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 |
|
A1 F17 I0 R2
|
276 |
45.3 |
3729697 |
93.0% |
3468618 |
60.6 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
2,669,838 |
T→C |
66.1% |
V92A (GTT→GCT) |
hcaC → |
3‑phenylpropionate dioxygenase, predicted ferredoxin subunit |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 2,669,838 | 0 | T | C | 66.1%
| 68.9
/ 53.4
| 59 | V92A (GTT→GCT) | hcaC | 3‑phenylpropionate dioxygenase, predicted ferredoxin subunit |
| Reads supporting (aligned to +/- strand): ref base T (5/15); new base C (16/23); total (21/38) |
| Fisher's exact test for biased strand distribution p-value = 2.63e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.26e-01 |
CCTGAAAACGGGGAAAGCGTTATGCCTGCCCGCCACCGATCCGCTCACCACTTATCCAGTACACGTTGAAGGTGGTGACATTTTCATCGACTTACCGGAGGCGCAGCCATGAGCGATCTGCATAACGAG > W3110S.gb/2669773‑2669901
|
ccTGAAAACGGGGAAAGCGTTATGCCTGCCCGCCACCGATCCGCTCACCACTTATCCAGTACACGTTg < 1:691922/68‑1 (MQ=255)
cTGAAAACGGGGAAAGCGTTATGCCTGCCCGCCACCGATCCGCTCACCACTTATCCAGTACACGCTg < 1:3138202/67‑1 (MQ=255)
gAAAACGGGGAAAGCGTTATGCCTGCCCGCCACCGATCCGCTCACCACTTATCCAGTACACGCTGAAgg < 1:1152721/69‑1 (MQ=255)
aaCGGGGAAAGCGTTATGCCTGCCCGCCACCGATCCGCTCACCACTTATCCAGTACACGTTGAAggt < 1:2247145/67‑1 (MQ=255)
aaCGGGGAAAGCGTTATGCCTGCCCGCCACCGATCCGCTCACCACTTATCCAGTACACGTTGAAggt < 1:2526390/67‑1 (MQ=255)
aaCGGGGAAAGCGTTATGCCTGCCCGCCACCGATCCGCTCACCACTTATCCAGTACACGTTGAAggt < 1:3258830/67‑1 (MQ=255)
aaaGCGTTTTGCCTGCCCGCCTCCGATCCGCTCAGCAGTTATCCAGTACACGTTGAAGGTGGTGACAtt < 1:1171884/69‑1 (MQ=255)
aaaGCGTTATGCCTGCCCGCCACCGATCCGCTCACCACTTATCCAGTACACGTTGAAGGTGGTGACAtt < 1:1331410/69‑1 (MQ=255)
aGCGTTATGCCTGCCCGCCACCGATCCGCTCACCACTTATCCAGTACACGCTGAAGGTGGTGACAtttt > 1:1062101/1‑69 (MQ=255)
aGCGTTATGCCTGCCCGCCACCGATCCGCTCACCACTTATCCAGTACACGCTGAAGGTGGTGACAtttt > 1:2949640/1‑69 (MQ=255)
aGCGTTATGCCTGCCCGCCACCGATCCGCTCACCACTTATCCAGTACACGCTGAAGGTGGTGACAtttt > 1:1030325/1‑69 (MQ=255)
cGTTATGCCTGCCCGCCACCGATCCGCTCACCACTTATCCAGTACACGTTGAAGGTGGTGACATTTTCa > 1:2904703/1‑69 (MQ=255)
aTGCCTGCCCGCCACCGATCCGCTCACCACTTATCCAGTACACGCTGAAGGTGGTGACATTTTCATc < 1:340052/67‑1 (MQ=255)
