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 |
1,015,667 |
A→G |
25.5% |
G134G (GGT→GGC) |
fumA ← |
aerobic Class I fumarate hydratase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,015,667 | 0 | A | G | 25.5%
| 69.8
/ 25.8
| 47 | G134G (GGT→GGC) | fumA | aerobic Class I fumarate hydratase |
| Reads supporting (aligned to +/- strand): ref base A (26/9); new base G (4/8); total (30/17) |
| Fisher's exact test for biased strand distribution p-value = 1.65e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.77e-01 |
CTTTATACATATCCAGCGGCGCGTTTTGCGAGTAGCGCAGATTATCTTCGATATAAGTGTTATAGACACCGCGCGCCAGCGCCGCTTCATCACCACCACCGGTCCATACACGCTGCCCTTTTTTACCAACAATAATCG > minE/1015600‑1015737
|
cttTGTACATGTCCAGCGCCGCATTCTGTGAATAGCGCAGGTTATCTTCGATATAGGTGTTATAGACGcct > 1:3645695/1‑70 (MQ=255)
tataCATATCCAGCGGCGCGTTTTGCGAGTAGCGCAGATTATCTTCGATATAAGTGTTATAGACACcgc < 1:1219466/69‑1 (MQ=255)
tataCATATCCAGCGGCGCGTTTTGCGAGTAGCGCAGATTATCTTCGATATAAGTGTTATAGACACcgc < 1:4172446/69‑1 (MQ=255)
taCATATCCAGCGGCGCGTTTTGCGAGTAGCGCAGATTATCTTCGATATAAGTGTTATAGACACCgcgcgc > 1:4243451/1‑71 (MQ=255)
aCATATCCAGCGGCGCGTTTTGCGACTAGCGCAGATTATCTTCGATATAAGTGTTATAGACACCgcgcgc > 1:3526384/1‑70 (MQ=255)
cATATCCAGCGGCGCGTTTTGCGAGTAGCGCAGATTATCTTCGATATAAGTGTTATAGACACCGCGCGCCa < 1:4582949/71‑1 (MQ=255)
atCCAGCGGCGCGTTTTGCGAGTAGCGCAGATTATCTTCGATATAAGTGTTATAGACACCGCGCGCCAgcg > 1:3766262/1‑71 (MQ=255)
tCCAGCGGCGCGTTTTGCGAGTAGCGCAGATTATCTTCGATATAAGTGTTATAGaca > 1:3149096/1‑57 (MQ=255)
ccAGCGGCGCGTTTTGCGAGTAGCGCAGATTATCTTCGATATAAGTGTTATAGACACCGCGCGCCAGcgcc > 1:1071204/1‑71 (MQ=255)
ccAGCGGCGCGTTTTGCGAGTAGCGCAGATTATCTTCGATATAAGTGTTATAGACACCGCGCGCCAGcgcc > 1:5688093/1‑71 (MQ=255)
ccAGCGGCGCGTTTTGCGAGTAGCGCAGATTATCTTCGATATAAGTGTTATAGACACCGCGCGCCAGcgcc > 1:1919440/1‑71 (MQ=255)
cAGCGGCGCGTTTTGCGAGTAGCGCAGATTATCTTCGATATAAGTGTTATAGACACCGCGCGCCAGcgccg > 1:967218/1‑71 (MQ=255)
cAGCGGCGCGTTTTGCGAGTAGCGCAGATTATCTTCGATATAAGTGTTATAGACACCGCGCGCCAGcgccg > 1:4531729/1‑71 (MQ=255)
cggcgCGTTTTGCGAGTAGCGCAGATTATCTTCGATATAAGTGTTATAGACACCGCGCGCCAGCGCCGCtt < 1:2243750/71‑1 (MQ=255)
ggcgCGTTTTGCGAGTAGCGCAGATTATCTTCGATATAAGTGTTATAGacac > 1:389997/1‑52 (MQ=255)
tttGCGAGTAGCGCAGATTATCTTCGATATAAGTGTTATAGACACCGCGCGCCAGCGCCGCTTCATcacca > 1:163289/1‑71 (MQ=255)
tttGCGAGTAGCGCAGATTATCTTCGATATAAGTGTTATAGACACCGCGCGCCAGCGCCGCTTCATcacca > 1:327459/1‑71 (MQ=255)
ttGCGAGTAGCGCAGATTATCTTCGATATAAGTGTTATAGACACCGCGCGCCAGCGCCGCTTCATcaccac > 1:4547975/1‑71 (MQ=255)
aGTAGCGCAGATTATCTTCGATATAAGTGTTATAGACACCGCGCGCCAgcgc < 1:3941957/52‑1 (MQ=255)
gTAGCGCAGATTATCTTCGATATAAGTGTTATAGACACCGCGCGCCAGCGCCGCTTCATCACCACCACCgg > 1:1569488/1‑71 (MQ=255)
cgcAGGTTATCTTCGATATAGGTGTTATAGACGCCTTTCGACAGCGTTTCTTCATCACCGCCGCCGGTCCa < 1:2678046/71‑1 (MQ=255)
cAGGTTATCTTCGATATAGGTGTTATAGACGCCTTTCGACAGCGTTTCTTCATCACCGCCGCCGGTCCaca > 1:5239332/1‑69 (MQ=255)
cAGATTATCTTCGATATAAGTGTTATAGACACCGCGCGCCAGCGCCGCTTCATCACCACCACCGGTCCATa > 1:707321/1‑71 (MQ=255)
