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 |
834,595 |
A→G |
17.6% |
D1018G (GAT→GGT) ‡ |
narG → |
nitrate reductase 1, alpha subunit |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 834,595 | 0 | A | G | 17.6%
| 143.9
/ 23.5
| 68 | D1018G (GAT→GGT) ‡ | narG | nitrate reductase 1, alpha subunit |
| Reads supporting (aligned to +/- strand): ref base A (30/26); new base G (6/6); total (36/32) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.68e-01 |
TCCGCTTCCGCGATATTCAGGCACAGCCGCGCAAAATTATCTCCAGCCCGACCTGGTCTGGTCTGGAAGATGAACACGTTTCTTACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTG > minE/834526‑834663
|
tCCGCTTCCGCGATATTCAGGCACAGCCGCGCAAAATTATCTCCAGCCCGACCTGGTCTGGTCTGGAAGAt < 1:2317952/71‑1 (MQ=255)
cgcgATATTCAGGCACAGCCGCGCAAAATTATCTCCAGCCCGACCTGGTCTGGTCTGGAAGATGAACACg < 1:1001419/70‑1 (MQ=255)
cgcgATATTCAGGCACAGCCGCGCAAAATTATCTCCAGCCCGACCTGGTCTGGTCTGGAAGATGAACACGt > 1:4343050/1‑71 (MQ=255)
cgcgATATTCAGGCACAGCCGCGCAAAATTATCTCCAGCCCGACCTGGTCTGGTCTGGAAGATGAACACGt > 1:4414918/1‑71 (MQ=255)
gATATTCAGGCACAGCCGCGCAAAATTATCTCCAGCCCGACCTGGTCTGGTCTGGAAGATGAACACGTTTc < 1:1515092/71‑1 (MQ=255)
atatTCAGGCACAGCCGCGCAAAATTATCTCCAGCCCGACCTGGTCTGGTCTGGAAGATGAACACGTTTCt < 1:4720274/71‑1 (MQ=255)
ttCAGGCACAGCCGCGCAAAATTATCTCCAGCCCGACCTGGTCTGGTCTGGAAGATGAACACGTTTCTTa > 1:3980592/1‑70 (MQ=255)
cAGGCACAGCCGCGCAAAATTATCTCCAGCCCGACCTGGTCTGGTCTGGAAGATGAACACGTTTCTTACaa > 1:913106/1‑71 (MQ=255)
cAGGCACAGCCGCGCAAAATTATCTCCAGCCCGACCTGGTCTGGTCTGGAAGATGAACACGTTTCTTACa < 1:3276936/70‑1 (MQ=255)
cAGGCACAGCCGCGCAAAATTATCTCCAGCCCGACCTGGTCTGGTCTGGAAGATGAACACGTTTCTTACa < 1:19916/70‑1 (MQ=255)
gCACAGCCGCGCAAAATTATCTCCAGCCCGACCTGGTCTGGTCTGGAAGAt > 1:3828071/1‑51 (MQ=255)
cacaGCCGCGCAAAATTATCTCCAGCCCGACCTGGTCTGGTCTGGAAGATGAACACGTTTCTTACAACGcc > 1:5485810/1‑71 (MQ=255)
gcaGCCGCGTAAAATTATCTCCAGCCCCACCTGGTCCGGTCTGGAAAGCGATCACGTCTCCTATAACGcgg < 1:1426495/70‑3 (MQ=255)
acaGCCGCGCAAAATTATCTCCAGCCCGACCTGGTCTGGTCTGGAAGATGAACACGTTTCTTACAACGCCg > 1:2810182/1‑71 (MQ=255)
acaGCCGCGCAAAATTATCTCCAGCCCGACCTGGTCTGGTCTGGAAGATGAACACGTTTCTTACAACGCCg > 1:775879/1‑71 (MQ=255)
acaGCCGCGCAAAATTATCTCCAGCCCGACCTGGTCTGGTCTGGAAGATGAACACGTTTCTTACAACGCCg > 1:3431265/1‑71 (MQ=255)
aGCCGCGCAAAATTATCTCCAGCCCGACCTGGTCTGGTCTGGAAGATGAACACGTTTCTTACAACGCCGGt < 1:3199465/71‑1 (MQ=255)
aGCCGCGCAAAATTATCTCCAGCCCGACCTGGTCTGGTCTGGAAGATGAACACGTTTCTTACAACGCCGGt < 1:4438733/71‑1 (MQ=255)
ccGCGCAAAATTATCTCCAGCCCGACCTGGTCTGGTCTGGAAGATGaa > 1:314518/1‑48 (MQ=255)
ccGCGCAAAATTATCTCCAGCCCGACCTGGTCTGGTCTGGAAGATGaa > 1:1951803/1‑48 (MQ=255)
