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 |
|
A6 F1 I0 R1
|
2892 |
75.3 |
5698161 |
66.1% |
3766484 |
59.5 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
854,876 |
T→C |
25.0% |
Q38Q (CAA→CAG) |
yciG ← |
hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 854,876 | 0 | T | C | 25.0%
| 89.9
/ 33.2
| 60 | Q38Q (CAA→CAG) | yciG | hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base T (24/21); new base C (7/8); total (31/29) |
| Fisher's exact test for biased strand distribution p-value = 7.69e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.61e-01 |
AATCAGGATTTGCCTGATTTATTACCACCGCTTTGTTGACCGCCTTTTTTACCCGCTTCAGATGCGCGTTGCGGATCATTTTTAAAATTACCGCCGCTATGCTGACCGCCTTTACGGCCTGCGTCGGATGCCTTCTCA > minE/854808‑854945
|
aaTCAGGATTTGCCTGATTTATTACCACCGCTTTGTTGACCGCCTTTTTTACCCGCTTCAGATGCGCGTTg < 1:2085009/71‑1 (MQ=255)
aaTCAGGATTTGCCTGATTTATTACCACCGCTTTGTTGACCGCCTTTTTTACCCGCTTCAGATGCGCGTTg > 1:1928582/1‑71 (MQ=255)
aaTCAGGATTTGCCTGATTTATTACCACCGCTTTGTTGACCGCCTTTTTTACCCGCTTCAGATGCGCGTTg > 1:5177215/1‑71 (MQ=255)
tCAGGATTTGCCTGATTTATTACCACCGCTTTGTTGACCGCCTTTTTTACCCGCTTCAGATGCGCGTTGCg < 1:4809467/71‑1 (MQ=255)
gATTTGCCTGATTTATTACCACCGCTTTGTTGACCGCCTTTTTTACCCGCTTCAGATGCGCGTTg < 1:5578218/65‑1 (MQ=255)
tttCCCTGATTTATTACCACCGCTTTGTTGACCGCCTTTTTTACCCGCTTCAGATGCGCGTTGCGGATCAt < 1:706094/71‑1 (MQ=255)
tGCCTGATTTATTACCACCGCTTTGTTGACCGCCTTTTTTACCCGCTTCAGATGCGCGTTGCGGATCAttt > 1:1673781/1‑71 (MQ=255)
ccTGATTTATTACCACCGCTTTGTTGACCGCCTTTTTTACCCGCTTCAGATGCGCGTTGCg < 1:1303607/61‑1 (MQ=255)
tGATTTATTACCACCGCTTTGTTGACCGCCTTTTTTACCCGCTTCAGATGCGCGTTGCgg > 1:1222567/1‑60 (MQ=255)
tGATTTATTACCACCGCTTTGTTGACCGCCTTTTTTACCCGCTTCAGATGCGCGTTGCGGATCATTTTTa > 1:1199558/1‑70 (MQ=255)
aTTTATTACCACCGCTTTGTTGACCGCCTTTTTTACCCGCTTCAGATGCGCGTTGCGGATCATTTTTaa < 1:4841389/69‑1 (MQ=255)
tattaCCACCGCTTTGTTGACCGCCTTTTTTACCCGCTTCAGATGCGCGTTGCGGATCATTTTTAAAATTa > 1:4708965/1‑71 (MQ=255)
ttaCCACCGCTTTGTTGACCGCCTTTTTTACCCGCTTCAGATGCGCGTTGCGGATCATTTTTAAAATTAc < 1:4865645/70‑1 (MQ=255)
ccaccGCTTTGTTGACCGCCTTTTTTACCCGCTTCAGATGCGCGTTGCGGATCATTTTTAAAATTAccgc < 1:1450435/70‑1 (MQ=255)