aTGCCTGCCCGCCACCGATCCGCTCACCACTTATCCAGTACACGCTGAAGGTGGTGACATTTTCATc < 1:1997809/67‑1 (MQ=255)
aTGCCTGCCCGCCACCGATCCGCTCACCACTTATCCAGTACACGCTGAAGGTGGTGACATTTTCATCGa > 1:1752736/1‑69 (MQ=255)
aTGCCTGCCCGCCACCGATCCGCTCACCACTTATCCAGTACACGCTGAAGGTGGTGACATTTTCATCGa > 1:1998467/1‑69 (MQ=255)
gcctgccCGCCACCGATCCGGTCACCACTTATCCAGTACACGTTGAAGGTGGTGACATTTTCATCGACt > 1:2150505/1‑69 (MQ=255)
gcctgccCGCCACCGATCCGCTCACCACTTATCCAGTACACGTTGAAGGTGGTGACATTTTCATCGACt > 1:1107436/1‑69 (MQ=255)
cctgccCGCCACCGATCCGCTCACCACTTATCCAGTACACGCTGaa > 1:3302062/1‑46 (MQ=255)
cctgccCGCCACCGATCCGCTCACCACTTATCCAGTACACGCTGAAGGTGGTGACATTTTCATCGACtt < 1:142301/69‑1 (MQ=255)
aCCGATCCGCTCACCACTTATCCAGTACACGCTGAAGGTGGTGACATTTTCATCGACTTACCGGAgg > 1:2259457/1‑67 (MQ=255)
gATCCGCTCACCACTTATCCAGTACACGTTGAAGGTGGTGACATTTTCATCg < 1:1749106/52‑1 (MQ=255)
gATCCGCTCACCACTTATCCAGTACACGTTGAAGGTGGTGACATTTTCATCg > 1:510022/1‑52 (MQ=255)
gATCCGCTCACCACTTATCCAGTACACGCTGAAGGTGGTGACATTTTCATCGACTTACCGGAGGCGCa > 1:2259543/1‑68 (MQ=255)
gATCCGCTCACCACTTATCCAGTACACGCTGAAGGTGGTGACATTTTCATCGACTTACCGGAGGCGCa > 1:595796/1‑68 (MQ=255)
aTCCGCTCACCACTTATCCAGTACACGTTGAAGGTGGTGACATTTTCATCGACTTACCGGAGGCGCAGc < 1:1775150/69‑1 (MQ=255)
aTCCGATCACCACTTATCCAGTACACGTTGAAGGTGGTGACATTTTCATCGACTTACCGGAGGCGCAGc < 1:148281/69‑1 (MQ=255)
cGCTCACCACTTATCCAGTACACGCTGAAGGTGGTGACATTTTCATCGACTTACCGGAGGCGCAGCCAt < 1:2446632/69‑1 (MQ=255)
cGCTCACCACTTATCCAGTACACGCTGAAGGTGGTGACATTTTCATCGACTTACCGGAGGCGCAGCCAt < 1:3261648/69‑1 (MQ=255)
cGCTCACCACTTATCCAGTACACGCTGAAGGTGGTGACATTTTCATCGACTTACCGGAGGCGCAGCCAt < 1:3609856/69‑1 (MQ=255)
cGCTCACCACTTATCCAGTACACGCTGAAGGTGGTGACATTTTCATCGACTTACCGGAGGCGCAGCCAt < 1:2271338/69‑1 (MQ=255)
cGCTCACCACTTATCCAGTACACGCTGAAGGTGGTGACATTTTCATCGACTTACCGGAGGCGCAGCCAt < 1:622768/69‑1 (MQ=255)
gCTCACCACTTATCCAGTACACGCTGAAGGTGGTGACATTTTCATCGACTTACCGGAGGCGCAGCCAt < 1:3566055/68‑1 (MQ=255)
ccacTTATCCAGTACACGCTGAAGGTGGTGACATTTTCATCGACtt < 1:1889157/46‑1 (MQ=255)
ccacTTATCCAGTACACGCTGAAGGTGGTGACATTTTCATCGACtt < 1:642321/46‑1 (MQ=255)
ccacTTATCCAGTACACGCTGAAGGTGGTGACATTTTCATCGACtt < 1:646887/46‑1 (MQ=255)
