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 F2 I194 R1
|
197 |
32.2 |
1845014 |
95.2% |
1756453 |
85.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
2,536,106 |
T→C |
E261G (GAA→GGA) |
cysP ← |
thiosulfate/sulfate ABC transporter substrate‑binding protein CysP |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 2,536,106 | 0 | T | C | 100.0%
| 119.5
/ NA
| 34 | E261G (GAA→GGA) | cysP | thiosulfate/sulfate ABC transporter substrate‑binding protein CysP |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (22/12); total (22/12) |
GTTATTCACGCGGTAGTAATAGTCGGTGATGATGGTTTGCGCCTGCGGGCTATAGAGCCAGTTCAGATAGGCTTTGGCGGCTTTTTCCGTACCGTTGGCCTGCACGTTTTTATCAACCCACGCCACCGGGAATTCCGCCAGAATGTTGGTTTTCGGAATCACCACTTCAA > NZ_CP009273/2536021‑2536190
|
gTTATTCACGCGGTAGTAATAGTCGGTGATGATGGTTTGCGCCTGCGGGCTATAGAGCCAGTTCAGATAGGCTTTGGCGGCTTTTCCCGt < 1:156002/90‑1 (MQ=255)
gTTATTCACGCGGTAGTAATAGTCGGTGATGATGGTTTGCGCCTGCGGGCTATAGAGCCAGTTCAGATAGGCTTTGGCGGCTTTTCCCGt < 1:871172/90‑1 (MQ=255)
cgcgGTAGTAATAGTCGGTGATGATGGTTTGCGCCTGCGGGCTATAGAGCCAGTTCAGATAGGCTTTGGCGGCTTTTCCCGTACCGTTgg > 2:592363/1‑90 (MQ=255)
gcgGTAGTAATAGTCGGTGATGATGGTTTGCGCCTGCGGGCTATAGAGCCAGTTCAGATAGGCTTTGGCGGCTTTTCCCGTACCGTTGGc > 2:519461/1‑90 (MQ=255)
aGTCGGTGATGATGGTTTGCGCCTGCGGGCTATAGAGCCAGTTCAGATAGGCTTTGGCGGCTTTTCCCGTACCGTTGGCCTGCACGtttt > 2:251357/1‑90 (MQ=255)
tCGGTGATGATGGTTTGCGCCTGCGGGCTATAGAGCCAGTTCAGATAGGCTTTGGCGGCTTTTCCCGTACCGTTGGCCTGCACGTTTTTa > 2:523229/1‑90 (MQ=255)
tCGGTGATGATGGTTTGCGCCTGCGGGCTATAGAGCCAGTTCAGATAGGCTTTGGCGGCTTTTCCCGTACCGTTGGCCTGCACGTTTTTa > 1:318727/1‑90 (MQ=255)
tCGGTGATGATGGTTTGCGCCTGCGGGCTATAGAGCCAGTTCAGATAGGCTTTGGCGGCTTTTCCCGTACCGTTGGCCTGCACGTTTTTa > 2:336556/1‑90 (MQ=255)
tCGGTGATGATGGTTTGCGCCTGCGGGCTATAGAGCCAGTTCAGATAGGCTTTGGCGGCTTTTCCCGTACCGTTGGCCTGCACGTTTTTa > 2:201776/1‑90 (MQ=255)
tCGGTGATGATGGTTTGCGCCTGCGGGCTATAGAGCCAGTTCAGATAGGCTTTGGCGGCTTTTCCCGTACCGTTGGCCTGCACGTTTTTa > 1:758204/1‑90 (MQ=255)