gcAAAATTATCTCCAGCCCGCCCTGGTCTGGTCTGGAAGATGAACACGTTTCTTACAACGCCGGTTacac > 1:1316838/1‑70 (MQ=255)
gcAAAATTATCTCCAGCCCGACCTGGTCTGGTCTGGAAGATGAACACGTTTCTTACAACGCCGGTTacac > 1:4136311/1‑70 (MQ=255)
taaaaTTATCTCCAGCCCCACCTGGTCCGGTCTGGAAAGCGATCACGTCTCCTATAACGCGGGATACAcc > 1:2529333/2‑70 (MQ=255)
cAAAATTATCTCCAGCCCGACCTGGTCTGGTCTGGAAGATGAACACGTTTCTTACa > 1:1576026/1‑56 (MQ=255)
aaaaTTATCTCCAGCCCCACCTGGTCCGGTCTGGAAAGCGATCACGTCTCCTATAACGCggg > 1:2979045/1‑62 (MQ=255)
aaaTTATCTCCAGCCCCACCTGGTCCGGTCTGGAAAGCGATCACGTCTCCTATAACGCGGGATACACCAAc > 1:692219/1‑71 (MQ=255)
aaTTATCTCCAGCCCGACCTGGTCTGGTCTGGAAGATGAACACGTTTCTTACAACGCCGGTTACACCAACg > 1:5147618/1‑71 (MQ=255)
ttATCTCCAGCCCGACCTGGTCTGGTCTGGAAGATGAACACGTTTCTTACAACGCCGGTTACACCAACGtt < 1:4566101/71‑1 (MQ=255)
tctcCAGCCCGACCTGGTCTGGTCTGGAAGATGAACACGTTTCTTACAACGCCGGTTACACCAACGTTCAc > 1:3109015/1‑71 (MQ=255)
tctcCAGCCCGACCTGGTCTGGTCTGGAAGATGAACACGTTTCTTACAACGCCGGTTACACCAACGTTCAc > 1:422689/1‑71 (MQ=255)
cAGCCCGACCTGGTCTGGTCTGGAAGATGAACATGTTTCTTACAACGCCGGTTACACCAACGTTCAc < 1:3874263/67‑1 (MQ=255)
cAGCCCGACCTGGTCTGGTCTGGAAGATGAACACGTTTCTTACAACGCCGGTTACACCAACGTTCACGAga < 1:3325402/71‑2 (MQ=255)
cAGCCCGACCTGGTCTGGTCTGGAAGATGAACACGTTTCTTACAACGCCGGTTACACCAACGTTCACGAGc > 1:3771642/1‑71 (MQ=255)
cAGCCCGACCTGGTCTGGTCTGGAAGATGAACACGTTTCTTACAACGCCGGTTACACCAACGTTCACGAGc > 1:2279472/1‑71 (MQ=255)
cAGCCCCACCTGGTCCGGTCTGGAAAGCGATCACGTCTCCTATAACGCGGGATACACCAACGTTCATGAgt > 1:3245122/1‑70 (MQ=255)
aGCCCCACCTGGTCCGGTCTGGAAAGCGATCACGTCTCCTATAACGCGGGATACACCAACGTTCATGAgtt < 1:3154329/71‑3 (MQ=255)
cGACCTGGTCTGGTCTGGAAGATGAACACGTTTCTTACAACGCCGGTTACACCAACGTTCACGa > 1:5564691/1‑64 (MQ=255)
aCCTGGTCTGGTCTGGAAGATGAACACGTTTCTTACAACGCCGGTTACACCAACGTTCACGAGCTGATcc > 1:3053275/1‑70 (MQ=255)
ccTGGTCTGGTCTGGAAGATGAACACGTTTCTTACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCa < 1:2859978/71‑1 (MQ=255)
ctggtccggtCTGGAAAGCTATCACGTCTCCTATAACGCGGGATACACCAACGtt < 1:1773061/55‑1 (MQ=255)
ctggtccggtCTGGAAAGCGATCACGTCTCCTATAACGCGGGATACACCAACGtt < 1:4670662/55‑1 (MQ=255)
tggtctggtcTGGAAGATGAACACGTTTCTTACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCATg > 1:4345503/1‑71 (MQ=255)
gtctggtctgGAAGATGAACACGTTTCTTACAACGCCGGTTACACCAACGTTCACGAGCTg < 1:4221275/61‑1 (MQ=255)
gtctggtctgGAAGATGAACACGTTTCTTACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCATGGc > 1:1666562/1‑71 (MQ=255)
gtccggtctgGAAAGCGATCACGTCTCCTATAACGCGGGATACACCAACGTTCATGAGTTAATTCCGTgg < 1:4443603/70‑1 (MQ=255)
