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 |
|
A1 F5 I97 R1
|
275 |
44.0 |
1733530 |
96.5% |
1672856 |
122.0 |
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%
| 74.6
/ NA
| 21 | Q678Q (CAA→CAG) | pdeI | EAL domain‑containing protein |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (9/12); total (9/12) |
CATGAGCGTTTTACCACCATCATGAAAGAAAATGGCCTGAAGGCGAACAGCCTCTGTGTTGAGATCACTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAAGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAGACAGCATAAAGGTGGACTCGCAATTCACCGGCGATATTTTCGGTACTGCGGGAAA > NZ_CP009273/870337‑870596
|
cATGAGCGTTTTACCACCATCATGAAAGAAAATGGCCTGAAGGCGAACAGCCTCTGTGTTGAGATCACTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTa < 1:498501/138‑1 (MQ=255)
cGTTTTACCACCATCATGAAAGAAAATGGCCTGAAGGCGAACAGCCTCTGTGTTGAGATCACTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGatat < 2:727531/139‑1 (MQ=255)
gCCTCTGTGTTGAGATCACTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATtgat < 1:139231/104‑1 (MQ=255)
gCCTCTGTGTTGAGATCACTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATtgat > 2:139231/1‑104 (MQ=255)
ttGAGATCACTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGaaa < 2:345419/138‑1 (MQ=255)
aCTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATc > 1:214607/1‑136 (MQ=255)
aCTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATc > 1:826957/1‑136 (MQ=255)
aCTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCa < 1:853332/138‑1 (MQ=255)
cTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAGa < 1:611723/139‑1 (MQ=255)
cTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAGa < 2:214607/139‑1 (MQ=255)
aaaCCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGCCTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAGAc < 2:369511/137‑1 (MQ=255)
aaCCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAGACAg > 1:312409/1‑138 (MQ=255)
aGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAGACAGCATAAAGGTGGa > 1:484114/1‑139 (MQ=255)
cGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAGACAGCATAAAGGTGGACt < 2:644401/139‑1 (MQ=255)
tATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAGACAGCATAAAGGTGGACTCGCAATTCACCGGCGat < 2:76941/138‑1 (MQ=255)
cTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAGa < 1:551920/86‑1 (MQ=255)
cTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAGa > 2:551920/1‑86 (MQ=255)
cTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAGACAGCATAAAGGTGGACTCGCAATTCACCGGCGATATTTTCGGTACTGCGGGa > 1:564091/1‑138 (MQ=255)
gCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAGACAGCATAAAGGTGGACTCGCAATTCACCGGCGATATTTTCGGTACTGCGGGaaa > 2:274953/1‑138 (MQ=255)
cGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAGa > 1:131543/1‑83 (MQ=255)
cGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAGa < 2:131543/83‑1 (MQ=255)
|
CATGAGCGTTTTACCACCATCATGAAAGAAAATGGCCTGAAGGCGAACAGCCTCTGTGTTGAGATCACTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAAGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAGACAGCATAAAGGTGGACTCGCAATTCACCGGCGATATTTTCGGTACTGCGGGAAA > NZ_CP009273/870337‑870596
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ 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
GTTAAACGAACCACACTTTCATGAGCGTTTTACCACCATCATGAAAGAAAATGGCCTGAAGGCGAACAGCCTCTGTGTTGAGATCACTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAAGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAGACAGCATAAAGGTGGACTCGCAATTCACCGGCGATATTTTCGGTACTGCGGGAAAAATTGTGCGCATTATTTTCGAC > NZ_CP009273/870318‑870618
|
GTTAAACGAACCACACTTTCATGAGCGTTTTACCACCATCATGAAAGAAAATGGCCTGAAGGCGAACAGCCTCTGTGTTGAGATCACTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAG < SRR3722120.363255/151‑1 (MQ=60)
gatgtgtataagagacaGTTTTACCACCATCATGAAAGAAAATGGCCTGAAGGCGAACAGCCTCTGTGTTGAGATCACTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGG < SRR3722120.706212/134‑1 (MQ=60)
TCATGAGCGTTTTACCACCATCATGAAAGAAAATGGCCTGAAGGCGAACAGCCTCTGTGTTGAGATCACTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGAT < SRR3722120.505663/150‑1 (MQ=60)
gctcggagatgtgtataagagacagGAAGGCGAACAGCCTCTGTGTTGAGATCACTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCAC < SRR3722120.141115/126‑1 (MQ=60)
atatttcaggttgtttttttttttttttcaagcagaagacggcatacgagattcgccttagtctcgtgggctcggagatgtgtataagagacagATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCAC < SRR3722120.149868/55‑1 (MQ=60)
GTGTTGAGATCACTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCC > SRR3722120.838079/1‑148 (MQ=60)
GTGTTGAGATCACTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCC > SRR3722120.217575/1‑148 (MQ=60)
GAGATCACTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAGACAGC > SRR3722120.316938/1‑150 (MQ=60)
CACTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAGACAGCATAAA < SRR3722120.864766/150‑1 (MQ=60)
ACTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAGACAGCATAAAGG < SRR3722120.620205/151‑1 (MQ=60)
tcgccttagtctcgtgggctcggagatgtgtataagagacagATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAGACAGCATAAAGG < SRR3722120.559690/108‑1 (MQ=60)
AACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAGACAGCATAAAGGTGGAC > SRR3722120.491085/1‑151 (MQ=60)
ATATTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAGACAGCATAAAGGTGGACTCGCAATTCACCGGCGATATTTTCGGTACTGCGGGAA > SRR3722120.571982/1‑150 (MQ=60)
TTGAACAACTGCGTAAACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAGACAGCATAAAGGctgtctcttatacacatctccgagcccacgagactaaggcgaatct > SRR3722120.133317/1‑105 (MQ=60)
AACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAGACAGCATAAAGGTGGACTCGCAATTCACCGGCGATATTTTCGGTACTGCGGGAAAAATTGTGCGCATTATTTT > SRR3722120.228124/1‑151 (MQ=60)
AACAGGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAGACAGCATAAAGGTGGACTCGCAATTCACCGGCGATATTTTCGGTACTGCGGGAAAAATTGTGCGCATTATTTT > SRR3722120.179140/1‑151 (MQ=60)
GGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAGACAGCATAAAGGTGGACTCGCAATTCACCGGCGATATTTTCGGTACTGCGGGAAAAATTGTGCGCATTATTTTCGAC > SRR3722120.689110/1‑151 (MQ=60)
|
GTTAAACGAACCACACTTTCATGAGCGTTTTACCACCATCATGAAAGAAAATGGCCTGAAGGCGAACAGCCTCTGTGTTGAGATCACTGAAACCGTGATCGAGCGAATTAATGAACATTTTTATCTCAATATTGAACAACTGCGTAAACAAGGGGTACGGATATCGATTGATGACTTTGGCACCGGTTTGTCAAACCTGAAACGTTTTTATGAAATTAATCCAGACAGCATAAAGGTGGACTCGCAATTCACCGGCGATATTTTCGGTACTGCGGGAAAAATTGTGCGCATTATTTTCGAC > NZ_CP009273/870318‑870618
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