tCGGTGATGATGGTTTGCGCCTGCGGGCTATAGAGCCAGTTCAGATAGGCTTTGGCGGCTTTTCCCGTACCGTTGGCCTGCACGTTTTTa > 1:808409/1‑90 (MQ=255)
gcGGTGATGACGGTTTGCGCCTGCGGGCTATAGAGCCAGTTCAGATAGGCTTTGGCGGCTTTTCCCGTACCCTTGGCCTGCACGTTTTTa > 2:474158/2‑90 (MQ=255)
ggTGATGATGGTTTGCGCCTGCGGGCTATAGAGCCAGTTCAGATAGGCTTTGGCGGCTTTTCCCGTACCGTTGGCCTGCACGTTTTTATc < 2:836665/90‑1 (MQ=255)
ggTGATGATGGTTTGCGCCTGCGGGCTATAGAGCCAGTTCAGATAGGCTTTGGCGGCTTTTCCCGTACCGTTGGCCTGCACGTTTTTATc < 1:336556/90‑1 (MQ=255)
gTGATGATGGTTTGCGCCTGCGGGCTATAGAGCCAGTTCAGATAGGCTTTGGCGGCTTTTCCCGTACCGTTGGCCTGCACGTTTTTATCa > 2:507828/1‑90 (MQ=255)
gatgGTTTGCGCCTGCGGGCTATAGAGCCAGTTCAGATAGGCTTTGGCGGCTTTTCCCGTACCGTTGGCCTGCACGTTTTTATCAACCCa > 2:21043/1‑90 (MQ=255)
tttGCGCCTGCGGGCTATAGAGCCAGTTCAGATAGGCTTTGGCGGCTTTTCCCGTACCGTTGGCCTGCACGTTTTTATCAACCCACGCCa > 2:736/1‑90 (MQ=255)
tGCGCCTGCGGGCTATAGAGCCAGTTCAGATAGGCTTTGGCGGCTTTTCCCGTACCGTTGGCCTGCa > 1:258515/1‑67 (MQ=255)
tGCGCCTGCGGGCTATAGAGCCAGTTCAGATAGGCTTTGGCGGCTTTTCCCGTACCGTTGGCCTGCa < 2:258515/67‑1 (MQ=255)
tGCGGGCTATAGAGCCAGTTCAGATAGGCTTTGGCGGCTTTTCCCGTACCGTTGGCCTGCACGTTTTTATCAACCCACGCCACCGGGAAt > 2:52859/1‑90 (MQ=255)
cTATAGAGCCAGTTCAGATAGGCTTTGGCGGCTTTTCCCGTACCGTTGGCCTGCACGTTTTTATCAACCCACGCCACCGGGAATTCCGcc < 2:758204/90‑1 (MQ=255)
aGTTCAGATAGGCTTTGGCGGCTTTTCCCGTACCGTTGGCCTGCACGTTTTTATCAACCCACGCCACCGGGAATTCCGCCAGAATGTTgg > 1:911198/1‑90 (MQ=255)
aGTTCAGATAGGCTTTGGCGGCTTTTCCCGTACCGTTGGCCTGCACGTTTTTATCAACCCACGCCACCGGGAATTCCGCCAGAATGTTgg > 1:216994/1‑90 (MQ=255)
aGTTCAGATAGGCTTTGGCGGCTTTTCCCGTACCGTTGGCCTGCACGTTTTTATCAACCCACGCCACCGGGAATTCCGCCAGAATGTTgg > 2:384171/1‑90 (MQ=255)
aGTTCAGATAGGCTTTGGCGGCTTTTCCCGTACCGTTGGCCTGCACGTTTTTATCAACCCACGCCACCGGGAATTCCGCCAGAATGTTgg > 2:116795/1‑90 (MQ=255)
gTTCAGATAGGCTTTGGCGGC‑TTTCCCGTACCGTTGGCCTGCACGTTTTTATCAACCCACGCCACCGGGAATTCCGCCAGAATGTTGGtt > 1:694455/1‑90 (MQ=255)
aGATAGGCTTTGGCGGCTTTTCCCGTACCGTTGGCCTGCACGTTTTTATCAACCCACGCCACCGGGAATTCCGCCAGAATGTTGGTTTTc > 1:111369/1‑90 (MQ=255)
aGGCTTTGGCGGCTTTTCCCGTACCGTTGGCCTGCACGTTTTTATCAACCCACGCCACCGGGAATTCCGCCAGAATGTTGGTTTTCGGaa < 1:736/90‑1 (MQ=255)
