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 I211 R1
|
223 |
18.0 |
1007644 |
96.3% |
970361 |
85.7 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
1,952,429 |
T→C |
intergenic (‑40/+348) |
torY ← / ← cutC |
NapC/NirT family cytochrome c/copper homeostasis protein CutC |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,952,429 | 0 | T | C | 100.0%
| 39.6
/ NA
| 13 | intergenic (‑40/+348) | torY/cutC | NapC/NirT family cytochrome c/copper homeostasis protein CutC |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (4/9); total (4/9) |
AACCGCTATCAGCAAAAACAATAACCCAATGCGTTTTTTCCCTCGCATAGATTCCTCTAATTAAATTACTGGACACCGAAATCATTGTATAATTAAATATACAACGAATTAACCGCTTGCATAATTAGGCACAACACTGCCTGAAACAATCGATAAAGAATATGATTTATTACA > NZ_CP009273/1952342‑1952515
|
aaCCGCTATCAGCAAAAACAATAACCCAATGCGTTTTTTCCCTCGCATAGATTCCTCTAATTAAATTACTGGACACCGAAATCATTGcat < 2:280360/90‑1 (MQ=255)
aTGCGTTTTTTCCCTCGCATAGATTCCTCTAATTAAATTACTGGACACCGAAATCATTGCATAATTAAATATACAACGAATTAACCGCt < 1:233668/89‑1 (MQ=255)
aTGCGTTTTTTCCCTCGCATAGATTCCTCTAATTAAATTACTGGACACCGAAATCATTGCATAATTAAATATACAACGAATTAACCGCt > 2:233668/1‑89 (MQ=255)
ttCCCTCGCATAGATTCCTCTAATTAAATTACTGGACACCGAAATCATTGCATAATTAAATATACAACGAATTAACCGCTTGCATAATTa < 1:310835/90‑1 (MQ=255)
tAGATTCCTCTAATTAAATTACTGGACACCGAAATCATTGCATAATTAAATATACAACGAATTAACCGCTTGCATAATTAGGCACAacac < 2:228754/90‑1 (MQ=255)
aattaCTGGACACCGAAATCATTGCATAATTAAATATACAACGAATTAACCGCTTGCATAATTAGGCACAACACTGCCTGAAACAATCGa > 1:6244/1‑90 (MQ=255)
taCTGGACACCGAAATCATTGCATAATTAAATATACAACGAATTAACCGCTTGCATAATTAGGCACAACACTGCCTGAAACAATCGATaa > 1:15197/1‑90 (MQ=255)
taCTGGACACCGAAATCATTGCATAATTAAATATACAACGAATTAACCGCTTGCATAATTAGGCACAACACTGCCTGAAACAATCGATaa < 2:310638/90‑1 (MQ=255)
cTGGACACCGAAATCATTGCATAATTAAATATACAACGAATTAACCGCTTGCATAATTAGGCACAACACTGCCTGAAACAATCGATAAAg < 2:319634/90‑1 (MQ=255)
cacCGAAATCATTGCATAATTAAATATACAACGAATTAACCGCTTGCATAATTAGGCACAACACTGCCTGAAACAATCGATAAAGAatat < 1:149944/90‑1 (MQ=255)
ccGAAATCATTGCATAATTAAATATACAACGAATTAACCGCTTGCATAATTAGGCACAACACTGCCTGAAACAATCGATAAAGAATATGa > 2:196643/1‑90 (MQ=255)
gAAATCATTGCATAATTAAATATACAACGAATTAACCGCTTGCATAATTAGGCACAACACTGCCTGAAACAATCGATAAAGAATATGAtt < 2:111253/90‑1 (MQ=255)
aaaTCATTGCATAATTAAATATACAACGAATTAACCGCTTGCATAATTAGGCACAACACTGCCTGAAACAATCGATAAAGAATATGAttt < 2:108649/90‑1 (MQ=255)
ttGCATAATTAAATATACAACGAATTAACCGCTTGCATAATTAGGCACAACACTGCCTGAAACAATCGATAAAGAATATGATTTATTACa < 1:352899/90‑1 (MQ=255)
|
AACCGCTATCAGCAAAAACAATAACCCAATGCGTTTTTTCCCTCGCATAGATTCCTCTAATTAAATTACTGGACACCGAAATCATTGTATAATTAAATATACAACGAATTAACCGCTTGCATAATTAGGCACAACACTGCCTGAAACAATCGATAAAGAATATGATTTATTACA > NZ_CP009273/1952342‑1952515
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
AATGCGTTTTTTCCCTCGCATAGATTCCTCTAATTAAATTACTGGACACCGAAATCATTGTATAATTAAATATACAACGAATTAACCGCTTGCATAATTAGGCACAACACTGCCTGAAACAATCGATAAAGAATATGATTTATTACAATGTAATCAT > NZ_CP009273/1952369‑1952525
|
AATGCGTTTTTTCCCTCGCATAGATTCCTCTAATTAAATTACTGGACACCGAAATCATTGCATAATTAAATATACAACGAATTAACCGCTTGCATAATTA < SRR3722094.236943/100‑1 (MQ=60)
TTCCCTCGCATAGATTCCTCTAATTAAATTACTGGACACCGAAATCATTGCATAATTAAATATACAACGAATTAACCGCTTGCATAATTAGGCACAACAC < SRR3722094.315713/100‑1 (MQ=60)
CCTCTAATTAAATTACTGGACACCGAAATCATTGCATAATTAAATATACAACGAATTAACCGCTTGCATAATTAGGCACAACACTGCCTGAAACAATCGA > SRR3722094.6341/1‑100 (MQ=60)
CTAATTAAATTACTGGACACCGAAATCATTGCATAATTAAATATACAACGAATTAACCGCTTGCATAATTAGGCACAACACTGCCTGAAACAATCGATAA > SRR3722094.15427/1‑100 (MQ=60)
CACCGAAATCATTGCATAATTAAATATACAACGAATTAACCGCTTGCATAATTAGGCACAACACTGCCTGAAACAATCGATAAAGAATATGATTTATTAC < SRR3722094.152039/100‑1 (MQ=60)
TTGCATAATTAAATATACAACGAATTAACCGCTTGCATAATTAGGCACAACACTGCCTGAAACAATCGATAAAGAATATGATTTATTACAATGTAATCAT < SRR3722094.358795/100‑1 (MQ=60)
|
AATGCGTTTTTTCCCTCGCATAGATTCCTCTAATTAAATTACTGGACACCGAAATCATTGTATAATTAAATATACAACGAATTAACCGCTTGCATAATTAGGCACAACACTGCCTGAAACAATCGATAAAGAATATGATTTATTACAATGTAATCAT > NZ_CP009273/1952369‑1952525
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
