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 |
2,559,844 |
T→C |
31.6% |
V139V (GTA→GTG) |
yibK ← |
predicted rRNA methylase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,559,844 | 0 | T | C | 31.6%
| 31.3
/ 17.8
| 41 | V139V (GTA→GTG) | yibK | predicted rRNA methylase |
| Reads supporting (aligned to +/- strand): ref base T (14/14); new base C (6/7); total (20/21) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.45e-02 |
TACAGTAACTAATCTCTCAATACCGCTCCCGGATACCCCAACTGCCGCCAGGCTTCATACACCACTACCGACACCGCATTGGACAGATTCATGCTGCGGCTGTCCGGCACCATCGGAATGCGAATTTTTTGTTC > minE/2559779‑2559912
|
tACAGTAACTAATCTCTCAATACCGCTCCCGGATACCCCAACTGCCGCCAGGCTTCATACACCACTAcc < 1:2487556/69‑1 (MQ=255)
aCTAATCTCTCAATACCGCTCCCGGATACCCCAACTGCCGCCAGGCTTCATACACCACTACCGACACCg > 1:2576912/1‑69 (MQ=255)
tcAATACCGCTCCCGGATACCCCAACTGCCGCCAGGCTTCATACACCACTACCGa < 1:411076/55‑1 (MQ=255)
tcAATACCGCTCCCGGATACCCCAACTGCCGCCAGGCTTCATACACCACTACCGa < 1:3202159/55‑1 (MQ=255)
tcAATACCGCTCCCGGATACCCCAACTGCCGCCAGGCTTCATACACCACTACCGa < 1:1848064/55‑1 (MQ=255)
tcAATACCGCTCCCGGATACCCCAACTGCCGCCAGGCTTCATACACCACTACCGa < 1:2297215/55‑1 (MQ=255)
aCCGCTCCCGGATACCCCAACTGCCGCCAGGCTTCATACACCACTACCGACACCGCATTGGACAGATTc < 1:2813138/69‑1 (MQ=255)
ggATACCCCAACTGCCGCCAGGCTTCATACACCACTACCGACACCGCATTGGACAGATTCATGCTGCgg > 1:2867067/1‑69 (MQ=255)
ggATACCCCAACTGCCGCCAGGCTTCATACACCACTACCGACACCGCATTGGACAGATTCATGCTGCg < 1:3012036/68‑1 (MQ=255)
tACCCCAACTGCCGCCAGGCTTCATACACCACTACCGACACCGCATTGGACAGATTCATGCTGCGGCTg < 1:345661/69‑1 (MQ=255)
ccAACTGCCGCCAGGCTTCATACACCACTACCGACACCGCATTGGACAGATTCATGCTGCGGCTGTcc < 1:3380849/68‑1 (MQ=255)
ccAACTGCCGCCAGGCTTCATACACCACTACCGACACCGCATTGGACAGATTCATGCTGCGGCTGTcc < 1:1993543/68‑1 (MQ=255)
ccAACTGCCGCCAGGCTTCATACACCACTACCGACACCGCATTGGACAGATTCATGCTGCGGCTGTcc < 1:2588753/68‑1 (MQ=255)
ggcgccAGGCTTCATACACCACCACCGACACCGCATTGGACAGGTTCATGCTGCGGCTGTCCGGCACCa < 1:1290125/67‑1 (MQ=255)
ggcgccAGGCTTCATACACCACCACCGACACCGCATTGGACAGGTTCATGCTGCGGCTGTCCGGCACCa < 1:3399388/67‑1 (MQ=255)
ggcgccAGGCTTCATACACCACCACCGACACCGCATTGGACAGGTTCATGCTGCGGCTGTCCGGCACCa < 1:2584407/67‑1 (MQ=255)
ggcgccAGGCTTCATACACCACCACCGACACCGCATTGGACAGGTTCATGCTGCGGCTGTCCGGCACCa < 1:1932028/67‑1 (MQ=255)
ggcgccAGGCTTCATACACCACCACCGACACCGCATTGGACAAGTTCATGCTGCGGCTGTCCGGCACCa < 1:704522/67‑1 (MQ=255)
ggcgcaAGGCTTCATACACCACCACCGACACCGCATTGGACAGGTTCATGCTGCGGCTGTCCGGCACCa < 1:1574066/67‑1 (MQ=255)
gccgccAGGCTTCATACACCACTACCGACACCGCATTGGACAGATTCATGCTGCGGCTGTCCGGCACCa > 1:3162192/1‑69 (MQ=255)