gCTTTGGCGGCTTTTCCCGTACCGTTGGCCTGCACGTTTTTATCAACCCACGCCACCGGGAATTCCGCCAGAATGTTGGTTTTCGGAATc > 2:822154/1‑90 (MQ=255)
ttGGCGGCTTTTCCCGTACCGTTGGCCTGCACGTTTTTATCAACCCACGCCACCGGGAATTCCGCCAGAATGTTGGTTTTCGGAATcacc < 1:289369/90‑1 (MQ=255)
ttGGCGGCTTTTCCCGTACCGTTGGCCTGCACGTTTTTATCAACCCACGCCACCGGGAATTCCGCCAGAATGTTGGTTTTCGGAATcacc < 2:24167/90‑1 (MQ=255)
ttGGCGGCTTTTCCCGTACCGTTGGCCTGCACGTTTTTATCAACCCACGCCACCGGGAATTCCGCCAGAATGTTGGTTTTCGGAATcaac < 1:504503/90‑3 (MQ=255)
cTTTTCCCGTACCGTTGGCCTGCACGTTTTTATCAACCCACGCCACCGGGAATTCCGCCAGAATGTTGGTTTTCGGAATCACCACTTCaa < 1:523229/90‑1 (MQ=255)
cTTTTCCCGTACCGTTGGCCTGCACGTTTTTATCAACCCACGCCACCGGGAATTCCGCCAGAATGTTGGTTTTCGGAATCACCACTTCaa < 2:733301/90‑1 (MQ=255)
|
GTTATTCACGCGGTAGTAATAGTCGGTGATGATGGTTTGCGCCTGCGGGCTATAGAGCCAGTTCAGATAGGCTTTGGCGGCTTTTTCCGTACCGTTGGCCTGCACGTTTTTATCAACCCACGCCACCGGGAATTCCGCCAGAATGTTGGTTTTCGGAATCACCACTTCAA > NZ_CP009273/2536021‑2536190
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
GTTATTCACGCGGTAGTAATAGTCGGTGATGATGGTTTGCGCCTGCGGGCTATAGAGCCAGTTCAGATAGGCTTTGGCGGCTTTTTCCGTACCGTTGGCCTGCACGTTTTTATCAACCCACGCCACCGGGAATTCCGCCAGAATGTTGGTTTTCGGAATCACCACTTCAAAGCCCTGCGCTTC > NZ_CP009273/2536021‑2536203
|
GTTATTCACGCGGTAGTAATAGTCGGTGATGATGGTTTGCGCCTGCGGGCTATAGAGCCAGTTCAGATAGGCTTTGGCGGCTTTTCCCGTACCGTTGGCC < SRR3722072.158741/100‑1 (MQ=60)
GTTATTCACGCGGTAGTAATAGTCGGTGATGATGGTTTGCGCCTGCGGGCTATAGAGCCAGTTCAGATAGGCTTTGGCGGCTTTTCCCGTACCGTTGGCC < SRR3722072.886175/100‑1 (MQ=60)
GTAGTAATAGTCGGTGATGATGGTTTGCGCCTGCGGGCTATAGAGCCAGTTCAGATAGGCTTTGGCGGCTTTTCCCGTACCGTTGGCCTGCACGTTTTTA > SRR3722072.324306/1‑100 (MQ=60)
GTAGTAATAGTCGGTGATGATGGTTTGCGCCTGCGGGCTATAGAGCCAGTTCAGATAGGCTTTGGCGGCTTTTCCCGTACCGTTGGCCTGCACGTTTTTA > SRR3722072.822504/1‑100 (MQ=60)
GTAGTAATAGTCGGTGATGATGGTTTGCGCCTGCGGGCTATAGAGCCAGTTCAGATAGGCTTTGGCGGCTTTTCCCGTACCGTTGGCCTGCACGTTTTTA > SRR3722072.771580/1‑100 (MQ=60)
