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 I102 R1
|
278 |
39.1 |
2251254 |
95.8% |
2156701 |
87.1 |
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%
| 156.4
/ NA
| 43 | D124G (GAT→GGT) | ybgQ | fimbrial biogenesis outer membrane usher protein |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (22/21); total (22/21) |
ATGTAGAGGGGGGAGCCCAGTTTTCTGAGTGCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGATCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCTATCTGTGGCAAGGACTGACGGATATCTGGTT > NZ_CP009273/747181‑747345
|
aTGTAGAGGGGGGAGCCCAGTTTTCTGAGTGCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAAtt > 2:73665/1‑91 (MQ=255)
gagGGGGGAGCCCAGTTTTCTGAGTGCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAaga > 2:503095/1‑91 (MQ=255)
ggggggAGCCCAGTTTTCTGAGTGCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGc > 1:718654/1‑91 (MQ=255)
ggggggAGCCCAGTTTTCTGAGTGCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGc < 1:344558/91‑1 (MQ=255)
ggggggAGCCCAGTTTTCTGAGTGCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGc < 1:403644/91‑1 (MQ=255)
gggAGCCCAGTTTTCTGAGTGCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCAtt > 2:171301/1‑91 (MQ=255)
gggAGCCCAGTTTTCTGAGTGCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCAtt > 2:444676/1‑91 (MQ=255)
gAGCCCAGTTTTCTGAGTGCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCAtttt > 2:390145/1‑90 (MQ=255)
gAGCCCAGTTTTCTGAGTGCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTc > 1:564971/1‑91 (MQ=255)
gCCCAGTTTTCTGAGTGCCACGCCAGCCAGGCTTGCGGCATACTAATATTCAGTTGCTGATTGGCTTGCCCGCAATTTAAGAGCATTTCAg > 2:214917/1‑91 (MQ=255)
cAGTTTTCTGAGTGCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAgggc > 2:398258/1‑89 (MQ=255)
aGTTTTCTGAGTGCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCg < 2:608146/91‑1 (MQ=255)
aGTTTTCTGAGTGCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCg < 1:332920/91‑1 (MQ=255)
aGTTTTCTGAGTGCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCg < 1:796138/91‑1 (MQ=255)
ttttCTGAGTGCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCggg < 1:481590/91‑1 (MQ=255)
tGCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGGCGGGAACTGAAAt > 2:266583/1‑91 (MQ=255)
gCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATc < 2:628288/91‑1 (MQ=255)
cACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCaa < 1:444676/91‑1 (MQ=255)
cACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCaa < 1:73665/91‑1 (MQ=255)
cACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCaa < 1:171301/91‑1 (MQ=255)
aCGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAAt > 1:88249/1‑91 (MQ=255)
agccagGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACAcc < 1:207671/91‑1 (MQ=255)
ggCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGatct > 2:964014/1‑91 (MQ=255)
ggCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGatct > 1:300649/1‑91 (MQ=255)
ttGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGatctatc < 1:868700/91‑1 (MQ=255)
gCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCTATCtg > 1:346958/1‑91 (MQ=255)
aTACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCTATCTGTGGCa > 2:729123/1‑91 (MQ=255)
aCTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAagag > 2:871542/1‑42 (MQ=255)
aCTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAagag < 1:871542/42‑1 (MQ=255)
aCTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCTATCTGTGGCAAg < 1:749397/91‑1 (MQ=255)
aaTATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCTATCTGTGGCAAGGAc < 1:214917/91‑1 (MQ=255)
aaTATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCTATCTGTGGCAAGGAc < 2:761451/91‑1 (MQ=255)
aaTATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCTATCTGTGGCAAGGAc < 2:564971/91‑1 (MQ=255)
atatTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCTATCTGTGGCAAGGACt < 2:221885/91‑1 (MQ=255)
tCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCTATCTGTGGCAAGGACTGACg > 2:770885/1‑91 (MQ=255)
tCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCTATCTGTGGCAAGGACTGACg < 2:817611/91‑1 (MQ=255)
aGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCTATCTGTGGCAAGGACTGACGGa > 1:835357/1‑91 (MQ=255)
aGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCTATCTGTGGCAAGGACTGACGGa > 2:1003023/1‑91 (MQ=255)
gTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCTATCTGTGGCAAGGACTGACGGat > 1:574762/1‑91 (MQ=255)
gTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCTATCTGTGGCAAGGACTGACGGat > 2:220092/1‑91 (MQ=255)
tGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCTATCTGTGGCAAGGACTGAc > 1:88053/1‑85 (MQ=255)
tGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCTATCTGTGGCAAGGACTGAc < 2:88053/85‑1 (MQ=255)
tGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCTATCTGTGGCAAGGACTGACGGATATCTg < 1:27223/91‑1 (MQ=255)
ttGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCTATCTGTGGCAAGGACTGACGGATATCTGGtt > 2:875642/1‑91 (MQ=255)
|
ATGTAGAGGGGGGAGCCCAGTTTTCTGAGTGCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGATCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCTATCTGTGGCAAGGACTGACGGATATCTGGTT > NZ_CP009273/747181‑747345
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 31 ≤ 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
TCCATGTAGAGGGGGGAGCCCAGTTTTCTGAGTGCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGATCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCTATCTGTGGCAAGGACTGACGGATATCTGGTTTTAAACC > NZ_CP009273/747178‑747352
|
TCCATGTAGAGGGGGGAGCCCAGTTTTCTGAGTGCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGC > SRR3722125.734164/1‑101 (MQ=60)
GTAGAGGGGGGAGCCCAGTTTTCTGAGTGCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTC > SRR3722125.577062/1‑101 (MQ=60)
gcctagtctcgtgggctcggagatgtgtataagagacaGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGT < SRR3722125.890797/63‑1 (MQ=60)
GGGGGGAGCCCAGTTTTCTGAGTGCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTC < SRR3722125.351719/101‑1 (MQ=60)
GGGGGGAGCCCAGTTTTCTGAGTGCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTC < SRR3722125.412128/101‑1 (MQ=60)
AGTTTTCTGAGTGCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAA < SRR3722125.813517/101‑1 (MQ=60)
AGTTTTCTGAGTGCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAA < SRR3722125.339811/101‑1 (MQ=60)
TTTTCTGAGTGCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATC < SRR3722125.491750/101‑1 (MQ=60)
TCTGAGTGCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAAT > SRR3722125.89894/1‑101 (MQ=60)
CACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATC < SRR3722125.454064/101‑1 (MQ=60)
CACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATC < SRR3722125.75036/101‑1 (MQ=60)
CACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATC < SRR3722125.174619/101‑1 (MQ=60)
ACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCT > SRR3722125.306802/1‑101 (MQ=60)
AGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCTATCTG > SRR3722125.354158/1‑101 (MQ=60)
AGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCTATCTG < SRR3722125.211771/101‑1 (MQ=60)
TTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCTATCTGTGGCAAGG < SRR3722125.887885/101‑1 (MQ=60)
ACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCTATCTGTGGCAAGGACTGACGGA < SRR3722125.765574/101‑1 (MQ=60)
ACTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCTATCTGTGGCAAGGACTGACGGA > SRR3722125.853713/1‑101 (MQ=60)
CTAATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCTATCTGTGGCAAGGACTGACGGAT > SRR3722125.587068/1‑101 (MQ=60)
AATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCTATCTGTGGCAAGGACTGACGGATAT < SRR3722125.219157/101‑1 (MQ=60)
AATATTCAGTTGCTGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCTATCTGTGGCAAGGACTGACGGATAT > SRR3722125.89695/1‑101 (MQ=60)
TGATTGGCTTGACCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCTATCTGTGGCAAGGACTGACGGATATCTGGTTTTAAACC < SRR3722125.27706/101‑1 (MQ=60)
|
TCCATGTAGAGGGGGGAGCCCAGTTTTCTGAGTGCCACGCCAGCCAGGCTTGCGGAATACTAATATTCAGTTGCTGATTGGCTTGATCGAAATTGAAGAGCATTTCAGGTCGGGAACTGAAATCAATACACCGATCTATCTGTGGCAAGGACTGACGGATATCTGGTTTTAAACC > NZ_CP009273/747178‑747352
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