accGCTTTGTTGACCGCCTTTTTTACCCGCTTCAGATGCGCGTTGCGGATCATTTTTAAAATTACcgccgc < 1:4981776/71‑1 (MQ=255)
cGCTTTGTTGACCGCCTTTTTTACCCGCTTCAGATGCGCGTTGCGGATCATTTTTAAAATTACCGCCGCTa < 1:2394448/71‑1 (MQ=255)
cTTTGTTGACCGCCTTTTTTACCCGCTTCAGATGCGCGTTGCGGATCATTTTTAAAATTACCGCCGCTATg > 1:1814136/1‑71 (MQ=255)
tgttgACCGCCTTTTTTACCCGCTTCAGATGCGCGTTGCGGATCATTTTTAAAATTACCGCCGCTATGCt > 1:599170/1‑70 (MQ=255)
ttaccaccTTTTTTACCTGCTTCAGATGCGCGCTGCGGGTCATTCTTGAAATTAccccc > 1:2537712/3‑59 (MQ=255)
taccaccTTTTTTACCTGCTTCAGATGCGCGCTGCGGGTCATTCTTGAAATTACCCCCGCTGTGCTGTcca > 1:5201179/2‑70 (MQ=255)
gACCGCCTTTTTTACCCGCTTCAGATGCGCGTTGCGGATCATTTTTAAAATTACCGCCGCTa < 1:262660/62‑1 (MQ=255)
accaccTTTTTTACCTGCTTCAGATGCGCGCTGCGGGTCAtt > 1:4085450/1‑42 (MQ=25)
accaccTTTTTTACCTGCTTCAGATGCGCGCTGCGGGTCATTCTTGAAATTACCCCCGCTGTGCTgtc < 1:2902977/68‑3 (MQ=255)
accaccTTTTTTACCTGCTTCAGATGCGCGCTGCGGGTCATTCTTGAAATTACCCCCGCTGTGCTGTccac > 1:2807254/1‑69 (MQ=255)
accaccTTTTTTACCTGCTTCAGATGCGCGCTGCGGGTCATTCTTGAAATTACCCCCGCTGTGCTGTcca < 1:1115050/70‑2 (MQ=255)
accaccTTTTTTACCTGCTTCAGATGCGCGCTGCGGGTCATTCTTGAAATTACCCCCGCTGTGCTGTcca < 1:2414555/70‑2 (MQ=255)
accaccTTTTTTACCTGCTTCAGATGCGCGCTGCGGGTCATTCTTGAAATTACCCCCGCTGTGCTGTcca < 1:2408153/70‑2 (MQ=255)
aCCGCCTTTTTTACCCGCTTCAGATGCGCGTTGCGGATCATTTTTAAAATTACCGCCGCTATGCTGAcctc > 1:574382/1‑69 (MQ=255)
ccGCCTTTTTTACCCGCTTCAGATGCGCGTTGCGGAt > 1:2708169/1‑37 (MQ=255)
gCCTTTTTTACCCGCTTCAGATGCGCGTTGCGTATCATTTTTAAAATTACCGCCGCTATGCTGACCGCCtt < 1:3742697/71‑1 (MQ=255)
gCCTTTTTTACCCGCTTCAGATGCGCGTTGCGGATCATTTTTAAAATTACCGCCGCTATGCTGACCGCCtt < 1:49739/71‑1 (MQ=255)
gCCTTTTTTACCCGCTTCAGATGCGCGTTGCGGATCATTTTTAAAATTACCGCCGCTATGCTGACCGCCtt < 1:3456577/71‑1 (MQ=255)
ccTTTTTTACCTGCTTCAGATGCGCGCTGCGGGTCATTCTTGAAATTACCCCCGCTGTGCTGTCCACCttt > 1:504233/1‑71 (MQ=255)
cTTTTTTACCCGCTTCAGATGCGCGTTGCGGATCATTTTTAAAATTACCGCCGCTATGCTGACCGCCttt < 1:1081837/70‑1 (MQ=255)
ttttttACCCGCTTCAGATGCGCGTTGCGGATCATTTTTAAAATTACCGCCGCTATGCTGACCGc < 1:3452642/65‑1 (MQ=255)
ttttttACCCGCTTCAGATGCGCGTTGCGGATCATTTTTAAAATTACCGCCGCTATGCTGACCGCCTTTAc > 1:226188/1‑71 (MQ=255)
tttttACCTGCTTCAGATGCGCGCTGCGGGTCATTCTTGAAAt < 1:3374548/43‑1 (MQ=255)