ctggtctggAAGATGAACACGTTTCTTACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCATGGCg > 1:1296049/1‑70 (MQ=255)
ccggtctggAAAGAGATCACGTCTCCTATAACGCGGGATACACCAACGTTCATGAGTTAATTCCGTGGc > 1:2991480/3‑69 (MQ=255)
tggtctggAAGATGAACACGTTTCTTACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCa < 1:997608/64‑1 (MQ=255)
tggtctggAAGATGAACACGTTTCTTACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCa < 1:1082990/64‑1 (MQ=255)
tggtctggAAGATGAACACGTTTCTTACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCa < 1:1249383/64‑1 (MQ=255)
tggtctggAAGATGAACACGTTTCTTACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCa < 1:1256267/64‑1 (MQ=255)
ggtctggAAAGCGATCACGTCTCCTATAACGCGGGATACACCAACGTTCATGAGTTAATTCCGTGGCGCAc < 1:4005560/71‑1 (MQ=255)
gtctggAAGATGAACACGTTTCTTACAACGCCGGTTaca > 1:4015644/1‑39 (MQ=255)
gtctggAAGATGAACACGTTTCTTACAACGCCGGTTaca > 1:3717928/1‑39 (MQ=255)
gtctggAAGATGAACACGTTTCTTACAACGCCGGTTa > 1:4715456/1‑37 (MQ=255)
gtctggAAGATGAACACGTTTCTTACAACGCCGGTTa > 1:1806213/1‑37 (MQ=255)
gtctggAAGATGAACACGTTTCTTACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCATGGCGt < 1:191628/68‑1 (MQ=255)
gtctggAAGATGAACACGTTTCTTACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCATGGCGTAc < 1:4367756/70‑1 (MQ=255)
gtctggAAGATGAACACGTTTCTTACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCATGGCGTAc < 1:3967120/70‑1 (MQ=255)
gtctggAAAGCGATCACGTCTCCTATAACGCGGGATACACCAACGTTCATGAGTTAATTCCGTGGCGCACg > 1:4241321/1‑71 (MQ=255)
tctggATGATGAACACGTTTCTTACAACGCCGGTTACACCAACGTTCACGAGCTg < 1:3257601/55‑1 (MQ=255)
ctggAAGATGAACACGTTTCTTACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCATGGCGTACGct > 1:2064287/1‑71 (MQ=255)
tggAAGATGAACACGTTTCTTACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCATGGCGTACGc < 1:4808438/69‑1 (MQ=255)
gAAGATGAACACGTTTCTTACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCATGGCGTACGctctc < 1:1764458/71‑1 (MQ=255)
gAAGATGAACACGTTTCTTACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCATGGCGTACGctctc < 1:1157887/71‑1 (MQ=255)
gAAGATGAACACGTTTCTTACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCATGGCGTACGctctc > 1:5173350/1‑71 (MQ=255)
aGATGAACACGTTTCTTACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTg < 1:1013436/71‑1 (MQ=255)
gATGAACACGTTTCTTACAACGCCGGTTACACCAACGTTCACGAGCTGATcc < 1:5523829/52‑1 (MQ=255)
|
TCCGCTTCCGCGATATTCAGGCACAGCCGCGCAAAATTATCTCCAGCCCGACCTGGTCTGGTCTGGAAGATGAACACGTTTCTTACAACGCCGGTTACACCAACGTTCACGAGCTGATCCCATGGCGTACGCTCTCTG > minE/834526‑834663
|
| 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
