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 |
|
A12 F56 I1 R1
|
165 |
53.8 |
2611523 |
96.4% |
2517508 |
99.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
2,457,953 |
T→C |
K403E (AAA→GAA) |
fadJ ← |
enoyl‑CoA hydratase/epimerase and isomerase/3‑hydroxyacyl‑CoA dehydrogenase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 2,457,953 | 0 | T | C | 92.1%
| 110.0
/ 1.0
| 38 | K403E (AAA→GAA) | fadJ | enoyl‑CoA hydratase/epimerase and isomerase/3‑hydroxyacyl‑CoA dehydrogenase |
| Reads supporting (aligned to +/- strand): ref base T (1/2); new base C (20/15); total (21/17) |
| Fisher's exact test for biased strand distribution p-value = 5.77e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.30e-01 |
TGAGCGGCGATATCACCAATCGGTAAAGATGACGTATTCGAAGCAAAGATGGTATGAGCGGCGCAATTTTGCTCAACTTCCGCCACCATCTGTTGTTTCAATTCGAGATTTTCAAACACCGCTTCAATAATCAGATCGCGATGGGCAAAGCCGCGATAGTCCGTCGTTCCGGAGATTAATGCCAGCTGTTTGTC > NC_000913/2457856‑2458049
|
tgAGCGGCGATATCACCAATCGGTAAAGATGACGTATTCGAAGCAAAGATGGTATGAGCGGCGCAATTTTGCTCAACTTCCGCCACCATCTGTTGTTTCa < 2:516083/100‑1 (MQ=255)
gAGCGGCGATATCACCAATCGGTAAAGATGACGTATTCGAAGCAAAGATGGTATGAGCGGCGCAATTTTGCTCAACTTCCGCCACCATCTGTTGTTCCaa > 2:92253/1‑100 (MQ=255)
gAGCGGCGATATCACCAATCGGTAAAGATGACGTATTCGAAGCAAAGATGGTATGAGCGGCGCAATTTTGCTCAACTTCCGCCACCATCTGTTGTTCCaa < 2:55930/100‑1 (MQ=255)
gcggcgATATCACCAATCGGTAAAGATGACGTATTCGAAGCAAAGATGGTATGAGCGGCGCAATTTTGCTCAACTTCCGCCACCATCTGTTGTTCCAAtt < 1:441171/100‑1 (MQ=255)
atCACCAATCGGTAAAGATGACGTATTCGAAGCAAAGATGGTATGAGCGGCGCAATTTTGCTCAACTTCCGCCACCATCTGTTGTTCCAATTCGAGAttt < 1:630937/100‑1 (MQ=255)
atCACCAATCGGTAAAGATGACGTATTCGAAGCAAAGATGGTATGAGCGGCGCAATTTTGCTCAACTTCCGCCACCATCTGTTGTTCCAATTCGAGAttt < 2:103202/100‑1 (MQ=255)
aCCAATCGGTAAAGATGACGTATTCGAAGCAAAGATGTTATGAGCGGCGCAATTTTGCTCAACTTCCGCCACCATCTGTTGTTCCAATTCGAGATTTTCa < 1:520072/100‑1 (MQ=255)
ccAATCGGTAAAGATGACGTATTCGAAGCAAAGATGGTATGAGCGGCGCAATTTTGCTCAACTTCCGCCACCATCTGTTGTTCCAATTCGAGATTTTCaa < 1:994587/100‑1 (MQ=255)
