGAATAAAGAAGACGAGAAGATCCGCTTCCGCGATATTCAGGCACAGCCGCGCaaa < 1:444828/71‑1 (MQ=255)
cccATCTGGCGCTGCACAAAGAGGACGAGAAGATTCGCTTTCGCGATATTCAGGCGCAGCCGCGTAAAAt > 1:726047/3‑70 (MQ=255)
gCATCTGGCGCTGAATAAAGAAGACGAGAAGATCCGCTTCCGCGATATTCAGGCACAGCCGCGCAAAATTa < 1:1798718/71‑1 (MQ=255)
ccATCTGGCGCTGCACAAAGAGGACGAGAAGATTCGCTTTCGCGATATTCAGGCGCAGCcgc > 1:71946/2‑62 (MQ=255)
cATCTGGCGCTGCACAAAGAGGACGAGAAGATTCGCTTTCGCGATATTCAGGCGCAGCCGCGTAAAATTAt < 1:501873/71‑1 (MQ=255)
cATCTGGCGCTGCACAAAGAGGACGAGAAGATTCGCTTTCGCGATATTCAGGCGCAGCCGCGTAAAATTAt < 1:2869360/71‑1 (MQ=255)
aTCTGGCGCTGCACAAAGAGGACGAGAAGATTCGCTTTCGCGATATTCAGGCGCAGCCGCGTAAAAtt > 1:2402586/1‑68 (MQ=255)
aTCTGGCGCTGCACAAAGAGGACGAGAAGATTCGCTTTCGCGATATTCAGGCGCAGCCGCGTAAAATTAtc < 1:1834838/71‑1 (MQ=255)
gcgcTGAATAAAGAAGACGAGAAGATCCGCTTCCGCGATATTCAGGCACAGCCGCGCAAAATTATCTcc < 1:715014/69‑1 (MQ=255)
cgcTGCACAAAGAGGACGAGAAGATTCGCTTTCGCGATATTCAGGCGCAGCCGCGTAAAATTATCTCCAGc > 1:3406273/1‑71 (MQ=255)
gAATAAAGAAGACGAGAAGATCCGCTTCCGCGATATTCAGGCACAGCCGCGCAAAATTATCTCCAGCCCGa > 1:1145938/1‑71 (MQ=255)
aagaggACGAGAAGATTCGCTTTCGCGATATTCAGGCGCAGCCGCGTAAAATTATCTCCAGCCCCAc > 1:3447536/1‑67 (MQ=255)
aagaggACGAGAAGATTCGCTTTCGCGATATTCAGGCGCAGCCGCGTAAAATTATCTCCAGCCCCACctgg > 1:2264364/1‑71 (MQ=255)
aagaggACGAGAAGATTCGCTTTCGCGATATTCAGGCGCAGCCGCGTAAAATTATCTCCAGCCCCACctgg < 1:946677/71‑1 (MQ=255)
aagaggACGAGAAGATTCGCTTTCGCGATATTCAGGCGCAGCCGCGTAAAATTATCTCCAGCCCCACctgg > 1:1272132/1‑71 (MQ=255)
aagaagACGAGAAGATCCGCTTCCGCGATATTCAGGCACAGCCGCGCAAAATTATCTCCAGCCCGACctgg > 1:1483700/1‑71 (MQ=255)
agaggaCGAGAAGATTCGCTTTCGCGATATTCAGGCGCAGCCGCGTAAAATTATCTCCAGCCCCACctggt > 1:3512271/1‑71 (MQ=255)
agaagaCGAGAAGATCCGCTTCCGCGATATTCAGGCACAGCCGCGCAAAATTAtctc < 1:1289726/57‑1 (MQ=255)
gaagaCGAGAAGATCCGCTTCCGCGATATTCAGGCACAGCCGCGCAAAATTATCTCCAGCCCGACctggtc > 1:1206579/1‑71 (MQ=255)
