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 |
|
A4 F21 I0 R1
|
1009 |
73.8 |
4146436 |
87.4% |
3623985 |
60.3 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
1,789,035 |
T→C |
25.7% |
S58P (TCC→CCC) |
ygaF → |
hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,789,035 | 0 | T | C | 25.7%
| 55.1
/ 21.2
| 35 | S58P (TCC→CCC) | ygaF | hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base T (18/8); new base C (7/2); total (25/10) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.80e-01 |
AGAGTCCGCCCCGGCCTGTCACCAGACGGGCCACAACAGCGGCGTGATCCATGCCGGGGTCTATTACACGTCCGGCAGCCTGAAGGCGCAGTTTTGCCTGGCGGGAAACCGCGCCACCAAAGCCTTTTGCGATCAA > minE/1788965‑1789100
|
agagTCCGCCCCGGCCTGTCACCAGACGGGCCACAACAGCGGCGTGATCCATGCCGGGGTCTATTACACGt > 1:2123046/1‑71 (MQ=255)
cGCCCCGGCCTGTCACCAGCCGGGCCACAACAGCGGCGTGATCCATGCCGGGGTCTATTACACGCCCgg > 1:1544560/1‑69 (MQ=255)
cGGCCTGTCACCAGACGGGCCACAACAGCGGCGTGATCCATGCCGGGGTCTATTACACGTCCGGCAGCCTg < 1:1649032/71‑1 (MQ=255)
cGGCCTGTCACCAGACGGGCCACAACAGCGGCGTGATCCATGCCGGGGTCTATTACACGCCCGGCAGCCTg < 1:1321758/71‑1 (MQ=255)
tCACCAGACGGGCCACAACAGCGGCGTGATCCATGCCGGGGTCTATTACACGTCCGGCAGCCTGAAGgcg > 1:672795/1‑70 (MQ=255)
cACCAGACGGGCCACAACAGCGGCGTGATCCATGCCGGGGTCTATTACACGTCCGGCAGCCTGAAGgcg > 1:4031374/1‑69 (MQ=255)
cACCAGACGGGCCACAACAGCGGCGTGATCCATGCCGGGGTCTATTACACGCCCGGCAGCCTGaa > 1:2381090/1‑65 (MQ=255)
cACCAGACGGGCCACAACAGCGGCGTGATCCATGCCGGGGTCTATTACACGCCCGGCAGCCTGa > 1:329857/1‑64 (MQ=255)
aCCAGACGGGCCACAACAGCGGCGTGATCCATGCCGGGGTCTATTACACGTCCGGCAGCCt > 1:1015832/1‑61 (MQ=255)
aCCAGACGGGCCACAACAGCGGCGTGATCCATGCCGGGGTCTATTACACGTCCGGCAGCCt > 1:1108811/1‑61 (MQ=255)
aCCAGACGGGCCACAACAGCGGCGTGATCCATGCCGGGGTCTATTACACGTCCGGCAGCCTGAAGGCGCAg < 1:3975843/71‑1 (MQ=255)
aGACGGGCCACAACAGCGGCGTGATCCATGCCGGGGTCTATTACACCCCCGGCAGCCTg < 1:3133289/59‑1 (MQ=39)
aCGGGCCACAACAGCGGCGTGATCCATGCCGGGGTCTATTACACGTCCg < 1:839174/49‑1 (MQ=255)
cacaACAGCGGCGTGATCCATGCCGGGGTCTATTACACGTCCGGCAGCCTGAAGGCGCAGTTTTGCCTGGc > 1:986627/1‑71 (MQ=255)
caacaGCGGCGTGATCCATGCCGGGGTCTATTACACGCCCGGCAGCCTGAAGGCGCAGTTTTGCCTGGCgg > 1:3432951/1‑71 (MQ=255)
acaGCGGCGTGATCCATGCCGGGGTCTATTACACGTCCGGCAGCCTGaa > 1:2710127/1‑49 (MQ=255)