ggTAAAGATGACGTATTCGAAGCAAAGATGGTATGAGCGGCGCAATTTTGCTCAACTTCCGCCACCATCTGTTGTTCCAATTCGAGATTTTCAAACACCg > 1:1152434/1‑100 (MQ=255)
aGATGACGTATTCGAAGCAAAGATGGTATGAGCGGCGCAATTTTGCTCAACTTCCGCCACCATCTGTTGTTCCAATTCGAGATTTTCAAACACCGCTTCa < 2:1112797/100‑1 (MQ=255)
gACGTATTCGAAGCAAAGATGGTATGAGCGGCGCAATTTTGCTCAACTTCCGCCACCATCTGTTGTTCCAATTCGAGATTTTCAAACACCGCTTCaataa > 2:1145820/1‑100 (MQ=255)
aCGTATTCGAAGCAAAGATGGTATGAGCGGCGCAATTTTGCTCAACTTCCGCCACCATCTGTTGTTCCAATTCGAGATTTTCAAACACCGCTTCaataat < 2:1040898/100‑1 (MQ=255)
cGTATTCGAAGCAAAGATGGTATGAGCGGCGCAATTTTGCTCAACTTCCGCCACCATCTGTTGTTCCAATTCGAGATTTTCAAACACCGCTTCAATAATc > 1:456225/1‑100 (MQ=255)
cGTATTCGAAGCAAAGATGGTATGAGCGGCGCAATTTTGCTCAACTTCCGCCACCATCTGTTGTTCCAATTCGAGATTTTCAAACACCGCTTCAATAATc < 2:5443/100‑1 (MQ=255)
aTTCGAAGCAAAGATGGTATGAGCGGCGCAATTTTGCTCAACTTCCGCCACCATCTGTTGTTCCAATTCGAGATTTTCAAACACCGCTTCAATAATCAGa > 1:1270793/1‑100 (MQ=255)
aTTCGAAGCAAAGATGGTATGAGCGGCGCAATTTTGCTCAACTTCCGCCACCATCTGTTGTTCCAATTCGAGATTTTCAAACACCGCTTCAATAATCAGa > 2:596640/1‑100 (MQ=255)
cGAAGCAAAGATGGTATGAGCGGCGCAATTTTGCTCAACTTCCGCCACCATCTGTTGTTCCAATTCGAGATTTTCAAACACCGCTTCAATAATCAGATcg > 2:884781/1‑100 (MQ=255)
cGAAGCAAAGATGGTATGAGCGGCGCAATTTTGCTCAACTTCCGCCACCATCTGTTGTTCCAATTCGAGATTTTCAAACACCGCTTCAATAATCAGATcg > 2:53291/1‑100 (MQ=255)
gAAGCAAAGATGGTATGAGCGGCGCAATTTTGCTCAACTTCCGCCACCATCTGTTGTTTCAATTCGAGATTTTCAAACACCGCTTCAATAATCAGATcgc > 1:352680/1‑100 (MQ=255)
aaGCAAAGATGGTATGAGCGGCGCAATTTTGCTCAACTTCCGCCACCATCTGTTGTTCCAATTCGAGATTTTCAAACACCGCTTCAATAATCAGATcgcg > 2:35738/1‑100 (MQ=255)
aGCAAAGATGGTATGAGCGGCGCAATTTTGCTCAACTTCCGCCACCATCTGTTGTTCCAATTCGAGATTTTCAAACACCGCTTCAATAATCAGATCGCGa < 1:1090113/100‑1 (MQ=255)
cAAAGATGGTATGAGCGGCGCAATTTTGCTCAACTTCCGCCACCATCTGTTGTTCCAATTCGAGATTTTCAAACACCGCTTCAATAATCAGATCGCGATg < 2:890237/100‑1 (MQ=255)
aaGATGGTATGAGCGGCGCAATTTTGCTCAACTTCCGCCACCATCTGTTGTTCCAATTCGAGATTTTCAAACACCGCTTCAATAATCAGATCGCGATggg < 2:1140772/100‑1 (MQ=255)
aTGAGCGGCGCAATTTTGCTCAACTTCCGCCACCATCTGTTGTTCCAATTCGAGATTTTCAAACACCGCTTCAATAATCAGATCGCGATGGGCAAAGCcg > 2:616940/1‑100 (MQ=255)