ttttACCTGCTTCAGATGCGCGCTGCGGGTCATTCTTGAAATTa > 1:223896/1‑44 (MQ=255)
ttttACCTGCTTCAGATGCGCGCTGCGGGTCATTCTTGAAATTACCCCCGCTGTGCTGTCCACCttttt < 1:3709759/69‑3 (MQ=255)
ttttACCTGCTTCAGATGCGCGCTGCGGGTCATTCTTGAAATTACCCCCGCTGTGCTGTCCACCttttt < 1:1200742/69‑3 (MQ=255)
ttttACCTGCTTCAGATGCGCGCTGCGGGTCATTCTTGAAATTACCCCCGCTGTGCTGTCCACCttttt < 1:2860583/69‑3 (MQ=255)
ttttACCCGCTTCAGATGCGCGTTGCGGATCATTTTTaaaa > 1:2976150/1‑41 (MQ=255)
ttttACCCGCTTCAGATGCGCGTTGCGGATCATTTTTa > 1:3626140/1‑38 (MQ=255)
ttttACCCGCTTCAGATGCGCGTTGCGGATCATTTTTa > 1:2882276/1‑38 (MQ=255)
ttttACCCGCTTCAGATGCGCGTTGCGGATCATTTTTAAAATTa > 1:4627231/1‑44 (MQ=255)
ttttACCCGCTTCAGATGCGCGTTGCGGATCATTTTTAAAATTa > 1:4983566/1‑44 (MQ=255)
ttttACCCGCTTCAGATGCGCGTTGCGGATCATTTTTAAAATTa > 1:4340307/1‑44 (MQ=255)
ttttACCCGCTTCAGATGCGCGTTGCGGATCATTTTTAAAATTa > 1:3777310/1‑44 (MQ=255)
ttttACCCGCTTCAGATGCGCGTTGCGGATCATTTTTAAAATTAc > 1:4608047/1‑45 (MQ=255)
ttttACCCGCTTCAGATGCGCGTTGCGGATCATTTTTAAAATTAc > 1:1949034/1‑45 (MQ=255)
ttttACCCGCTTCAGATGCGCGTTGCGGATCATTTTTAAAATTACCGCCGCTATGCTGACCGCCTTTACgg > 1:1301709/1‑71 (MQ=255)
tACCCGCTTCAGATGCGCGTTGCGGATCATTTTTAAAATTACCGCCGCTATGCTGACCGCCtt < 1:1418166/63‑1 (MQ=255)
aCCCGCTTCAGATGCGCGTTGCGGATCATTTTTAAAATTACCGCCGCTATGCTGACCGCCTTTACGGCCt < 1:2288744/70‑1 (MQ=255)
cGCTTCAGATGCGCGTTGCGGATCATTTTTAAAATTACCGCCGCTa > 1:276554/1‑46 (MQ=255)
ttCAGATGCGCGCTGCGGGTCATTCTTGAAATTACCCCCGCTGTGCt > 1:4389781/1‑47 (MQ=255)
cAGATGCGCGTTGCGGATCATTTTTAAAATTACCGCCGCTATGCTGACCGCCTTTACGGCCTGCGTCGGAt > 1:3225039/1‑71 (MQ=255)
cAGATGCGCGTTGCGGATCATTTTTAAAATTACCGCCGATATGCTGACCGCCTTTACGGCCTGCGTCGGAt > 1:4576986/1‑71 (MQ=255)
aTGCGCGTTGCGGATCATTTTTAAAATTACCGCCGCTATGCTGACCGCCTTTACGGCCTGCGTCGGATGcc < 1:2214833/71‑1 (MQ=255)
gTTGCGGATCATTTTTAAAATTACCGCCGCTATGCTGACCGCCTTTACGGCCTGCGTCGGATGCCTtctaa < 1:4430476/71‑3 (MQ=255)
gTTGCGGATCATTTTTAAAATTACCGCCGCTATGCTGACCGCCTTTACGGCCTGCGTCGGATGCCTTCTCa < 1:1577361/71‑1 (MQ=255)
|
AATCAGGATTTGCCTGATTTATTACCACCGCTTTGTTGACCGCCTTTTTTACCCGCTTCAGATGCGCGTTGCGGATCATTTTTAAAATTACCGCCGCTATGCTGACCGCCTTTACGGCCTGCGTCGGATGCCTTCTCA > minE/854808‑854945
|
| 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