gaCGAGAAGATCCGCTTCCGCGATATTCAGGCACAGCCGCGCAAAATTATCTCCAGCCCGACctggtctgg > 1:3154823/1‑71 (MQ=255)
gaCGAGAAGATCCGCTTCCGCGATATTCAGGCACAGCCGCGCAAAATTATCTCCAGCCCGACctggtctgg > 1:92992/1‑71 (MQ=255)
cGAGAAGATTCGCTTTCGCGATATTCAGGCGCAGCCGCGTAAAATTATCTCCAGCCCCACCtggtccggtc > 1:3442243/1‑71 (MQ=255)
gagaAGATTCGCTTTCGCGATATTCAGGCGCAGCcgc < 1:584969/37‑1 (MQ=25)
gagaAGATTCGCTTTCGCGATATTCAGGCGCAGCCGCGTAAAATTATCTCCAGCCCCACCtggtccggtc < 1:1052559/70‑1 (MQ=255)
gagaAGATCCGCTTCCGCGATATTCAGGCACAGCCGCGCa > 1:719255/1‑40 (MQ=255)
gagaAGATCCGCTTCCGCGATATTCAGGCACAGCCGCGCa > 1:795493/1‑40 (MQ=255)
gaagaTTCGCTTTCGCGATATTCAGGCGCAgcggcgt > 1:2152428/1‑36 (MQ=16)
gaagaTCCGCTTCCGCGATATTCAGGCACAGCCGCGCAAAATTATCTCCAGCCCGACCTGgtctggtctg > 1:2688955/1‑70 (MQ=255)
agaTCCGCTTCCGCGATATTCAGGCACAGCCGCGCAAAATTATCTCCAGCCCGACCTGGTCTGGTCTGGa < 1:2507330/70‑1 (MQ=255)
gaTTCGCTTTCGCGATATTCAGGCGCAGCCGCGTAAAATTATCTCCAGCCCCACCTGGTCCGGTCTGGa > 1:2016113/1‑69 (MQ=255)
gaTCCGCTTCCGCGATATTCAGGCACAGCCGCGCAAAATTATCTCCAGCCCGACCTGgtct‑gtctgg < 1:1862095/67‑1 (MQ=255)
tCCGCTTCCGCGATATTCAGGCACAGCCGCGCAAAATTATCTCCAGCCCGACCTGGTCTGGTCTGGaa > 1:272111/1‑68 (MQ=255)
tCCGCTTCCGCGATATTCAGGCACAGCCGCGCAAAATTATCTCCAGCCCGACCTGGTCTGGTCTGGAAGAt > 1:2720303/1‑71 (MQ=255)
tCCGCTTCCGCGATATTCAGGCACAGCCGCGCAAAATTATCTCCAGCCCGACCTGGTCTGGTCTGGAAGAt > 1:2658065/1‑71 (MQ=255)
tcGCTTTCGCGATATTCAGGCGCAGCCGCGTAAAAtt < 1:958024/36‑1 (MQ=25)
cGCTTCCGCGATATTCAGGCACAGCCGCGCAAAATTATCTCCAGCCCGACCTGGTCTGGTCTGGAAGATGa < 1:579043/71‑1 (MQ=255)
gCTTCCGCGATATTCAGGCACAGCCGCGCAAAATTAt > 1:1614774/1‑37 (MQ=255)
gCTTCCGCGATATTCAGGCACAGCCGCGCAAAATTATCTCCAGCCCGACCTGGTCTGGTCTGGAAGATGaa < 1:597578/71‑1 (MQ=255)
cTTCCGCGATATTCAGGCACAGCCGCGCAAAATTATCTCCAGCCCGACCTGGTCTGGTCTGGAAGATGAac < 1:17509/71‑1 (MQ=255)
ttCCGCGATATTCAGGCACAGCCGCGCAAAATTAt < 1:3553451/35‑1 (MQ=255)
ttCCGCGATATTCAGGCACAGCCGCGCAAAATTATCTCCAGCCCGACctgg > 1:3934788/1‑51 (MQ=255)
