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 F4 I96 R1
|
227 |
23.3 |
882352 |
98.0% |
864704 |
126.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
747,264 |
T→C |
D124G (GAT→GGT) |
ybgQ ← |
fimbrial biogenesis outer membrane usher protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 747,264 | 0 | T | C | 100.0%
| 88.2
/ NA
| 25 | D124G (GAT→GGT) | ybgQ | fimbrial biogenesis outer membrane usher protein |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (13/12); total (13/12) |
GCAAACAAGTTGTAATCCATCAGGACACCGGCAACACCTTCTTTCCATGTAGAGGGGGGAGCCCAGTTTTCTGAGTGCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGATCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCTATCTGTGGCAAGGACTGACGGATATCTGGTTTTAAACCAAATTTATCGACCAGTGAATCATTGATGCATGGAATGGTT > NZ_CP009273/747135‑747392
|
gCAAACAAGTTGTAATCCATCAGGACACCGGCAACACCTTCTTTCCATGTAGAGGGGGGAGCCCAGTTTTCTGAGTGCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTg < 1:144102/138‑1 (MQ=255)
cATCAGGACACCGGCAACACCTTCTTTCCATGTAGAGGGGGGAGCCCAGTTTTCTGAGTGCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCgg < 1:56562/139‑1 (MQ=255)
cATCAGGACACCGGCAACACCTTCTTTCCATGTAGAGGGGGGAGCCCAGTTTTCTGAGTGCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCg < 2:427686/138‑1 (MQ=255)
aTCAGGACACCGGCAACACCTTCTTTCCATGTAGAGGGGGGAGCCCAGTTTTCTGAGTGCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCgg > 2:56562/1‑138 (MQ=255)
ccGGCAACACCTTCTTTCCATGTAGAGGGGGGAGCCCAGTTTTCTGAGTGCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAAt > 1:133982/1‑139 (MQ=255)
tGTAGAGGGGGGAGCCCAGTTTTCTGAGTGCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTc > 1:198873/1‑102 (MQ=255)
tGTAGAGGGGGGAGCCCAGTTTTCTGAGTGCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTc < 2:198873/102‑1 (MQ=255)
gagGGGGGAGCCCAGTTTTCTGAGTGCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCTATCTGTGGCa < 1:28269/139‑1 (MQ=255)
gggtAGCCCAGTTTTCTGAGTGCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTTGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCTATCTGTGGCAAGGa < 2:143834/139‑1 (MQ=255)
gggAGCCCAGTTTTCTGAGTGCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCTATCTGTGGCAAGGAc < 1:40896/139‑1 (MQ=255)
gggAGCCCAGTTTTCTGAGTGCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCTATCTGTGGCAAGGAc > 2:314742/1‑139 (MQ=255)
aGCCCAGTTTTCTGAGTGCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCTATCTGTGGCAAGGACTGa > 1:152524/1‑139 (MQ=255)
aGCCCAGTTTTCTGAGTGCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCTATCTGTGGCAAGGACTGa > 1:204221/1‑139 (MQ=255)
cTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCTATCTGTGGCa > 2:69702/1‑99 (MQ=255)
cTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCTATCTGTGGCa < 1:69702/99‑1 (MQ=255)
cTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCTATCTGTGGCAAGGACTGACGGATATCTGGTTTTAAACCAAATTTATCGAc < 2:204221/139‑1 (MQ=255)
gCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCTATCTGTGGCAAGGACTGACGGATATCTGGTTTTAAACCAAATTTATCGAcc < 2:160750/137‑1 (MQ=255)
cGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCTATCTGTGGCAAGGACTGACGGATATCTGGTTTTAAACCAAATTTATCGACCAGt < 2:45009/139‑1 (MQ=255)
tACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCTATCTGTGGCAAGGACTGACGGATATCTGGTTTTAAACCAAATTTATCGACCAGTGAAt > 2:198767/1‑138 (MQ=255)
ttCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCTATCTGTGGCAAGGACTGACGGATATCTGGTTTTAAACCAAATTTATCGACCAGTGAATCATTGATg > 1:59879/1‑138 (MQ=255)
ttCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCTATCTGTGGCAAGGACTGACGGATATCTGGTTTTAAACCAAATTTATCGACCAGTGAATCATTGATg > 1:188940/1‑138 (MQ=255)
cAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCTATCTGTGGCAAGGAc < 2:131750/85‑1 (MQ=255)
cAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCTATCTGTGGCAAGGAc > 1:131750/1‑85 (MQ=255)
gCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCTATCTGTGGCAAGGACTGACGGATATCTGGTTTTAAACCAAATTTATCGACCAGTGAATCATTGATGCATGGAAt > 1:277852/1‑139 (MQ=255)
aTTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCTATCTGTGGCAAGGACTGACGGATATCTGGTTTTAAACCAAATTTATCGACCAGTGAATCATTGATGCATGGAATGGtt > 2:26506/1‑139 (MQ=255)
|
GCAAACAAGTTGTAATCCATCAGGACACCGGCAACACCTTCTTTCCATGTAGAGGGGGGAGCCCAGTTTTCTGAGTGCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGATCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCTATCTGTGGCAAGGACTGACGGATATCTGGTTTTAAACCAAATTTATCGACCAGTGAATCATTGATGCATGGAATGGTT > NZ_CP009273/747135‑747392
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ 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: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
GGCAAACAAGTTGTAATCCATCAGGACACCGGCAACACCTTCTTTCCATGTAGAGGGGGGAGCCCAGTTTTCTGAGTGCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGATCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCTATCTGTGGCAAGGACTGACGGATATCTGGTTTTAAACCAAATTTATCGACCAGTGAATCATTGATGCATGGAATGGTTTTGTCACCCTTTTTTTGCC > NZ_CP009273/747134‑747411
|
GGCAAACAAGTTGTAATCCATCAGGACACCGGCAACACCTTCTTTCCATGTAGAGGGGGGAGCCCAGTTTTCTGAGTGCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTC < SRR3722119.145592/150‑1 (MQ=60)
CCATCAGGACACCGGCAACACCTTCTTTCCATGTAGAGGGGGGAGCCCAGTTTTCTGAGTGCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATC > SRR3722119.135384/1‑151 (MQ=60)
CCATCAGGACACCGGCAACACCTTCTTTCCATGTAGAGGGGGGAGCCCAGTTTTCTGAGTGCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATC < SRR3722119.57086/151‑1 (MQ=60)
CATTCTTTCCATGTAGAGGGGGGAGCCCAGTTTTCTGAGTGCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACctgtctcttatacacatctccgagccc > SRR3722119.200993/1‑124 (MQ=60)
GTAGAGGGGGGAGCCCAGTTTTCTGAGTGCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCTATCTGTGGCAAGGACTGAC > SRR3722119.154088/1‑151 (MQ=60)
GTAGAGGGGGGAGCCCAGTTTTCTGAGTGCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCTATCTGTGGCAAGGACTGAC > SRR3722119.206405/1‑151 (MQ=60)
cgtgggctcggagatgtgtataagagacagCGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCTATCTGTGGCAAGGACTGACGG < SRR3722119.70384/121‑1 (MQ=60)
AGAGGGGGGAGCCCAGTTTTCTGAGTGCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCTATCTGTGGCAAGGACTGACGG < SRR3722119.28519/151‑1 (MQ=60)
GGGGAGCCCAGTTTTCTGAGTGCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCTATCTGTGGCAAGGACTGACGGATATC < SRR3722119.41254/151‑1 (MQ=60)
GAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCTATCTGTGGCAAGGACTGACGGATATCTGGTTTTAAACCAAATTTATCGACCAGTGAATCATTGATGC > SRR3722119.190923/1‑150 (MQ=60)
GAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCTATCTGTGGCAAGGACTGACGGATATCTGGTTTTAAACCAAATTTATCGACCAGTGAATCATTGATGC > SRR3722119.60437/1‑150 (MQ=60)
ATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCTATCTGTGGCAAGGACTGACGGATATCctgtctcttatacacatctccgagcccacgagactaaggcgaat > SRR3722119.133089/1‑107 (MQ=60)
AATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCTATCTGTGGCAAGGACTGACGGATATCTGGTTTTAAACCAAATTTATCGACCAGTGAATCATTGATGCATGGAATG > SRR3722119.280725/1‑151 (MQ=60)
ACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCTATCTGTGGCAAGGACTGACGGATATCTGGTTTTAAACCAAATTTATCGACCAGTGAATCATTGATGCATGGAATGGTTTTGTCACCCTTTTTTTGCC > SRR3722119.164538/1‑149 (MQ=60)
|
GGCAAACAAGTTGTAATCCATCAGGACACCGGCAACACCTTCTTTCCATGTAGAGGGGGGAGCCCAGTTTTCTGAGTGCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGATCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCTATCTGTGGCAAGGACTGACGGATATCTGGTTTTAAACCAAATTTATCGACCAGTGAATCATTGATGCATGGAATGGTTTTGTCACCCTTTTTTTGCC > NZ_CP009273/747134‑747411
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