gccgccAGGCTTCATACACCACTACCGACACCGCATTGGACAGATTCATGCTGCGGCTGTCCGGCACCa > 1:266644/1‑69 (MQ=255)
gccgccAGGCTTCATACACCACTACCGACACCGCATTGGACAGATTCATGCTGCGGCTGTCCGGCACCa > 1:289074/1‑69 (MQ=255)
gccgccAGGCTTCATACACCACTA‑CTACACCGCATTGGACAGATTCATGCTGCGGCTGTCCGGCACCAt > 1:3329502/1‑69 (MQ=255)
gcgccAGGCTTCATACACCACCACCGACACCGCATTGGACAGGTTCATGCTGCGGCTGTCCGGCACCa < 1:1758825/67‑1 (MQ=255)
gccAGGCTTCATACACCACCACCGACACCGCATTGGACAgg > 1:2252102/1‑40 (MQ=38)
gccAGGCTTCATACACCACCACCGACACCGCATTGGACAgg > 1:767607/1‑40 (MQ=38)
gccAGGCTTCATACACCACCACCGACACCGCATTGGACAgg > 1:539125/1‑40 (MQ=38)
gccAGGCTTCATACACCACCACCGACACCGCATTGGACAgg > 1:1867907/1‑40 (MQ=38)
gccAGGCTTCATACACCACCACCGACACCGCATTGGACAgg > 1:2910282/1‑40 (MQ=38)
gccAGGCTTCATACACCACCACCGACACCGCATTGGACAgg > 1:1803036/1‑40 (MQ=38)
ccAGGCTTCATACACCACTACCGACACCGCATTGGACAGATTCATGCTGCGGCTGTCCGGCACCATCgg < 1:2285734/69‑1 (MQ=255)
ccAGGCTTCATACACCACTACCGACACCGCATTGGACAGATTCATGCTGCGGCTGTCCGGCACCATCgg < 1:262890/69‑1 (MQ=255)
cAGGCTTCATACACCACTACCGACACCGCATTGGACAGATTCATGCTGCGGCTGTCCGGCACCATCgg < 1:2135879/68‑1 (MQ=255)
caccacTACCGACACCGCATTGGACAGATTCATGCTGCGGCTGTCCGGCACCATCGGAATGCGAAtttt > 1:2142076/1‑69 (MQ=255)
caccacTACCGACACCGCATTGGACAGATTCATGCTGCGGCTGTCCGGCACCATCGGAATGCGAAtttt > 1:1558279/1‑69 (MQ=255)
cTACCGACACCGCATTGGACAGATTCATGCTGCGGCTGTCCGGCACCATCGGAATGCGAATTTTTTg > 1:505260/1‑67 (MQ=255)
cTACCGACACCGCATTGGACAGATTCATGCTGCGGCTGTCCGGCACCATCGGAATGCGAATTTTTTg > 1:400124/1‑67 (MQ=255)
cTACCGACACCGCATTGGACAGATTCATGCTGCGGCTGTCCGGCACCATCGGAATGCGAATTTTTTg > 1:2366495/1‑67 (MQ=255)
cTACCGACACCGCATTGGACAGATTCATGCTGCGGCTGTCCGGCACCATCGGAATGCGAATTTTTTg > 1:1787915/1‑67 (MQ=255)
cTACCGACACCGCATTGGACAGATTCATGCTGCGGCTGTCCGGCACCATCGGAATGCGAATTTTTTg > 1:2175166/1‑67 (MQ=255)
cTACCGACACCGCATTGGACAGATTCATGCTGCGGCTGTCCGGCACCATCGGAATGCGAATTTTTTg > 1:2518344/1‑67 (MQ=255)
tACCGACACCGCATTGGACAGATTCATGCTGCGGCTGTCCGGCACCATCGGAATGGGAATTTTTTGTTc > 1:2940382/1‑69 (MQ=255)
tACCGACACCGCATTGGACAGATTCATGCTGCGGCTGTCCGGCACCATCGGAATGCGAATTTTTTGtt > 1:663229/1‑68 (MQ=255)
tACCGACACCGCATTGGACAGATTCATGCTGCGGCTGTCCGGCACCATCGGAATGCGAATTTTTTGTTc > 1:117572/1‑69 (MQ=255)
tACCGACACCGCATTGGACAGATTCATGCTGCGGCTGTCCGGCACCATCCGAATGCGAATTTTTTGtt > 1:2788316/1‑68 (MQ=255)
|
TACAGTAACTAATCTCTCAATACCGCTCCCGGATACCCCAACTGCCGCCAGGCTTCATACACCACTACCGACACCGCATTGGACAGATTCATGCTGCGGCTGTCCGGCACCATCGGAATGCGAATTTTTTGTTC > minE/2559779‑2559912
|
| 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