tCCGCGATATTCAGGCACAGCCGCGCAAAATTATCTCCAGCCCGACCTGGTCTGGTCTGGAAGATGaa > 1:3157990/1‑68 (MQ=255)
tCCGCGATATTCAGGCACAGCCGCGCAAAATTATCTCCAGCCCGACCTGGTCTGGTCTGGAAGATGAacac > 1:162863/1‑71 (MQ=255)
ccGCGATATTCAGGCACAGCCGCGCAAAATTATCTCCAGCCCGACCTGGTCTGGTCTGGAAGATGAacac > 1:1261589/1‑70 (MQ=255)
ccGCGATATTCAGGCACAGCCGCGCAAAATTATCTCCAGCCCGACCTGGTCTGGTCTGGAAGATGAacac < 1:250499/70‑1 (MQ=255)
atatTCAGGCACAGCCGCGCAAAATTATCTCCAGCCCGACCTGGTCTGGTCTGGAAGATGAACACGTTTCt < 1:3872957/71‑1 (MQ=255)
tatTCAGGCACAGCCGCGCAAAATTATCTCCAGCCCGACCTGGTCTGGTCTGGAAGATGAACACGTTTCtt < 1:1375015/71‑1 (MQ=255)
ttCAGGCGCAGCCGCGTAAAATTATCTCCAGCCCCACCtggtccggtc < 1:366804/48‑1 (MQ=255)
ttCAGGCACAGCCGCGCAAAATTATCTCCAGCCCGACctggtctg < 1:283827/45‑1 (MQ=255)
cAGGCACAGCCGCGCAAAATTATCTCCAGCCCGACCTGGTCTGGTCTGGAAGATGAACACGTTTCTTa > 1:3752800/1‑68 (MQ=255)
cAGGCACAGCCGCGCAAAATTATCTCCAGCCCGACCTGGTCTGGTCTGGAAGATGAACACGTTTCTTa > 1:653439/1‑68 (MQ=255)
cAGGCACAGCCGCGCAAAATTATCTCCAGCCCGACCTGGTCTGGTCTGGAAGATGAACACGTTTCTTACa < 1:1228092/70‑1 (MQ=255)
cggCACAGCCGCGCAAAATTATCTCCAGCCCGACCTGGTCTGGTCTGGAAGATGAACACGTTTCTTAc < 1:550323/67‑1 (MQ=255)
aGGCACAGCCGCGCAAAATTATCTCCAGCCCGACCTGGTCTGGTCTGGAAGATGAACACGTTTCTTACAAc > 1:1431713/1‑71 (MQ=255)
acaGCCGCGCAAAATTATCTCCAGCCCGACCTGGTCTGGTCTGGAAGATGAACACGTTTCTTACAACGcc < 1:710114/70‑1 (MQ=255)
acaGCCGCGCAAAATTATCTCCAGCCCGACCTGGTCTGGTCTGGAAGATGAACACGTTTCTTACAACGCCg > 1:526679/1‑71 (MQ=255)
acaGCCGCGCAAAATTATCTCCAGCCCGACCTGGTCTGGTCTGGAAGATGAACACGTTTCTTACAACGCCg > 1:3223269/1‑71 (MQ=255)
acaGCCGCGCAAAATTATCTCCAGCCCGACCTGGTCTGGTCTGGAAGATGAACACGTTTCTTACAACGCCg > 1:3656926/1‑71 (MQ=255)
|
CGGTCGTGACCATACGCATCTGGCGCTGAATAAAGAAGACGAGAAGATCCGCTTCCGCGATATTCAGGCACAGCCGCGCAAAATTATCTCCAGCCCGACCTGGTCTGGTCTGGAAGATGAACACGTTTCTTACAACGCCG > minE/834479‑834618
|
| 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
