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 |
|
A2 F1 I0 R1
|
4577 |
57.4 |
3436498 |
77.7% |
2670158 |
63.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
1,069,145 |
C→T |
29.4% |
D14D (GAC→GAT) |
cfa → |
cyclopropane fatty acyl phospholipid synthase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,069,145 | 0 | C | T | 29.4%
| 41.7
/ 16.5
| 44 | D14D (GAC→GAT) | cfa | cyclopropane fatty acyl phospholipid synthase |
| Reads supporting (aligned to +/- strand): ref base C (11/20); new base T (10/3); total (21/23) |
| Fisher's exact test for biased strand distribution p-value = 1.99e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.94e-01 |
GATCACCGACCAGTGATGGAGAAACTATGAGTTCATCGTGTATAGAAGAAGTCAGTGTACCGGATGACAACTGGTACCGTATCGCCAACGAATTACTTAGCCGTGCCGGTATAGCCATTAACGGTTCTGCCCC > minE/1069078‑1069210
|
gATCACCGACCAGTGATGTAGAAACTATGAGTTCATCGTGTATAGAAGAAGTCAGTGTACCGGATGAc < 1:2923377/68‑1 (MQ=255)
gATCACCGACCAGTGATGGAGAAACTATGAGTTCATCGTGTATAGAAGAAGTCAGTGTACCGGATGAc < 1:1395530/68‑1 (MQ=255)
gATCACCGACCAGTGATGGAGAAACTATGAGTTCATCGTGTATAGAAGAAGTCAGTGTACCGGATGAc < 1:2253651/68‑1 (MQ=255)
gATCACCGACCAGTGATGGAGAAACTATGAGTTCATCGTGTATAGAAGAAGTCAGTGTACCGGATGAc < 1:2149819/68‑1 (MQ=255)
gATCACCGACCAGTGATGGAGAAACTATGAGTTCATCGTGTATAGAAGAAGTCAGTGTACAGGATGAc < 1:1448595/68‑1 (MQ=255)
aGTGATGGAGAAACTATGAGTTCATCGTGTATAGAAGAAGTCAGTGTACCGGATGACAACTGGTACCGt < 1:1240453/69‑1 (MQ=255)
aGTGATGGAGAAACTATGAGTTCATCGTGTATAGAAGAAGTCAGTGTACCGGATGACAACTGGTACCGt < 1:1270639/69‑1 (MQ=255)
aGTGATGGAGAAACTATGAGTTCATCGTGTATAGAAGAAGTCAGTGTACCGGATGACAACTGGTACCGt < 1:613935/69‑1 (MQ=255)
aGTGATGGAGAAACTATGAGTTCATCGTGTATAGAAGAAGTCAGTGTACCGGATGACAACTGGTACCGt < 1:3297121/69‑1 (MQ=255)
aGTGATGGAGAAACTATGAGTTCATCGTGTATAGAAGAAGTCAGTGTACCGGATGACAACTGGTACCGt < 1:2981186/69‑1 (MQ=255)
aGTGATGGAGAAACTATGAGTTCATCGTGTATAGAAGAAGTCAGTGTACCGGATGACAACTGGTACCGt < 1:2973380/69‑1 (MQ=255)
aGTGATGGAGAAACTATGAGTTCATCGTGTATAGAAGAAGTCAGTGTACCGGATGACAACTGGTACCGt < 1:1838412/69‑1 (MQ=255)
aaCTATGAGTTCATCGTGTATAGAAGAAGTCAGTGTACCGGATGACAACTGGTACCGTATCGCCAACGa < 1:2388809/69‑1 (MQ=255)
aaCTATGAGTTCATCGTGTATAGAAGAAGTCAGTGTACCGGATGACAACTGGTACCGTATCGCCAACGa < 1:686122/69‑1 (MQ=255)
aaCTATGAGTTCATCGTGTATAGAAGAAGTCAGTGTACCGGATGACAACTGGTACCGTATCGCCAACGa < 1:2223601/69‑1 (MQ=255)
aaCTATGAGTTCATCGTGTATAGAAGAAGTCAGTGTACCGGATGACAACTGGTACCGTATCGCCAACGa < 1:2062164/69‑1 (MQ=255)
aaCTATGAGTTCATCGTGTATAGAAGAAGTCAGTGTACCGGATGACAACTGGTACCGTATCGCCAACGa < 1:126617/69‑1 (MQ=255)
aaCTATGAGTTCATCGTGTATAGAAGAAGGCAGTGTACCGGATGACAACTGGTACCGTATCGCCAACGa < 1:67455/69‑1 (MQ=255)
cTATGAGTTCATCGTGTATAGAAGAAGTCAGTGTACCGGATGACAACTGGTACCGTATCGCCAACGAAt < 1:727027/69‑1 (MQ=255)
tATGAGTTCATCGTGTATAGAAGAAGTCAGTGTACCGGATGACAACTGGTACCGTATCGCCAACGAAtt < 1:1906507/69‑1 (MQ=255)
