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 I2 R1
|
758 |
59.3 |
2864096 |
93.9% |
2689386 |
105.7 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
2,358,163 |
G→A |
A228V (GCG→GTG) |
rhmA ← |
2‑keto‑3‑deoxy‑L‑rhamnonate aldolase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 2,358,163 | 0 | G | A | 97.7%
| 130.2
/ ‑6.4
| 43 | A228V (GCG→GTG) | rhmA | 2‑keto‑3‑deoxy‑L‑rhamnonate aldolase |
| Reads supporting (aligned to +/- strand): ref base G (0/1); new base A (26/16); total (26/17) |
| Fisher's exact test for biased strand distribution p-value = 3.95e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.99e-01 |
GGCCTTTGATATCAATAACTACCTTTTATGCGTGGCCCATTTTTGCCTGATTTAAACATCGCCAGTCGTTGATCCAGGGCATCGCTGTAGAGCATCGTGTCAACGCCAACAGCGACAAAGTTCGCTCCCCACGCCAGGCATTG‑CTGCGCCATATCAGGAGCCACAGCCAGAAAACCAGCCGCTTTACCCGCAGCACGGATCCGCCGAATACTGGTTTCAATAATTCGCTGCACTTCCGGGTGCCCGGCGTTATCCGGGTAGCCCAACG > NC_000913/2358031‑2358298
|
ggCCTTTGATATCAATAACTACCTTTTATGCGTGGCCCATTTTTGCCTGATTTAAACATCGCCAGTCGTTGATCCAGGGCATCGCTGTAGAGCATCGTGTCAACGCCAACAGCGACAAAGTTCGCTCCCCACACCAGGc < 2:1183833/139‑1 (MQ=255)
cTTTTATGCGTGGCCCATTTTTGCCTGATTTAAACATCGCCAGTCGTTGATCCAGGGCATCGCTGTAGAGCATCGTGTCAACGCCAACAGCGACAAAGTTCGCTCCCCACACCAGGCATTG‑CTGCGCCATATCAGGAGc > 1:47469/1‑139 (MQ=255)
ttATGCGTGGCCCATTTTTGCCTGATTTAAACATCGCCAGTCGTTGATCCAGGACATCGCTGTAGAGCATCGTGTCAACGCCAACAGCGACACAGTTCGCTCCCCACACCAGGAATTG‑CTGCGCCATATCAGGAGCcac > 1:810343/1‑139 (MQ=255)
tGGCCCATTTTTGCCTGATTTAAACATCGCCAGTCGTTGATCCAGGGCATCGCTGTAGAGCATCGTGTCAACGCCAACAGCGACAAAGTTCGCTCCCCACACCAGGCATTGCCTGCGCCATATCAGGAGCCACAGCCAg > 2:390821/1‑139 (MQ=255)
tGGCCCATTTTTGCCTGATTTAAACATCGCCAGTCGTTGATCCAGGGCATCGCTGTAGAGCATCGTGTCAACGCCAACAGCGACAAAGTTCGCTCCCCACACCAGGCATTG‑CTGCGCCATATCAGGAGCCACAGCCAGa > 2:1116717/1‑139 (MQ=255)
tGGCCCATTTTTGCCTGATTTAAACATCGCCAGTCGTTGATCCAGGGCATCGCTGTAGAGCATCGTGTCAACGCCAACAGCGACAAAGTTCGCTCCCCACACCAGGCATTG‑CTGCGCCATATCAGGAGCCACAGCCAGa > 1:265541/1‑139 (MQ=255)
gCCTGATTTAAACATCGCCAGTCGTTGATCCAGGGCATCGCTGTAGAGCATCGTGTCAACGCCAACAGCGACAAAGTTCGCTCCCCACACCAGGCATTG‑CTGCGCCATATCAGGAGCCACAGCCAGAAAACCAGCCGCt < 2:47469/139‑1 (MQ=255)
tttAAACATCGCCAGTCGTTGATCCAGGGCATCGCTGTAGAGCATCGTGTCAACGCCAACAGCGACAAAGTTCGCTCCCCACACCAGGCATTG‑CTGCGCCATATCAGGAGCcac > 2:613445/1‑114 (MQ=255)
tttAAACATCGCCAGTCGTTGATCCAGGGCATCGCTGTAGAGCATCGTGTCAACGCCAACAGCGACAAAGTTCGCTCCCCACACCAGGCATTG‑CTGCGCCATATCAGGAGCcac < 1:613445/114‑1 (MQ=255)
cATCGCCAGTCGTTGATCCAGGGCACCGCTGCAGAGCACCGTGTCAACGCCCACAGCGACAAAGTTCGCTCCCCACACCAGGCATTG‑CTGCGCCATATCAGGCGCCACAGCCAGAAAACCAGCCGCTTTACCCgcagca < 2:265541/139‑1 (MQ=255)