ggttATCTTCGATATAGGTGTTATAGACGCCTTTCGACAGCGTTTCTTCATCACCGCCGCCGGTCCacac > 1:2203505/3‑70 (MQ=255)
aTTATCTTCGATATAAGTGTTATAGACACCGCGCGCCAGCGCCGCTTCATCACCACCACCGGTcc < 1:141177/65‑1 (MQ=255)
ttATCCTCGATATAAGTGTTATAGACACCGCGCGcc > 1:2181820/1‑36 (MQ=255)
ttATCCTCGATATAAGTGTTATAGACACCGCGCGCCAGCGCCGCTTCATcacc > 1:2000193/1‑53 (MQ=255)
tATCTTCGATATAGGTGTTATAGACGCCTTTCGACAGCGTTTCTTCATCACCGCCGCCGGTCCACACgcgc > 1:2326450/1‑71 (MQ=255)
aTCTTCGATATAAGTGTTATAGACACCGCGCGCCAGCGCCGCTtca > 1:4562658/1‑46 (MQ=255)
tCTTCGATATAAGTGTTATAGACACCGCGCGCCAGCGCCGCTTCATCACCACCACCGGTCCATACACGCTg > 1:3654795/1‑71 (MQ=255)
cTTCGATATAGGTGTTATAGACGCCTTTCGACAGCGTTTCTTCATcaccgc < 1:963907/51‑3 (MQ=255)
cTTCGATATAAGTGTTATAGACACCGCGCGCCAGCGCCGCTTCATcaccaccac < 1:2301525/54‑1 (MQ=255)
gATATAGGTGTTATAGACGCCTTTCGACAGCGTTTCTTCATCACCGCCGCCGGTCCACACGCGCTGGCCtt < 1:1704682/71‑1 (MQ=255)
gATATAAGTGTTATAGACACCGCGCGCCAGCGCCGCTtcat > 1:5581721/1‑41 (MQ=255)
gATATAAGTGTTATAGACACCGCGCGCCAGCGCCGCTtcat > 1:4994944/1‑41 (MQ=255)
gATATAAGTGTTATAGACACCGCGCGCCAGCGCCGCTTCATCACCACCACCGGTCCAt > 1:1070353/1‑58 (MQ=255)
atatAGGTGTTATAGACGCCTTTCGACAGCGTTTCTTCATCACCGCCGCCGGTCCACACGCGCTGGCCttt < 1:1647556/71‑1 (MQ=255)
atatAGGTGTTATAGACGCCTTTCGACAGCGTTTCTTCATCACCGCCGCCGGTCCACACGCGCTGGCCttt < 1:2118962/71‑1 (MQ=255)
atatAGGTGTTATAGACGCCTTTCGACAGCGTTTCTTCATCACCGCCGCCGGTCCACACGCGCTGGCCttt < 1:1357801/71‑1 (MQ=255)
tataGGTGTTATAGACGCCTTTCGACAGCGTTTCTTCATCACCGCCGCCGGTCCACACGCGCTGGCCttt < 1:1981250/70‑1 (MQ=255)
ataAGTGTTATAGACACCGCGCGCCAGCGCCGCTCCATCACCACCACCGGTCCATACACGCTGCCCttttt > 1:4085079/1‑71 (MQ=255)
taAGTGTTATAGACACCGCGCGCCAGCGCCGCTTCATCACCACCACCGGTCCa < 1:4237096/53‑1 (MQ=255)
aGTGTTATAGACACCGCGCGCCAGCGCCGCTTCATCACCACCACCGGTCCATACACGCTGCCCTTTTTTAc > 1:2649153/1‑71 (MQ=255)
gtgtTATAGACGCCTTTCGACAGCGTTTCTTCATCACCGCCGCCGGTCCACACGCGCTGGCCTTTTTTAcc < 1:5075048/71‑1 (MQ=255)
ataGACACCGCGCGCCAGCGCCGCTTCATCACCACCACCGGTCCATACACGCTGCCCTTTTTTACcaaca > 1:5127351/1‑70 (MQ=255)
taGACACCGCGCGCCAGCGCCGCTTCATCACCACCACCGGTCCATACACGCTGCCCTTTTTTACcaacaa > 1:3402511/1‑70 (MQ=255)
taGACACCGCGCGCCAGCGCCGCTTCATCACCACCACCGGTCCATACACGCTGCCCTTTTTTACcaacaa > 1:2528372/1‑70 (MQ=255)
taGACACCGCGCGCCAGCGCCGCTTCATCACCACCACCGGTCCATACACGCTGCCCTTTTTTACCAACaat < 1:4727397/71‑1 (MQ=255)
gACACCGCGCGCCAGCGCCGCTTCATCACCACCACCGGTCCATACACGCTGCCCTTTTTTACCAACaataa > 1:3811583/1‑71 (MQ=255)
acacCGCGCGCCAGCGCCGCTTCATCACCACCCCCGGTCCATACCCGCTGCCCTTTTTTACCAACaataat > 1:520643/1‑71 (MQ=255)
cacCGCGCGCCAGCGCCGCTTCATCACCACCACCGGTCCATACACGCTGCCCTTTTTTACCAACAATAATc < 1:3447993/71‑1 (MQ=255)
acCGCGCGCCAGCGCCGCTTCATCACCACCACCGGTCCATACACGCTGCCCTTTTTTACCAACAATAATcg < 1:2695996/71‑1 (MQ=255)
|
CTTTATACATATCCAGCGGCGCGTTTTGCGAGTAGCGCAGATTATCTTCGATATAAGTGTTATAGACACCGCGCGCCAGCGCCGCTTCATCACCACCACCGGTCCATACACGCTGCCCTTTTTTACCAACAATAATCG > minE/1015600‑1015737
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