GGTGATGATGGTTTGCGCCTGCGGGCTATAGAGCCAGTTCAGATAGGCTTTGGCGGCTTTTCCCGTACCGTTGGCCTGCACGTTTTTATCAACCCACGCC < SRR3722072.342484/100‑1 (MQ=60)
GATGATGGTTTGCGCCTGCGGGCTATAGAGCCAGTTCAGATAGGCTTTGGCGGCTTTTCCCGTACCGTTGGCCTGCACGTTTTTATCctgtctcttatac > SRR3722072.262894/1‑87 (MQ=60)
CTATAGAGCCAGTTCAGATAGGCTTTGGCGGCTTTTCCCGTACCGTTGGCCTGCACGTTTTTATCAACCCACGCCACCGGGAATTCCGCCAGAATGTTGG > SRR3722072.926860/1‑100 (MQ=60)
CTATAGAGCCAGTTCAGATAGGCTTTGGCGGCTTTTCCCGTACCGTTGGCCTGCACGTTTTTATCAACCCACGCCACCGGGAATTCCGCCAGAATGTTGG > SRR3722072.220682/1‑100 (MQ=60)
TATAGAGCCAGTTCAGATAGGCTTTGGCGGC‑TTTCCCGTACCGTTGGCCTGCACGTTTTTATCAACCCACGCCACCGGGAATTCCGCCAGAATGTTGGTT > SRR3722072.706874/1‑100 (MQ=60)
GAGCCAGTTCAGATAGGCTTTGGCGGCTTTTCCCGTACCGTTGGCCTGCACGTTTTTATCAACCCACGCCACCGGGAATTCCGCCAGAATGTTGGTTTTC > SRR3722072.113427/1‑100 (MQ=60)
CAGATAGGCTTTGGCGGCTTTTCCCGTACCGTTGGCCctgtctcttatacacatctccgagcccacgagacggccgattatctcgtatgccgtcttctgc > SRR3722072.777750/1‑37 (MQ=60)
AGGCTTTGGCGGCTTTTCCCGTACCGTTGGCCTGCACGTTTTTATCAACCCACGCCACCGGGAATTCCGCCAGAATGTTGGTTTTCGGAATCACCACTTC < SRR3722072.765/100‑1 (MQ=60)
TTGGCGGCTTTTCCCGTACCGTTGGCCTGCACGTTTTTATCAACCCACGCCACCGGGAATTCCGCCAGAATGTTGGTTTTCGGAATCACCACTTCAAAGC < SRR3722072.294365/100‑1 (MQ=60)
TTGGCGGCTTTTCCCGTACCGTTGGCCTGCACGTTTTTATCAACCCACGCCACCGGGAATTCCGCCAGAATGTTGGTTTTCGGAATCAACACTTCAAAGC < SRR3722072.513607/100‑1 (MQ=60)
CTTTTCCCGTACCGTTGGCCTGCACGTTTTTATCAACCCACGCCACCGGGAATTCCGCCAGAATGTTGGTTTTCGGAATCACCACTTCAAAGCCCTGCGC < SRR3722072.532648/100‑1 (MQ=60)
TTCCCGTACCGTTGGCCTGCACGTTTTTATCAACCCACGCCACCGGGAATTCCGCCAGAATGTTGGTTTTCGGAATCACCACTTCAAAGCCCTGCGCTTC > SRR3722072.31440/1‑100 (MQ=60)
TTCCCGTACCGTTGGCCTGCACGTTTTTATCAACCCACGCCACCGGGAATTCCGCCAGAATGTTGGTTTTCGGAATCACCACTTCAAAGCCCTGCGCTTC > SRR3722072.13540/1‑100 (MQ=60)
|
GTTATTCACGCGGTAGTAATAGTCGGTGATGATGGTTTGCGCCTGCGGGCTATAGAGCCAGTTCAGATAGGCTTTGGCGGCTTTTTCCGTACCGTTGGCCTGCACGTTTTTATCAACCCACGCCACCGGGAATTCCGCCAGAATGTTGGTTTTCGGAATCACCACTTCAAAGCCCTGCGCTTC > NZ_CP009273/2536021‑2536203
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