cGCCAGTCGTTGATCCAGGGCATCGCTGTAGAGCATCGTGTCAACGCCAACAGCGACAAAGTTCGCTCCCCACGCCAGGCATTG‑CTGCGCCATATCAGGAGCcaca < 1:914478/106‑1 (MQ=255)
cGCCAGTCGTTGATCCAGGGCATCGCTGTAGAGCATCGTGTCAACGCCAACAGCGACAAAGTTCGCTCCCCACACCAGGCATTG‑CTGCGCCATATCAGGAGCcaca > 2:914478/1‑106 (MQ=255)
cAGTCGTTGATCCAGGGCATCGCTGTAGAGCATCGTGTCAACGCCAACAGCGACAAAGTTCGCTCCCCACACCAGGCATTGCCTGCGCCATATCAGGAGCCACAGCCAGAAAACCAGCCGCTTTACCCGCAGCACGGAt < 1:390821/139‑1 (MQ=255)
gTCGTTGATCCAGGGCATCGCTGTAGAGCATCGTGTCAACGCCAACAGCGACAAAGTTCGCTCCCCACACCAGGCATTG‑CTGCGCCATATCAGGAGCCACAGCCAGAAAACCAGCCGCTTTACCCGCAGCACGGATccg < 2:770328/139‑1 (MQ=255)
ggCATCGCTGTAGAGCATCGTGTCAACGCCAACAGCGACAAAGTTCGCTCCCCACACCAGGCATTG‑CTGCGCCATATCAGGAGCCACAGCCAGAAAACCAGCCGCTTTACCCGCAGCACGGATCCGCCGAATACTGGtt > 2:1344476/1‑139 (MQ=255)
tCGCTGTAGAGCATCGTGTCAACGCCAACAGCGACAAAGTTCGCTCCCCACACCAGGCATTG‑CTGCGCCATATCAGGAGCCACAGCCAGAAAACCAGCCGCTTTACCCGCAGCACGGATCCGCCGAATACTGGTTTCaa > 1:1122705/1‑139 (MQ=255)
cATCGTGTCAACGCCAACAGCGACAAAGTTCGCTCCCCACACCAGGCATTG‑CTGCGCCATATCAGGAGc < 1:315026/69‑1 (MQ=255)
cATCGTGTCAACGCCAACAGCGACAAAGTTCGCTCCCCACACCAGGCATTG‑CTGCGCCATATCAGGAGc > 2:315026/1‑69 (MQ=255)
cGTGTCAACGCCAACAGCGACAAAGTTCGCTCCCCACACCAGGCATTG‑CTGCGCCATATCAGGAGCcaca > 2:1172505/1‑70 (MQ=255)
cGTGTCAACGCCAACAGCGACAAAGTTCGCTCCCCACACCAGGCATTG‑CTGCGCCATATCAGGAGCcaca < 1:1172505/70‑1 (MQ=255)
cGTGTCAACGCCAACAGCGACAAAGTTCGCTCCCCACACCAGGCATTG‑CTGCGCCATATCAGGAGCCACAGCCAGAAAACCAg < 2:1080970/83‑1 (MQ=255)
cGTGTCAACGCCAACAGCGACAAAGTTCGCTCCCCACACCAGGCATTG‑CTGCGCCATATCAGGAGCCACAGCCAGAAAACCAg > 1:1080970/1‑83 (MQ=255)
cGTGTCAACGCCAACAGCGACAAAGTTCGCTCCCCACACCAGGCATTG‑CTGCGCCATATCAGGAGCCACAGCCAGAAAACCAGCCGCTTTACCCGCAGCACGGATCCGCCGAATa < 1:714758/115‑1 (MQ=255)
cGTGTCAACGCCAACAGCGACAAAGTTCGCTCCCCACACCAGGCATTG‑CTGCGCCATATCAGGAGCCACAGCCAGAAAACCAGCCGCTTTACCCGCAGCACGGATCCGCCGAATa > 2:714758/1‑115 (MQ=255)
cGTGTCAACGCCAACAGCGACAAAGTTCGCTCCCCACACCAGGCATTG‑CTGCGCCATATCAGGAGCCACAGCCAGAAAACCAGCCGCTTTACCCGCAGCACGGATCCGCCGAATACTGGTTTCAATAATTCGCTGCACt > 2:98550/1‑139 (MQ=255)
tgtCAACGCCAACAGCGACAAAGTTCGCTCCCCACACCAGGCATTG‑CTGCGCCATATCAGGAGCCACAGCCAGAAAACCAGCCGCTTTACCCGCAGCACGGATCCGCCGAATACTGGTTTCAATAATTCGCTGCACTTc > 2:1040862/1‑139 (MQ=255)
tgtCAACGCCAACAGCGACAAAGTTCGCTCCCCACACCAGGCATTG‑CTGCGCCATATCAGGAGCCACAGCCAGAAAACCAGCCGCTTTACCCGCAGCACGGATCCGCCGAATACTGGTTTCAATAATTCGCTGCACTTc > 2:818526/1‑139 (MQ=255)
