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 F5 I184 R1
|
278 |
29.6 |
1166432 |
97.3% |
1134938 |
124.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
870,468 |
A→G |
Q678Q (CAA→CAG) |
pdeI → |
EAL domain‑containing protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 870,468 | 0 | A | G | 100.0%
| 71.1
/ NA
| 20 | Q678Q (CAA→CAG) | pdeI | EAL domain‑containing protein |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (12/8); total (12/8) |
TCATGAGCGTTTTACCACCATCATGAAAGAAAATGGCCTGAAGGCGAACAGCCTCTGTGTTGAGATCACTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAAGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAGACAGCATAAAGGTGGACTCGCAATTCACCGGCGATATTTTCGGTACTGCGGGAAAAATT > NZ_CP009273/870336‑870600
|
tCATGAGCGTTTTACCACCATCATGAAAGAAAATGGCCTGAAGGCGAACAGCCTCTGTGTTGAGATCACTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTa > 2:470694/1‑139 (MQ=255)
tcatGAAAGAAAATGGCCTGAAGGCGAACAGCCTCTGTGTTGAGATCACTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACtt > 1:538833/1‑139 (MQ=255)
gCCTGAAGGCGAACAGCCTCTGTGTTGAGATCACTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGt < 1:470694/138‑1 (MQ=255)
tgtTGAGATCACTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGa > 2:479461/1‑138 (MQ=255)
ttGAGATCACTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGaaa < 2:538833/138‑1 (MQ=255)
gagaTCACTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGt < 2:51135/108‑1 (MQ=255)
gagaTCACTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGt > 1:51135/1‑108 (MQ=255)
aTCACTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATc > 2:284485/1‑139 (MQ=255)
aCTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATc > 1:297236/1‑136 (MQ=255)
cTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAGa < 2:57623/139‑1 (MQ=255)
cTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAGa < 2:297236/139‑1 (MQ=255)
cTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAGa < 1:284485/139‑1 (MQ=255)
cTGAAACCGTGAGCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAGa < 2:12056/139‑1 (MQ=255)
aGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAGACAGCATAAAGGTGGa > 1:130032/1‑139 (MQ=255)
aaCATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAGACAGCATAAAGGTGGACTCGCAATTCa < 2:326793/138‑1 (MQ=255)
cTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAGACAGCATAAAGGTGGACTCGCAATTCACCGGCGATATTTTCGGTACTGCGGGa > 2:81066/1‑138 (MQ=255)
cTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAGACAGCATAAAGGTGGACTCGCAATTCACCGGCGATATTTTCGGTACTGCGGGa > 2:254313/1‑138 (MQ=255)
cTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAGACAGCATAAAGGTGGACTCGCAATTCACCGGCGATATTTTCGGTACTGCGGGa > 1:281785/1‑138 (MQ=255)
cGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAGACAGCATAAAGGTGGACTCGCAATTCACCGGCGATATTTTCGGTACTGCGGGaaaaa > 1:8316/1‑139 (MQ=255)
tAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAGACAGCATAAAGGTGGACTCGCAATTCACCGGCGATATTTTCGGTACTGCGGGAAAAAtt > 1:492870/1‑139 (MQ=255)
|
TCATGAGCGTTTTACCACCATCATGAAAGAAAATGGCCTGAAGGCGAACAGCCTCTGTGTTGAGATCACTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAAGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAGACAGCATAAAGGTGGACTCGCAATTCACCGGCGATATTTTCGGTACTGCGGGAAAAATT > NZ_CP009273/870336‑870600
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
GTTTTACCACCATCATGAAAGAAAATGGCCTGAAGGCGAACAGCCTCTGTGTTGAGATCACTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAAGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAGACAGCATAAAGGTGGACTCGCAATTCACCGGCGATATTTTCGGTACTGCGGGAAAAATTG > NZ_CP009273/870344‑870601
|
GTTTTACCACCATCATGAAAGAAAATGGCCTGAAGGCGAACAGCCTCTGTGTTGAGATCACTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATActgtctcttatac > SRR3722139.96742/1‑137 (MQ=60)
TTTTACCACCATCATGAAAGAAAATGGCCTGAAGGCGAACAGCCTCTGTGTTGAGATCACTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTT > SRR3722139.545013/1‑151 (MQ=60)
GGCCTGAAGGCGAACAGCCTCTGTGTTGAGATCACTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAA < SRR3722139.476180/150‑1 (MQ=60)
GCCTCTGTGTTGAGATCACTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTctgtctcttatacacatctcc > SRR3722139.51720/1‑130 (MQ=60)
GTGTTGAGATCACTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCC > SRR3722139.300956/1‑148 (MQ=60)
tttcaagcagaagacggcatacgagatctagtacggtctcgtgggctcggagatgtgtataagagacagAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAGAC < SRR3722139.5383/81‑1 (MQ=60)
ACTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAGACAGCATAAAGG < SRR3722139.288063/151‑1 (MQ=60)
AACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAGACAGCATAAAGGTGGAC > SRR3722139.131628/1‑151 (MQ=60)
ATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAGACAGCATAAAGGTGGACTCGCAATTCACCGGCGATATTTTCGGTACTGCGGGAA > SRR3722139.285335/1‑150 (MQ=60)
TTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAGACAGCATAAAGGTGGACTCGCAATTCACCGGCGATATTTTCGGTACTGCGGGAAAAAT > SRR3722139.8396/1‑151 (MQ=60)
GAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAGACAGCATAAAGGTGGACTCGCAATTCACCGGCGATATTTTCGGTACTGCGGGAAAAATTG > SRR3722139.498576/1‑151 (MQ=60)
|
GTTTTACCACCATCATGAAAGAAAATGGCCTGAAGGCGAACAGCCTCTGTGTTGAGATCACTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAAGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAGACAGCATAAAGGTGGACTCGCAATTCACCGGCGATATTTTCGGTACTGCGGGAAAAATTG > NZ_CP009273/870344‑870601
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