gAGCGGCGCAATTTTGCTCAACTTCCGCCACCATCTGTTGTTCCAATTCGAGATTTTCAAACACCGCTTCAATAATCAGATCGCGATGGGCAAAGCcgcg > 2:1247447/1‑100 (MQ=255)
gAGCGGCGCAATTTTGCTCAACTTCCGCCACCATCTGTTGTTCCAATTCGAGATTTTCAAACACCGCTTCAATAATCAGATCGCGATGGGCAAAGCcgcg > 2:739687/1‑100 (MQ=255)
ggcgCAATTTTGCTCAACTTCCGCCACCATCTGTTGTTCCAATTCGAGATTTTCAAACACCGCTTCAATAATCAGATCGCGATGGGCAAAGCCGCGATAg > 1:1218159/1‑100 (MQ=255)
aTTTTGCTCAACTTCCGCCACCATCTGTTGTTCCAATTCGAGATTTTCAAACACCGCTTCAATAATCAGATCGCGATGGCCAAAGCCGCGATAGTCcgtc > 1:1012540/1‑100 (MQ=255)
gCTCAACTTCCGCCACCATCTGTTGTTCCAATTCGAGATTTTCAAACACCGCTTCAATAATCAGATCGCGATGGGCAAAGCCGCGATAGTCCGTCGTTcc > 2:138087/1‑100 (MQ=255)
tCAACTTCCGCCACCATCTGTTGTTCCAATTCGAGATTTTCAAACACCGCTTCAATAATCAGTTCGCGATGGGCAAAGCCGCGATAGTCCGTCGTTCCgg < 2:700284/100‑1 (MQ=255)
ttCCGCCACCATCTGTTGTTCCAATTCGAGATTTTCAAACACCGCTTCAATAATCAGATCGCGATGGGCAAAGCCGCGATAGTCCGTCGTTCCGGAGAtt > 1:1196670/1‑100 (MQ=255)
gCCACCATCTGTTGTTCCAATTCGAGATTTTCAAACACCGCTTCAATAATCAGATCGCGATGGGCAAAGCCGCGATAGTCCGTCGTTCCGGAGATTaacg < 1:885614/100‑3 (MQ=255)
aTCTGTTGTTCCAATTCGAGATTTTCAAACACCGCTTCAATAATCAGATCGCGATGGGCAAAGCCGCGATAGTCCGTCGTTCCGGAGATTAATGCCAGCt > 1:815830/1‑100 (MQ=255)
tCTGTTGTTTCAATTCGAGATTTTCAAACACCGCTTCAATAATCAGATCGCGATGGGCAAAGCCGCGATAGTCCGTCGTTCCGGAGATTAATGCCAGCTg < 2:352677/100‑1 (MQ=255)
ttgttCCAATTCGAGATTTTCAAACACCGCTTCAATAATCAGATCGCGATGGGCAAAGCCGCGATAGTCCGTCGTTCCGGAGATTAATGCCAGCTGTTTg > 2:1164405/1‑100 (MQ=255)
gttCCAATTCGAGATTTTCAAACACCGCTTCAATAATCAGATCGCGATGGGCAAAGCCGCGATAGTCCGTCGTTCCGGAGATTAATGCCAGCTGTTTg < 2:117764/98‑1 (MQ=255)
gttCCAATTCGAGATTTTCAAACACCGCTTCAATAATCAGATCGCGATGGGCAAAGCCGCGATAGTCCGTCGTTCCGGAGATTAATGCCAGCTGTTTGTc > 2:511750/1‑100 (MQ=255)
gttCCAATTCGAGATTTTCAAACACCGCTTCAATAATCAGATCGCGATGGGCAAAGCCGCGATAGTCCGTCGTTCCGGAGATTAATGCCAGCTGTTTGTc > 2:192621/1‑100 (MQ=255)
|
TGAGCGGCGATATCACCAATCGGTAAAGATGACGTATTCGAAGCAAAGATGGTATGAGCGGCGCAATTTTGCTCAACTTCCGCCACCATCTGTTGTTTCAATTCGAGATTTTCAAACACCGCTTCAATAATCAGATCGCGATGGGCAAAGCCGCGATAGTCCGTCGTTCCGGAGATTAATGCCAGCTGTTTGTC > NC_000913/2457856‑2458049
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
