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 |
837,716 |
T→C |
12.2% |
F63F (TTT→TTC) |
narI → |
nitrate reductase 1, gamma (cytochrome b(NR)) subunit |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 837,716 | 0 | T | C | 12.2%
| 104.9
/ 5.6
| 41 | F63F (TTT→TTC) | narI | nitrate reductase 1, gamma (cytochrome b(NR)) subunit |
| Reads supporting (aligned to +/- strand): ref base T (20/16); new base C (2/3); total (22/19) |
| Fisher's exact test for biased strand distribution p-value = 6.49e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
GCCAGATGCTGGATCGCAAAGGGATGAACCTGGCGTCGAACCTGTTCCATATCGGGATTCTGGGGATTTTTGTCGGTCACTTCTTCGGTATGCTGACGCCGCACTGGATGTATGAAGCCTGGCTGCCGATTGAAGTGAAA > minE/837646‑837785
|
gccagATGCTGGATCGCAAAGGGATGAACCTGGCGTCGAACCTGTTCCATATCGGGATTCTGGGGAttttt > 1:1638939/1‑71 (MQ=255)
ccagATGCTGGATCGCAAAGGGATGAACCTGGCGTCGAACCTGTTCCATATCGGGATTCTGGGGATTTTTg < 1:3574448/71‑1 (MQ=255)
ccagATGCTGGATCGCAAAGGGATGAACCTGGCGTCGAACCTGTTCCATATCGGGATTCTGGGGATTTTTg < 1:2593375/71‑1 (MQ=255)
cagATGCTGGATCGCAAAGGGATGAACCTGGCGTCGAACCTGTTCCATATCGGGATTCTGGGGATTTTTGt < 1:3308032/71‑1 (MQ=255)
agATGCTGGATCGCAAAGGGATGAACCTGGCGTCGAACCTGTTCCATATCGGGATTCTGGGGATTTTTGTc > 1:846490/1‑71 (MQ=255)
agATGCTGGATCGCAAAGGGATGAACCTGGCGTCGAACCTGTTCCATATCGGGATTCTGGGGATTTTTGTc > 1:769442/1‑71 (MQ=255)
atgatgGATCGCAAAGGGATGAACCTGGCGTCGAACCTGTTCCATATCGGGATTCTGGGGATTTTTGTCgg > 1:3479523/1‑71 (MQ=255)
aTGCTGGATCGCAAAGGGATGAACCTGGCGTCGAACCTGTTCCATATCGGGATTCTGGGGATTTTTGTCgg > 1:1132658/1‑71 (MQ=255)
tCGCAAAGGGATGAACCTGGCGTCGAACCTGTTCCATATCGGGATTCTGGGGATTTTTGTCGGTCActtct < 1:3077969/71‑1 (MQ=255)
tCGCAAAGGGATGAACCTGGCGTCGAACCTGTTCCATATCGGGATTCTGGGGATTTTTGTCGGTCActtct > 1:2943459/1‑71 (MQ=255)
cGCAAAGGGATGAACCTGGCGTCGAACCTGTTCCATATCGGGATTCTGGGGATTTTTGt < 1:3488616/59‑1 (MQ=255)
aaaGGGATGAACCTGGCGTCGAACCTGTTCCATATCGGGATTCTGGGGATTTTTGTCGGTCACTTCTTCgg > 1:2214863/1‑71 (MQ=255)
aaGGGATGAACCTGGCGTCGAACCTGTTCCATATAGGGATTCTGGGGATTTTTGTCGGTCACTTCTTCgg > 1:3945069/1‑70 (MQ=255)
gggATGAACCTGGCGTCGCACCTGTTCCATATCGGGATTCTGGGGATTTTTGTCGGTCACTTCTTCgg > 1:338379/1‑68 (MQ=255)
tgATGAACCTGGCGTCGAACCTGTTCCATATCGGGATTCTGGGGATTTTTGTc < 1:2445750/52‑1 (MQ=255)
gATGAACCTGGCGTCGAACCTGTTCCATATCGGGATTCTGGGGATTTTTGTCGGTCACTTCTTCGGTATGc < 1:2548172/71‑1 (MQ=255)
aTGAACCTGGCGTCGAACCTGTTCCATATCGGGATTCTGGGGATTTTTGTCGGTCACTTCTTCGGTATGCt > 1:498578/1‑71 (MQ=255)
aTGAACCTGGCGTCGAACCTGTTCCATATCGGGATTCTGGGGATTTTTGTCGGTCACTTCTTCGGTATGCt > 1:174865/1‑71 (MQ=255)
aCCTGGCGTCGAACCTGTTCCATATCGGGATTCTGGGGATTTTTGTCGGTCa > 1:3327032/1‑52 (MQ=255)
ccTGGCGTCGAACCTGTTCCATATCGGGATTCTGGGGATTTTTGTCGGTCACTTCTTCGGTATGCTGAcgc > 1:2300660/1‑71 (MQ=255)
cTGGCGTCGAACCTGTTCCATATCGGGATTCTGGGGATTTTTGTCGGTCACTTCTTCGGTATGCTGAcgc < 1:3764346/70‑1 (MQ=255)
ggCGTCGAACCTGTTCCATATCGGGATTCTGGGGAttttt < 1:971649/40‑1 (MQ=255)