tCCATGCCGGGGTCTATTACACGTCCGGCAGCCTGAAGGCGCAGTTTTGCCTGGCGGGAAACCGCGccacc < 1:2595315/71‑1 (MQ=255)
ccATGCCGGGGTCTATTACACGTCCGGCAGCCTGAAGGCGCAGTTTTGCCTGGCGGGAAACCGCGccacc > 1:2458243/1‑70 (MQ=255)
tGCCGGGGTCTATTACACGTCCGGCAGCCTGAAGGCGCAGTTTTGCCTGGCGGGAAAcc > 1:1925573/1‑59 (MQ=255)
ccGGGGTCTATTACACGTCCGGCAGCCTGAAGGCGCAGTTTTGCCTGGCGGGAAACCGCGCCACCAAAGcc < 1:899337/71‑1 (MQ=255)
ccGGGGTCTATTACACGTCCGGCAGCCTGAAGGCGCAGTTTTGCCTGGCGGGAAACCGCGCCACCAAAGcc > 1:3249462/1‑71 (MQ=255)
gggTCTATTACACGTCCGGCAGCCTGAAGGCGCAGTTTTGCCTGGCGGGAAACCGCGCCACCAAAGCCttt < 1:3978914/71‑1 (MQ=255)
tATTACACGTCCGGCAGCCTGAAGGCGCAGTTTTGCCTGGCGGGAAACCGCGCCACCAAAGCCTTTTGCGa > 1:217172/1‑71 (MQ=255)
tATTACACGCCCGGCAGCCTGAAGGCGCAGTTTTGCCTGGCGGGAAACCGCGCCACCAAAGCCTTTTGCGa > 1:3744743/1‑71 (MQ=255)
tATTACACGCCCGGCAGCCTGAAGGCGCAGTTTTGCCTGGCGGGAAACCGCGCCACCAAAGCCTTTTGCGa > 1:2003395/1‑71 (MQ=255)
aTTACACGTCCGGCAGCCTGAAGGCGCAGTTTTGCCTGGCGGGAAACcgc < 1:2484917/50‑1 (MQ=255)
ttACACGTCCGGCAGCCTGAAGGCGCAGTTTTGcc > 1:2847498/1‑35 (MQ=255)
ttACACGTCCGGCAGCCTGAAGGCGCAGTTTTGCCTGGCGGGAAACCGCGCCACCAAAGCCTTTTGCGAt > 1:691023/1‑70 (MQ=255)
ttACACGCCCGGCAGCCTGAAGGCGCAGTTTTGCCTGGCGGGAAACCGCGCCACCAAAGCCTTTTGCGAt > 1:474509/1‑70 (MQ=255)
tACACGTCCGGCAGCCTGAAGGCGCAGTTTTGCCTGGCGGGAAACCGCGCCACCAAAGCCTTTTGCGATc > 1:799773/1‑70 (MQ=255)
acacGTCCGGCAGCCTGAAGGCGCAGTTTTGCCTGGCGGGAAACCGCGCCACCAAAGCCTTTTGCGATCa > 1:3692349/1‑70 (MQ=255)
acacGTCCGGCAGCCTGAAGGCGCAGTTTTGCCTGGCGGGAAACCGCGCCACCAAAGCCTTTTGCGATCa > 1:1995310/1‑70 (MQ=255)
acacGTCCGGCAGCCTGAAGGCGCAGTTTTGCCTGGCGGGAAACCGCGCCACCAAAGCCTTTTGCGATCa > 1:1106815/1‑70 (MQ=255)
cacGTCCGGCAGCCTGAAGGCGCAGTTTTGCCTGGCGGGAAACCGCGCCACCAAAGCCTTTTGCGATCaa > 1:3225136/1‑70 (MQ=255)
cacGTCCGGCAGCCTGAAGGCGCAGTTTTGCCTGGCGGGAAACCGCGCCACCAAAGCCTATTGCGATCaa > 1:3539320/1‑70 (MQ=255)
acGTCCGGCAGCCTGAAGGCGCAGTTTTGCCTGGCGGGAAACCGCGCCACCAAAGCCTTTTGCGATCaa < 1:2344730/69‑1 (MQ=255)
|
AGAGTCCGCCCCGGCCTGTCACCAGACGGGCCACAACAGCGGCGTGATCCATGCCGGGGTCTATTACACGTCCGGCAGCCTGAAGGCGCAGTTTTGCCTGGCGGGAAACCGCGCCACCAAAGCCTTTTGCGATCAA > minE/1788965‑1789100
|
| 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