tATGAGTTCATCGTGTATAGAAGAAGTCAGTGTACCGGATGACAACTGGTACCGTATCGCCAACGAAtt < 1:514516/69‑1 (MQ=255)
cGTGTATAGAAGAAGTCAGTGTACCGGATGATAACTGGTACCGTATCGCCAACGAATTACTTAGCCGTg < 1:967317/69‑1 (MQ=255)
cGTGTATAGAAGAAGTCAGTGTACCGGATGATAACTGGTACCGTATCGCCAACGAATTACTTAGCCGTg < 1:959260/69‑1 (MQ=255)
cGTGTATAGAAGAAGTCAGTGTACCGGATGATAACTGGTACCGTATCGCCAACGAATTACTTAGCCGTg < 1:2037747/69‑1 (MQ=255)
gaagaaGTCAGTGTACCGGATGACAACTGGTACCGTATCGCCAACGAATTACTTAGCCGTGCCGGtat < 1:946038/68‑1 (MQ=255)
gaagaaGTCAGTGTACCGGATGACAACTGGTACCGTATCGCCAACGAATTACTTAGCCGTGCCGGtat < 1:2772560/68‑1 (MQ=255)
gaagaaGTCAGTGTACCGGATGACAACTGGTACCGTATCGCCAACGAATTACTTAGCCGTGCCGGtat < 1:289902/68‑1 (MQ=255)
gaagaaGTCAGTGTACCGGATGACAACTGGTACCGTATCGCCAACGAATTACTTAGCCGTGCCGGtat < 1:3322335/68‑1 (MQ=255)
aagaagTCAGTGTACCGGATGACAACTGGTACCGTATCGCCAACGAATTa > 1:803223/1‑50 (MQ=255)
cAGTGTACCGGATGACAACTGGTACCGTATCGCCAACGAATTACTTAGCCGTGCCGGTATAGCCATTaa > 1:2393047/1‑69 (MQ=255)
tGATAACTGGTACCGTATCGCCAACGAATTACTTAGCCGTGCCGGTATAGCCATTAACGGTTCTGcccc > 1:604867/1‑69 (MQ=255)
tGATAACTGGTACCGTATCGCCAACGAATTACTTAGCCGTGCCGGTATAGCCATTAACGGTTCTGcccc > 1:1362848/1‑69 (MQ=255)
tGATAACTGGTACCGTATCGCCAACGAATTACTTAGCCGTGCCGGTATAGCCATTAACGGTTCTGcccc > 1:2987812/1‑69 (MQ=255)
tGATAACTGGTACCGTATCGCCAACGAATTACTTAGCCGTGCCGGTATAGCCATTAACGGTTCTGcccc > 1:1460742/1‑69 (MQ=255)
tGATAACTGGTACCGTATCGCCAACGAATTACTTAGCCGTGCCGGTATAGCCATTAACGGTTCTGcccc > 1:1678814/1‑69 (MQ=255)
tGATAACTGGTACCGTATCGCCAACGAATTACTTAGCCGTGCCGGTATAGCCATTAACGGTTCTGcccc > 1:1798671/1‑69 (MQ=255)
tGATAACTGGTACCGTATCGCCAACGAATTACTTAGCCGTGCCGGTATAGCCATTAACGGTTCTGcccc > 1:180942/1‑69 (MQ=255)
tGATAACTGGTACCGTATCGCCAACGAATTACTTAGCCGTGCCGGTATAGCCATTAACGGTTCTGcccc > 1:2276917/1‑69 (MQ=255)
tGATAACTGGTACCGTATCGCCAACGAATTACTTAGCCGTGCCGGTATAGCCATTAACGGTTCTGccc > 1:2143791/1‑68 (MQ=255)
tGATAACTGGTACCGTATCGCCAACGAATTACTTAGCCGTGCCGGTATAGCCATTAACGGTTCTGcc > 1:1859172/1‑67 (MQ=255)
aCAACTGGTACCGTATCGCCAACGAATTACTTAGCCGt > 1:1923999/1‑38 (MQ=255)
aCAACTGGTACCGTATCGCCAACGAATTACTTAGCCGTGCCGGTATAGCTATTAACgg > 1:2343976/1‑58 (MQ=255)
aCAACTGGTACCGTATCGCCAACGAATTACTTAGCCGTGCCGGTATAGCCATTAACgg > 1:3161422/1‑58 (MQ=255)
aCAACTGGTACCGTATCGCCAACGAATTACTTAGCCGTGCCGGTATAGCCATTAACgg > 1:436988/1‑58 (MQ=255)
aCAACTGGTACCGTATCGCCAACGAATTACTTAGCCGTGCCGGTATAGCCATTAACgg > 1:521890/1‑58 (MQ=255)
aCAACTGGTACCGTATCGCCAACGAATTACTTAGCCGTGCCGGTATAGCCATTAACgg > 1:2929725/1‑58 (MQ=255)
aCAACTGGTACCGTATCGCCAACGAATTACTTAGCCGTGCCGGTATAGCCATTAACgg > 1:1127688/1‑58 (MQ=255)
aCAACTGGTACCGTATCGCCAACGAATTACTTAGCCGTGCCGGTATAGCCATTAACgg > 1:2158893/1‑58 (MQ=255)
aCAACTGGTACCGTATCGCCAACCAATTACTTAGc > 1:3221447/1‑35 (MQ=255)
|
GATCACCGACCAGTGATGGAGAAACTATGAGTTCATCGTGTATAGAAGAAGTCAGTGTACCGGATGACAACTGGTACCGTATCGCCAACGAATTACTTAGCCGTGCCGGTATAGCCATTAACGGTTCTGCCCC > minE/1069078‑1069210
|
| 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
