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 |
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%
| 95.4
/ NA
| 28 | D124G (GAT→GGT) | ybgQ | fimbrial biogenesis outer membrane usher protein |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (13/15); total (13/15) |
ATCAGGACACCGGCAACACCTTCTTTCCATGTAGAGGGGGGAGCCCAGTTTTCTGAGTGCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGATCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCTATCTGTGGCAAGGACTGACGGATATCTGGTTTTAAACCAAATTTATCGACCAGTGAATCATTGATGCATGGA > NZ_CP009273/747153‑747386
|
aTCAGGACACCGGCAACACCTTCTTTCCATGTAGAGGGGGGAGCCCAGTTTTCTGAGTGCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAagag < 1:18394/125‑1 (MQ=255)
aTCAGGACACCGGCAACACCTTCTTTCCATGTAGAGGGGGGAGCCCAGTTTTCTGAGTGCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAagag > 2:18394/1‑125 (MQ=255)
tCAGGACACCGGCAACACCTTCTTTCCATGTAGAGGGGGGAGCCCAGTTTTCTGAGTGCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCggg > 1:390280/1‑138 (MQ=255)
aGGACACCGGCAACACCTTCTTTCCATGTAGAGGGGGGAGCCCAGTTTTCTGAGTGCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGaa < 1:102313/138‑1 (MQ=255)
ccGGCAACACCTTCTGTCCATGTAGAGGGGGGAGCCCAGTTTTCTGAGTGCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAAt < 1:310746/139‑1 (MQ=255)
gCAACACCTTCTTTCCATGTAGAGGGGGGAGCCCAGTTTTCTGAGTGCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCaa < 1:605250/139‑1 (MQ=255)
acCTTCTTTCCATGTAGAGGGGGGAGCCCAGTTTTCTGAGTGCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATacac < 2:12148/139‑1 (MQ=255)
acCTTCTTGCCATGTAGAGGGGGGAGCCCAGTTTTCTGAGTGCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATacac < 2:390280/139‑1 (MQ=255)
cttTCCATGTAGAGGGGGGAGCCCAGTTTTCTGAGTGCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGatc > 2:441352/1‑139 (MQ=255)
cATGTAGAGGGGGGAGCCCAGTTTTCTGAGTGCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGatctatct < 1:829537/139‑1 (MQ=255)
tGTAGAGGGGGGAGCCCAGTTTTCTGAGTGCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAag > 1:388758/1‑94 (MQ=255)
tGTAGAGGGGGGAGCCCAGTTTTCTGAGTGCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAag < 2:388758/94‑1 (MQ=255)
tGTAGAGGGGGGAGCCCAGTTTTCTGAGTGCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCTATCtgt > 1:225012/1‑139 (MQ=255)
gagGGGGGAGCCCAGTTTTCTGAGTGCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCTATCTGTGGCa < 2:179406/139‑1 (MQ=255)
gggAGCCCAGTTTTCTGAGTGCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCTATCTGTGGCAAGGAc < 1:702644/139‑1 (MQ=255)
ggAGCCCAGTTTTCTGAGTGCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCTATCTGTGGc < 1:424173/132‑1 (MQ=255)
ggAGCCCAGTTTTCTGAGTGCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCTATCTGTGGc > 2:424173/1‑132 (MQ=255)
aGCCCAGTTTTCTGAGTGCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCTATCTGTGGCAAGGACTGa > 1:734165/1‑139 (MQ=255)
cccAGTTTTCTGAGTGCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCTATCTGTGGCAAGGACTGACg > 2:256635/1‑139 (MQ=255)
ccAGTTTTCTGAGTGCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCTATCTGTGGCAAGGACTGACg > 1:501553/1‑138 (MQ=255)
tCTGAGTGCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCTATCTGTGGCAAGGACTGACGGATATCt < 2:501553/138‑1 (MQ=255)
tGAGTGCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCTATCTGTGGCAAGGACTGACGGATATCTGGt > 2:406587/1‑139 (MQ=255)
cTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCTATCTGTGGCAAGGACTGACGGATATCTGGTTTTAAACCAAATTTATCGAc > 2:293483/1‑139 (MQ=255)
atatTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCTATCTGTGGCAAGGACTGACGGATATCTGGTTTTAAACCAAATTTATCGACCAGTGAATCAtt < 1:256635/137‑1 (MQ=255)
ttCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCTATCTGTGGCAAGGACTGACGGATATCTGGTTTTAAACCAAATTTATCGACCAGTGAATCATTGATg > 2:616367/1‑138 (MQ=255)
cAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCTATCTGTGGCAAGGACTGACGGATATCTGGTTTTAAACCAAATTTATCGACCAGTGAATCATTGATGCa < 1:819948/138‑1 (MQ=255)
ttGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCTATCTGTGGCAAGGACTGACGGATATCTGGTTTTAAACCAAATTTATCGACCAGTGAATCATTGATGCATgg > 2:47586/1‑138 (MQ=255)
ttGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCTATCTGTGGCAAGGACTGACGGATATCTGGTTTTAAACCAAATTTATCGACCAGTGAATCATTGATGCATGGa < 1:139041/139‑1 (MQ=255)
