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 F21 I0 R1
|
476 |
35.3 |
2812105 |
96.7% |
2719305 |
61.2 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
4,361,585 |
C→T |
17.1% |
P571P (CCG→CCA) |
cadA ← |
lysine decarboxylase 1 |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 4,361,585 | 0 | C | T | 17.1%
| 99.9
/ 12.9
| 41 | P571P (CCG→CCA) | cadA | lysine decarboxylase 1 |
| Reads supporting (aligned to +/- strand): ref base C (24/10); new base T (4/3); total (28/13) |
| Fisher's exact test for biased strand distribution p-value = 6.59e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.52e-01 |
TATTCTGAGCCAGTTCCTGAATACGCATGTTTTCATAGAATTCAGGATCTTCACGATACAGAGACGGCAGCATGTTTTTCACACGCAGGTTCAGGTCGAACGCACGTTTAAAGTCAGTCAGAGCACGCAGCAG > W3110S.gb/4361521‑4361653
|
tatTCTGAGCCAGTTCCTGAATACGCATGTTTTCATAGAATTCAGGATCTTCACGATACAGAGATGgcagc < 1:704351/71‑1 (MQ=255)
atTCTGAGCCAGTTCCTGAATACGCATGTTTTCATAGAATTCAGGATCTTCACGATACAGAGACGgcagc > 1:856406/1‑70 (MQ=255)
tCTGAGCCAGTTCCTGAATACGCATGTTTTCATAGAATTCAGGATCTTCACGATACAGAGATGGCAGCATg > 1:2750132/1‑71 (MQ=255)
aGCCAGTTCCTGAATACGCATGTTTTCATAGAATTCAGGATCTTCACGATACAGAGACGGCAGCATg < 1:816068/67‑1 (MQ=255)
aGCCAGTTCCTGAATACGCATGTTTTCATAGAATTCAGGATCTTCACGATACAGAGACGGCAGCATg < 1:2060346/67‑1 (MQ=255)
ccTGAATACGCATGTTTTCATAGAATTCAGGATCTTCACGATACAGAGACGGCAGCATGTTTTTCACACg > 1:578682/1‑70 (MQ=255)
ccTGAATACGCATGTTTTCATAGAATTCAGGATCTTCACGATACAGAGACGGCAGCATGTTTTTCACACg > 1:2517798/1‑70 (MQ=255)
cTGAATACGCATGTTTTCATAGAATTCAGGATCTTCACGATACAGAGACGGCAGCATGTTTTTCACACGCa < 1:2319252/71‑1 (MQ=255)
aaTACGCATGTTTTCATAGAATTCAGGATCTTCACGATACAGAGACGGCAGCATGTTTTTCACACGCAGGt < 1:2437936/71‑1 (MQ=255)
aaTACGCATGTTTTCATAGAATTCACGATCTTCACGATACAGAGACGGCAGCATGTTTTTc > 1:560752/1‑61 (MQ=255)
tACGCTTGTTTTCATAGAATTCAGGATCTTCACGATACAGAGACGGCAGCATGTTTTTCACACGCAGGTTc < 1:1144171/71‑1 (MQ=255)
cGCATGTTTTCATAGAATTCAGGATCTTCACGATACAGAGACGGCAGCATGTTTTTCACACGCAGGTTCAg > 1:72469/1‑71 (MQ=255)
aTGTTTTCATAGAATTCAGGATCTTCACGATACAGAGACGGCAGCATGttttt < 1:430736/53‑1 (MQ=255)
tGTTTTCATAGAATTCAGGATCTTCACGATACAGAGACGGCAGCATGTTTTTCACACGCAGGTTCa > 1:1250535/1‑66 (MQ=255)
tGTTTTCATAGAATTCAGGATCTTCACGATACAGAGACGGCAGCATGTTTTTCACACGCAGGTTCAGGTCg < 1:1988846/71‑1 (MQ=255)
ttttCATAGAATTCAGGATCTTCACGATACAGAGATGGCAGCATGttttt > 1:799554/1‑50 (MQ=255)
ttttCATAGAATTCAGGATCTTCACGATACAGAGATGGCAGCATGTTTTTCACACGCAGGTTCAGGTCGaa > 1:1273645/1‑71 (MQ=255)