ggCGTCGAACCTGTTCCATATCGGGATTCTGGGGAttttt < 1:3577298/40‑1 (MQ=255)
ggCGTCGAACCTGTTCCATATCGGGATTCTGGGGATTTTTGTCGGTCACTTCTTCGGTATGCTGAcgccg > 1:1505350/1‑70 (MQ=255)
gCGTCGAACCTGTTCCATATCGGGATTCTGGGGATTTTTGTCGGTCACTTCTTCGGTATGCTGAcgccg < 1:2446114/69‑1 (MQ=255)
tCGAACCTGTTCCATATCGGGATTCTGGGGATTTTTGTCGGTCACTTCTTCGGTATGCTGACGCCGCACTg < 1:2020350/71‑1 (MQ=255)
gAATCTGTTCCATATCGGCATTTTGGGGATTTTCTTCGGGCACTTGTTCGGCATGTTAACGCCGCACTgg < 1:999754/70‑1 (MQ=255)
gAATCTGTTCCATATCGGCATTTTGGGGATTTTCTTCGGGCACTTGTGCGGCATGTTAACGCCGCACTg < 1:1437546/69‑1 (MQ=255)
gAACCTGTTCCATATCGGGATTCTGGGGATTTTTGTCGGTCACTTCTTCGGTATGCTGACGCCGCACTGGa > 1:1273085/1‑71 (MQ=255)
aCCTGTTCCATATCGGGATTCTGGGGATTTTTGTCGGTCACTTCTTCGGTATGCTGACGCCGCACTGGATg > 1:1463209/1‑71 (MQ=255)
tcTGTTCCATATCGGCATTTTGGGGATTTTCTTCGGGCACTTGTTCGGCATGTTAACGCCGCACTGGATg > 1:2560582/2‑70 (MQ=255)
tGTTCCATATCGGCATTTTGGGGATTTTCTTCGGGCACTTGTTCGGCATGTTAACGCCGCACTgg < 1:1092000/65‑1 (MQ=255)
ttCCATATCGGGATTCTGGGGATTTTTGTCGGTCACTTCTTCGGTATGCTGACGCCGCACTGGATGTATGa < 1:1064298/71‑1 (MQ=255)
tCCATTTCGGGATTCTGGGGATTTTTGTCGGTCAGTTCTTCGGTATGCTGACGCCGCACTGGATGTATGa < 1:2305298/70‑1 (MQ=255)
tCCATATCGGGATTCTGGGGATTTTTGTCGGTCACTTCTTCg > 1:3939225/1‑42 (MQ=255)
tCCATATCGGGATTCTGGGGATTTTTGTCGGTCACTTCTTCGGTATGCTGACGCCGCACTGGATGTATg > 1:3013147/1‑69 (MQ=255)
atCGGGATTCTGGGGATTTTTGTCGGTCACTTCTTCGGTATGCTGa < 1:2855573/46‑1 (MQ=255)
tGGGGATTTTCTTCGGGCACTTGTTCGGCATGTTAACGCCGCACTGGATGTa > 1:723555/1‑52 (MQ=255)
gggATTTTTGTCGGTCACTTCTTCGGTATGCTGACGCCGCACTGGATGTATGAAGCCTGGCt > 1:210283/1‑62 (MQ=255)
gggATTTTTGTCGGTCACTTCTTCGGTATGCTGACGCCGCACTGGATGTATGAAGCCTGGCt > 1:1730880/1‑62 (MQ=255)
gggATTTTTGTCGGTCACTTCTTCGGTATGCTGACGCCGCACTGGATGTATGAAGCCTGGCTGCCGATTGa < 1:766058/71‑1 (MQ=255)
ggATTTTTGTCGGTCACTTCTTCGGTATGCTGACGCCGCACTGGATGTATGAAGc > 1:941868/1‑55 (MQ=255)
aTTTTTGTCGGTCACTTCTTCGGTATGCTGACGCCGCACTGGATGTATGAAGCCTGGCTGCCGATTGAAGt < 1:1054019/71‑1 (MQ=255)
aTTTTTGTCGGTCACTTCTTCGGTATGCTGACGCCGCACTGGATGTATGAAGCCTGGCTGCCGATTGAAGt < 1:994830/71‑1 (MQ=255)
tttttGTCGGTCACTTCTTCGGTATGCTGACGCCGCACTGGATGTATGAAGCCTGGCTGCCGATTGAAGt > 1:3052113/1‑70 (MQ=255)
tttttGTCGGTCACTTCTTCGGTATGCTGACGCCGCACTGGATGTATGAAGCCTGGCTGCCGATTGAAGt > 1:3873386/1‑70 (MQ=255)
ttGTCGGTCACTTCTTCGGTATGCTGACGCCGCACTGGATGTATGAAGCCTGGCTGCCGATTGAAGTGaaa > 1:2970484/1‑71 (MQ=255)
ttGTCGGTCACTTCTTCGGTATGCTGACGCCGCACTGGATGTATGAAGCCTGGCTGCCGATTGAAGTGaa < 1:2830759/70‑1 (MQ=255)
tGTCGGTCACTTCTTCGGTATGCTGACGCCGCACTGGATGTATGAAGCCt > 1:3248328/1‑50 (MQ=255)
tGTCGGTCACTTCTTCGGTATGCTGACGCCGCACTGGATGTATGAAGCCt > 1:3079998/1‑50 (MQ=255)
|
GCCAGATGCTGGATCGCAAAGGGATGAACCTGGCGTCGAACCTGTTCCATATCGGGATTCTGGGGATTTTTGTCGGTCACTTCTTCGGTATGCTGACGCCGCACTGGATGTATGAAGCCTGGCTGCCGATTGAAGTGAAA > minE/837646‑837785
|
| 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