tgtCAACGCCAACAGCGACAAAGTTCGCTCCCCACACCAGGCATTG‑CTGCGCCATATCAGGAGCCACAGCCAGAAAACCAGCCGCTTTACCCGCAGCACGGATCCGCCGAATACTGGTTTCAATAATTCGCTGCACTTc > 2:1197797/1‑139 (MQ=255)
tgtCAACGCCAACAGCGACAAAGTTCGCTCCCCACACCAGGCATTG‑CTGCGCCATATCAGGAGCCACAGCCAGAAAACCAGCCGCTTTACCCGCAGCACGGATCCGCCGAATACTGGTTTCAATAATTCGCTGCACTTc > 1:328055/1‑139 (MQ=255)
gCCAACAGCGACAAAGTTCGCTCCCCACACCAGGCATTG‑CTGCGCCATATCAGGAGCCACAGCCAGAAAACCAGCCGCTTTACCCGCAGCACGGATCCGCCGAATACTGGTTTCAATAATTCGCTGCACTTCCGGGTGc > 2:1325868/1‑139 (MQ=255)
gCCAACAGCGACAAAGTTCGCTCCCCACACCAGGCATTG‑CTGCGCCATATCAGGAGCCACAGCCAGAAAACCAGCCGCTTTACCCGCAGCACGGATCCGCCGAATACTGGTTTCAATAATTCGCTGCACTTCCGGGTGc < 2:492316/139‑1 (MQ=255)
aaCAGCGACAAAGTTCGCTCCCCACACCAGGCATTG‑CTGCGCCATATCAGGAGCCACAGCCAGAAAACCAGCCGCTTTAcc > 2:190011/1‑81 (MQ=255)
aaCAGCGACAAAGTTCGCTCCCCACACCAGGCATTG‑CTGCGCCATATCAGGAGCCACAGCCAGAAAACCAGCCGCTTTAcc < 1:190011/81‑1 (MQ=255)
cAGCGACAAAGTTCGCTCCCCACACCAGGCATTG‑CTGCGCCATATCAGGAGCCACAGCCAGAAAACCAGCCGCTTTACCCGCAGCACGGATCCGCCGAATACTGGTTTCAATAATTCGCTGCACTTCCGGGTGCCCGGc < 1:1197797/139‑1 (MQ=255)
aCAAAGTTCGCTCCCCACACCAGGCATTG‑CTGCGCCATATCAGGAGCCACAGCCAGAAAACCAGCCGCTTTACCCg > 2:578865/1‑76 (MQ=255)
aCAAAGTTCGCTCCCCACACCAGGCATTG‑CTGCGCCATATCAGGAGCCACAGCCAGAAAACCAGCCGCTTTACCCg < 1:578865/76‑1 (MQ=255)
aCAAAGTTCGCTCCCCACACCAGGCATTG‑CTGCGCCATATCAGGAGCCACAGCCAGAAAACCAGCCGCTTTACCCGCAGCACGGATCCGCCGAATACTGGTTTCAATAATTCGCTGCACTTCCGGGTGCCCGGCGTTAt > 1:847533/1‑139 (MQ=255)
ttCGCTCCCCACACCAGGCATTG‑CTGCGCCATATCAGGAGCCACAGCCAGAAAACCAGCCGCTTTACCCGCAGCACGGATCCGCCGAATACTGGTTTCAATAATTCGCTGCACTTCCGGGTGCCCGGCGTTATCCGGGt > 2:144195/1‑139 (MQ=255)
cTCCCCACACCAGGCATTG‑CTGCGCCATATCAGGAGCCACAGGCAGAAAACCAGCCGCTTTACCCGCAGCACGGATCCGCCGAATACTGGTTTCAATAATTCGCTGCACTTCCGGGTGCCCGGCGTTATCCGGGTAGcc > 1:1414183/1‑139 (MQ=255)
tCCCCACACCAGGCATTG‑CTGCGCCATATCAGGAGcc > 1:1256186/1‑37 (MQ=255)
tCCCCACACCAGGCATTG‑CTGCGCCATATCAGGAGcc < 2:1256186/37‑1 (MQ=255)
tCCCCACACCAGGCATTG‑CTGCGCCATATCAGGAGCcaca > 1:1363419/1‑40 (MQ=255)
tCCCCACACCAGGCATTG‑CTGCGCCATATCAGGAGCcaca < 2:1363419/40‑1 (MQ=255)
cacaCCAGGCATTG‑CTGCGCCATATCAGGAGCCACAGCCAGAAAACCAGCCGCTTTACCCGCAGCACGGATCCGCCGAATACTGGTTTCAATAATTCGCTGCACTTCCGGGTGCCCGGCGTTATCCGGGTAGCCCAacg < 2:847533/139‑1 (MQ=255)
|
GGCCTTTGATATCAATAACTACCTTTTATGCGTGGCCCATTTTTGCCTGATTTAAACATCGCCAGTCGTTGATCCAGGGCATCGCTGTAGAGCATCGTGTCAACGCCAACAGCGACAAAGTTCGCTCCCCACGCCAGGCATTG‑CTGCGCCATATCAGGAGCCACAGCCAGAAAACCAGCCGCTTTACCCGCAGCACGGATCCGCCGAATACTGGTTTCAATAATTCGCTGCACTTCCGGGTGCCCGGCGTTATCCGGGTAGCCCAACG > NC_000913/2358031‑2358298
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
