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 I210 R1
|
226 |
19.6 |
1130256 |
95.4% |
1078264 |
84.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
1,854,126 |
T→C |
M121V (ATG→GTG) |
ydjK ← |
MFS transporter |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,854,126 | 0 | T | C | 100.0%
| 71.0
/ NA
| 23 | M121V (ATG→GTG) | ydjK | MFS transporter |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (9/14); total (9/14) |
TTCCACGATTTCTACCGGGCATATATTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCATCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGCAATATGAATGGCCTCATAG > NZ_CP009273/1854048‑1854208
|
ttCCACGATTTCTACCGGGCATATATTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACggc > 2:369616/1‑90 (MQ=255)
tCCACGATTTCTACCGGGCATATATTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACggca < 1:307962/90‑1 (MQ=255)
cTACCGGGCATATATTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAgg < 1:211272/90‑1 (MQ=255)
aCCGGGCATATATTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGaa < 1:369616/90‑1 (MQ=255)
gggCATATATTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATc > 1:145164/1‑90 (MQ=255)
atTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCg < 2:379567/90‑1 (MQ=255)
cGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTg > 2:454165/1‑90 (MQ=255)
gTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTgag > 2:165806/1‑90 (MQ=255)
aaCCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAg > 1:31285/1‑90 (MQ=255)
aGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCAcc > 2:312061/1‑90 (MQ=255)
aCAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACaa < 1:378322/90‑1 (MQ=255)
gCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCa > 2:378777/1‑90 (MQ=255)
tAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCg < 1:550081/90‑1 (MQ=255)
aCCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAg < 1:152872/90‑1 (MQ=255)
tAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAgg > 2:248253/1‑46 (MQ=255)
tAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAgg < 1:248253/46‑1 (MQ=255)
tCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGCAATATGAAt < 2:126896/90‑1 (MQ=255)
tCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGCAATATGAAt < 1:420181/90‑1 (MQ=255)
cAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGCAATATGAATGGc > 1:39705/1‑90 (MQ=255)
aGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGCAATATGAATGGcc < 2:145164/90‑1 (MQ=255)
aGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGCAATATGAATGGcc < 1:454165/90‑1 (MQ=255)
aGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGCAATATGAATGGcc < 1:378777/90‑1 (MQ=255)
aCTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGCAATATGAATGGCCTCATag < 2:231221/90‑1 (MQ=255)
|
TTCCACGATTTCTACCGGGCATATATTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCATCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGCAATATGAATGGCCTCATAG > NZ_CP009273/1854048‑1854208
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ 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: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
TCCACGATTTCTACCGGGCATATATTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCATCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGCAATATGAATGGCCTCATAGAGGATGAACGC > NZ_CP009273/1854049‑1854219
|
TCCACGATTTCTACCGGGCATATATTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGG < SRR3722092.313390/100‑1 (MQ=60)
GATTTCTACCGGGCATATATTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATC > SRR3722092.147602/1‑100 (MQ=60)
gtcgtcggcagcgtcagatgtgtataagagacagGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATAT < SRR3722092.252277/66‑1 (MQ=60)
CTACCGGGCATATATTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATAT < SRR3722092.214755/100‑1 (MQ=60)
ACCGGGCATATATTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTC < SRR3722092.376559/100‑1 (MQ=60)
TATTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAG > SRR3722092.31825/1‑100 (MQ=60)
ACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGC < SRR3722092.385483/100‑1 (MQ=60)
TAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGCAATATG < SRR3722092.561126/100‑1 (MQ=60)
ACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGCAATATGAA < SRR3722092.155442/100‑1 (MQ=60)
GTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGCAATATGAATGGC > SRR3722092.40392/1‑100 (MQ=60)
TCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGCAATATGAATGGCCTCATAG < SRR3722092.428313/100‑1 (MQ=60)
AGCCCAGCGCCCACCACAAAACGCCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGCAATATGAATGGCCTCATAGAGGA < SRR3722092.385949/100‑1 (MQ=60)
AGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGCAATATGAATGGCCTCATAGAGGA < SRR3722092.463118/100‑1 (MQ=60)
GCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGCAATATGAATGGCCTCATAGAGGAT > SRR3722092.210890/1‑100 (MQ=60)
CTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGCAATATGAATGGCCTCATAGAGGATGAACGC < SRR3722092.381085/100‑1 (MQ=60)
|
TCCACGATTTCTACCGGGCATATATTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCATCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGCAATATGAATGGCCTCATAGAGGATGAACGC > NZ_CP009273/1854049‑1854219
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