ttttCATAGAATTCAGGATCTTCACGATACAGAGACGGCAGCATg > 1:1768347/1‑45 (MQ=255)
ttttCATAGAATTCAGGATCTTCACGATACAGAGACGGCAGCATGTTTTTca > 1:1926197/1‑52 (MQ=255)
ttttCATAGAATTCAGGATCTTCACGATACAGAGACGGCAGCATGTTTTTca > 1:1698022/1‑52 (MQ=255)
ttttCATAGAATTCAGGATCTTCACGATACAGAGACGGCAGCATGTTTTTCACACGCAGGTTCAGGTCg > 1:316388/1‑69 (MQ=255)
ttttCATAGAATTCAGGATCTTCACGATACAGAGACGGCAGCATGTTTTTCACACGCAGGTTCAGGTCGaa > 1:1940968/1‑71 (MQ=255)
ttttCATAGAATTCAGGATCTTCACGATACAGAGACGGCAGCATGTTTTTCACACGCAGGTTCAGGTCGaa > 1:628732/1‑71 (MQ=255)
ttttCATAGAATTCAGGATCTTCACGATACAGAGACGGCAGCATGTTTTTCACACGCAGGTTCAGGTCGaa > 1:2022059/1‑71 (MQ=255)
ttttCATAGAATTCAGGATCTTCACGATACAGAGACGGCAGCATGTTTTTCACACGCAGGTTCAGGTCGaa > 1:2017659/1‑71 (MQ=255)
tCATAGAATTCAGGATCTTCACGATACAGAGACGGCAGCATGTTTTTCACACGCAGGTTCAGGTCGAACg < 1:1566011/70‑1 (MQ=255)
aaTTCAGGATCTTCACGATACAGAGATGGCAGCATGTTTTTCACACGCAGGTTc < 1:1915570/54‑1 (MQ=255)
aTTCAGGATCTTCACGATACAGAGACGGCAGCATGTTTTTCACACGCAGGTTCAGGTCGAACGCACGTTTa < 1:2510887/71‑1 (MQ=255)
ttCAGGATCTTCACGATACAGAGATGGCAGCATGTTTTTCACACGCAGGTTCAg > 1:2653182/1‑54 (MQ=255)
ttCAGGATCTTCACGATACAGAGACGGCAGCATGTTTTTCACACGCAGGTTCAGGTCGAACGCACGTTTa > 1:1373787/1‑70 (MQ=255)
tCTTCACGATACAGAGACGGCAGCATGTTTTTCACACGCAGGTTCAGGTCGAACGCACGTTTAAagtcagt > 1:542267/1‑71 (MQ=255)
tCTTCACGATACAGAGACGGAAGCATGTTTTTCACACGCAGGTTCAGGTCGAACGCACGTTTAAagtcagt > 1:985928/1‑71 (MQ=255)
cACGATACAGAGACGGCAGCATGTTTTTCACACGCAGGTTCAGGt > 1:547756/1‑45 (MQ=255)
cACGATACAGAGACGGCAGCATGTTTTTCACACGCAGGTTCAGGTCGAACGCACGTTTAAAgtcagtca > 1:1060069/1‑69 (MQ=255)
cACGATACAGAGACGGCAGCATGTTTTTCACACGCAGGTTCAGGTCGAACGCACGTTTAAAGtcagtcag < 1:21926/70‑1 (MQ=255)
gATACAGAGACGGCAGCATGTTTTTCACACGCAgg > 1:1232763/1‑35 (MQ=255)
tACAGAGATGGCAGCATGTTTTTCACACGCAGGTTCAGGTCGAACGCACGTTTAAAGTCAGTCAGAGCACg < 1:2774890/71‑1 (MQ=255)
tACAGAGACGGCAGCATGTTTATCACACGCAGGTTCAGGTCGAACGCACGTTTAAAGTCAGTCAGAGCACg > 1:137731/1‑71 (MQ=255)
cAGAGACGGCAGCATGTTTTTCACACGCAGGTTCAGGTCGAACGCACGtt > 1:2494136/1‑50 (MQ=255)
gagaCGGCAGCATGTTTTTCACACGCAGGTTCAGGTCGAACGCACGTTTAAAGTCAGTCAGAGCACgca > 1:2279146/1‑69 (MQ=255)
gaCGGCAGCATGTTTTTCACACGCAGGTTCAGGTCGAACGCACGTTTAAAGTCAGTCAGAGCACGcagcag > 1:460707/1‑71 (MQ=255)
|
TATTCTGAGCCAGTTCCTGAATACGCATGTTTTCATAGAATTCAGGATCTTCACGATACAGAGACGGCAGCATGTTTTTCACACGCAGGTTCAGGTCGAACGCACGTTTAAAGTCAGTCAGAGCACGCAGCAG > W3110S.gb/4361521‑4361653
|
| 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