|
ATCAGGACACCGGCAACACCTTCTTTCCATGTAGAGGGGGGAGCCCAGTTTTCTGAGTGCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGATCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCTATCTGTGGCAAGGACTGACGGATATCTGGTTTTAAACCAAATTTATCGACCAGTGAATCATTGATGCATGGA > NZ_CP009273/747153‑747386
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 35 ≤ 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
GTGGGCGGTAGCTGCTGGCAAACA‑AGTTGTAATCCATCAGGACACCGGCAACACCTTCTTTCCATGTAGAGGGGGGAGCCCAGTTTTCTGAGTGCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGATCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCTATCTGTGGCAAGGACTGACGGATATCTGGTTTTAAACCAAATTTATCGACCAGTGAATCATTGATGCATGGAATGGTTTTGTCACCCTTTTTTTGCC > NZ_CP009273/747118‑747411
|
GTGGGCGGTAGCTGCTGGCAAACA‑AGTTGTAATCCATCAGGACACCGGCAACACCTTCTTTCCATGTAGAGGGGGGAGCCCAGTTTTCTGAGTGCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGA > SRR3722120.33721/1‑150 (MQ=60)
GTAGCTGCTGGCAAACA‑AGTTGTAATCCATCAGGACACCGGCAACACCTTCTTTCCATGTAGAGGGGGGAGCCCAGTTTTCTGAGTGCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAG < SRR3722120.555731/151‑1 (MQ=60)
ACAGAGTTGTAATCCATCAGGACACCGGCAACACCTTCTTTCCATGTAGAGGGGGGAGCCCAGTTTTCTGAGTGCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTC < SRR3722120.18607/151‑1 (MQ=60)
GTTGTAATCCATCAGGACACCGGCAACACCTTCTTTCCATGTAGAGGGGGGAGCCCAGTTTTCTGAGTGCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGA > SRR3722120.396008/1‑150 (MQ=60)
CAGGACACCGGCAACACCTTCTTTCCATGTAGAGGGGGGAGCCCAGTTTTCTGAGTGCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAAT < SRR3722120.103681/150‑1 (MQ=60)
ACCGGCAACACCTTCTGTCCATGTAGAGGGGGGAGCCCAGTTTTCTGAGTGCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGA < SRR3722120.315254/151‑1 (MQ=60)
GGCAACACCTTCTTTCCATGTAGAGGGGGGAGCCCAGTTTTCTGAGTGCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCT < SRR3722120.613651/151‑1 (MQ=60)
CCTTCTTTCCATGTAGAGGGGGGAGCCCAGTTTTCTGAGTGCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGctgtctcttatacacatctccgagcccacgagact > SRR3722120.394464/1‑116 (MQ=60)
CCTTCTTTCCATGTAGAGGGGGGAGCCCAGTTTTCTGAGTGCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCTATCTGTG > SRR3722120.228165/1‑151 (MQ=60)
CCATGTAGAGGGGGGAGCCCAGTTTTCTGAGTGCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCTATCTGTGGCAAGGAC < SRR3722120.840689/151‑1 (MQ=60)
GTAGAGGGGGGAGCCCAGTTTTCTGAGTGCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCTATCTGTGGCAAGGACTGAC > SRR3722120.744098/1‑151 (MQ=60)
AGAGGGGGGAGCCCAGTTTTCTGAGTGCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCTATCTGTGGCAAGGACTGACG < SRR3722120.430367/150‑1 (MQ=60)
GAGGGGGGAGCCCAGTTTTCTGAGTGCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGctgtctcttatacacatctccgagcccacgagactaaggcgaatctcgtatgccgtcttct > SRR3722120.546104/1‑90 (MQ=60)
GAGGGGGGAGCCCAGTTTTCTGAGTGCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCTATCTGTGGCAAGGACTGACGG > SRR3722120.508734/1‑150 (MQ=60)
GGGGAGCCCAGTTTTCTGAGTGCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCTATCTGTGGCAAGGACTGACGGATATC < SRR3722120.712224/151‑1 (MQ=60)
AATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCTATCTGTGGCAAGGACTGACGGATATCTGGTTTTAAACCAAATTTATCGACCAGTGAATCATTGATGCATGGAA < SRR3722120.260351/149‑1 (MQ=60)
TCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCTATCTGTGGCAAGGACTGACGGATATCTGGTTTTAAACCAAATTTATCGACCAGTGAATCATTGATGCATGGAATGGTTT < SRR3722120.830980/150‑1 (MQ=60)
GTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCTATCTGTGGCAAGGACTGACGGATATCTGGTTTTAAACCAAATTTATCGACCAGTGAATCATTGATGCATGGAATGGTTTTGTC < SRR3722120.140922/151‑1 (MQ=60)
GACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCTATCTGTGGCAAGGACTGACGGATATCTGGTTTTAAACCAAATTTATCGACCAGTGAATCATTGATGCATGGAATGGTTTTGTCACCCTTTTTTTGCC > SRR3722120.308618/1‑150 (MQ=60)
|
GTGGGCGGTAGCTGCTGGCAAACA‑AGTTGTAATCCATCAGGACACCGGCAACACCTTCTTTCCATGTAGAGGGGGGAGCCCAGTTTTCTGAGTGCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGATCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCTATCTGTGGCAAGGACTGACGGATATCTGGTTTTAAACCAAATTTATCGACCAGTGAATCATTGATGCATGGAATGGTTTTGTCACCCTTTTTTTGCC > NZ_CP009273/747118‑747411
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