ccacTTATCCAGTACACGCTGAAGGTGGTGACATTTTCATCGACtt < 1:3148029/46‑1 (MQ=255)
ccacTTATCCAGTACACGCTGAAGGTGGTGACATTTTCATCGACtt < 1:731167/46‑1 (MQ=255)
cacTTATCCAGTACACGTTGAAGGTGGTGACATTTTCATCGACTTACCGGAGGCGCAGCCATGAGCg < 1:2402980/67‑1 (MQ=255)
cacTTATCCAGTACACGTTGAAGGTGGTGACATTTTCATCGACTTACCGGAGGCGCAGCCATGAGCg > 1:2469610/1‑67 (MQ=255)
cAGTACACGCTGAAGGTGGTGACATTTTCATCGACTTACCGGAGGCGCAGCCATGAGCg < 1:512228/59‑1 (MQ=255)
cAGTACACGCTGAAGGTGGTGACATTTTCATCGACTTACCGGAGGCGCAGCCATGAGCg < 1:2552768/59‑1 (MQ=255)
cAGTACACGCTGAAGGTGGTGACATTTTCATCGACTTACCGGAGGCGCAGCCATGAGCg < 1:3081423/59‑1 (MQ=255)
cAGTACACGCTGAAGGTGGTGACATTTTCATCGACTTACCGGAGGCGCAGCCATGAGCg < 1:1009824/59‑1 (MQ=255)
cAGTACACGCTGAAGGTGGTGACATTTTCATCGACTTACCGGAGGCGCAGCCATGAGCg < 1:2574186/59‑1 (MQ=255)
tACACGCTGAAGGTGGTGACATTTTCATCGACTTACCGGAGGCGCAGc < 1:295519/48‑1 (MQ=255)
tACACGCTGAAGGTGGTGACATTTTCATCGACTTACCGGAGGCGCAGc < 1:2819338/48‑1 (MQ=255)
acacGTTGAAGGTGGTGACATTTTCATCGACTTACCGGAGGCGCAGCCATg < 1:3311660/51‑1 (MQ=255)
acacGTTGAAGGTGGTGACATTTTCATCGACTTACCGGAGGCGCAGCCATg < 1:748934/51‑1 (MQ=255)
acacGTTGAAGGTGGTGACATTTTCATCGACTTACCGGAGGCGCAGCCATg < 1:1366741/51‑1 (MQ=255)
acacGTTGAAGGTGGTGACATTTTCATCGACTTACCGGAGGCGCAGCCATg < 1:1963927/51‑1 (MQ=255)
acacGTTGAAGGTGGTGACATTTTCATCGACTTACCGGAGGCGCAGCCATg < 1:421492/51‑1 (MQ=255)
cacGCTGAAGGTGGTGACATTTTCATCGACTTACCGGAGGCGCAGCCATGAGCg > 1:2584388/1‑54 (MQ=255)
cacGCTGAAGGTGGTGACATTTTCATCGACTTACCGGAGGCGCAGCCATGAGCg > 1:2428464/1‑54 (MQ=255)
cacGCTGAAGGTGGTGACATTTTCATCGACTTACCGGAGGCGCAGCCATGAGCg > 1:1732750/1‑54 (MQ=255)
cacGCTGAAGGTGGTGACATTTTCATCGACTTACCGGAGGCGCAGCCATGAGCg > 1:2901701/1‑54 (MQ=255)
cacGCTGAAGGTGGTGACATTTTCATCGACTTACCGGAGGCGCAGCCATGAGCg > 1:3404162/1‑54 (MQ=255)
cacGCTGAAGGTGGTGACATTTTCATCGACTTACCGGAGGCGCAGCCATGAGCGATCTGCATAACGAg > 1:1766612/1‑68 (MQ=255)
cacGCTGAAGGTGGTGACATTTTCATCGACTTACCGGAGGCGCAGCCATGAGCGATCTGCATAACGAg > 1:913590/1‑68 (MQ=255)
|
CCTGAAAACGGGGAAAGCGTTATGCCTGCCCGCCACCGATCCGCTCACCACTTATCCAGTACACGTTGAAGGTGGTGACATTTTCATCGACTTACCGGAGGCGCAGCCATGAGCGATCTGCATAACGAG > W3110S.gb/2669773‑2669901
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
