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 I199 R1
|
220 |
57.5 |
3163680 |
97.0% |
3068769 |
86.1 |
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 | 97.7%
| 129.7
/ ‑4.0
| 43 | M121V (ATG→GTG) | ydjK | MFS transporter |
| Reads supporting (aligned to +/- strand): ref base T (0/1); new base C (17/25); total (17/26) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.22e-01 |
CGTTCCACGATTTCTACCGGGCATATATTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCATCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGCAATATGAATGGCCTCATAGA > NZ_CP009273/1854046‑1854209
|
cGTTCCACGATTTCTACCGGGCATATATTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACg > 2:1154041/1‑90 (MQ=255)
cGTTCCACGATTTCTACCGGGCATATATTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACg > 1:1154263/1‑90 (MQ=255)
cGTTCCACGATTTCTACCGGGCATATATTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACg > 1:1060717/1‑90 (MQ=255)
ttCCACGATTTCTACCGGGCATATATTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACggc < 1:335276/90‑1 (MQ=255)
ccACGATTTCTCCCGGGCATATATTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACggcag < 2:731794/90‑1 (MQ=255)
ccACGATTTCTACCGGGCATATATTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACggcag < 1:1329687/90‑1 (MQ=255)
ccACGATTTCTACCGGGCATATATTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACggcag < 2:711656/90‑1 (MQ=255)
ccACGATTTCTACCGGGCATATATTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACggcag < 2:735386/90‑1 (MQ=255)
aCGATTTCTACCGGGCATATATTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACggcaggc < 2:1123344/90‑1 (MQ=255)
aCGATTTCTACCGGGCATATATTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACggcaggc > 1:786187/1‑90 (MQ=255)
tttCTACCGGGCATATATTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATa > 2:1371389/1‑90 (MQ=255)
tCTACCGGGCATATATTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAg > 2:19401/1‑90 (MQ=255)
tACCGGGCATATATTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGa > 2:840286/1‑90 (MQ=255)
tACCGGGCATATATTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGa > 2:354424/1‑90 (MQ=255)
tACCGGGCATATATTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGa > 1:973818/1‑90 (MQ=255)
aCCGGGCATATATTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCATCACAAAACGGCAGGCAATAAGGaa < 2:687065/90‑1 (MQ=255)
tatatTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCatat > 1:521563/1‑90 (MQ=255)
tCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCCGCCCAACTCCCACCCCAAAACGGCAGGCAATAAGGAAATCCATATTCGGt < 1:1180254/90‑1 (MQ=255)
cGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTg > 1:353712/1‑90 (MQ=255)
cGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTg > 1:993539/1‑90 (MQ=255)
cAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCAc < 2:1100160/90‑1 (MQ=255)
cGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCAt < 1:1086423/90‑1 (MQ=255)
gTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATc < 2:563838/90‑1 (MQ=255)
tAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCg < 2:1541286/90‑1 (MQ=255)
tAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCg < 1:1335813/90‑1 (MQ=255)
ccAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAgg < 2:1066664/90‑1 (MQ=255)
aGTAAAGCTCCCGGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGCa > 1:735119/1‑90 (MQ=255)
aGTAAAGCTCCCAGCCCAACTCCCCCCCCAAAACGGAAGGCAATAACGAAATCCATGTTCGGTGAGAAAGCACCGCCAACCATCGAGGCa < 1:876781/90‑1 (MQ=255)
gTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGCaa > 2:541366/1‑90 (MQ=255)
cTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGCAATATGaa > 1:658993/1‑90 (MQ=255)
tCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGCAATATGAAt < 2:893107/90‑1 (MQ=255)
tCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGCAATATGAAt < 1:810723/90‑1 (MQ=255)
tCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGCAATATGAAt < 2:632179/90‑1 (MQ=255)
tCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGCAATATGAAt < 2:483258/90‑1 (MQ=255)
tCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGCAATATGAAt < 2:353712/90‑1 (MQ=255)
tCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGCAATATGAAt < 1:963271/90‑1 (MQ=255)
tCCCAGCCCAACTCCCACCACAAAACGCCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGCAATATGAAt < 2:1191593/90‑1 (MQ=255)
ccAGACCAAATCCCACCAAAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGCAATATGAATgg < 1:523403/90‑1 (MQ=255)
aGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGCAATATGAATGGcc < 2:1546958/90‑1 (MQ=255)
cccAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGCAATATGAATGGCCTc < 1:1557470/90‑1 (MQ=255)
cAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGCAATATGAATGGCCTCAt < 2:472513/90‑1 (MQ=255)
aCTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGCAATATGAATGGCCTCATag > 2:1066154/1‑90 (MQ=255)
cTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGCAATATGAATGGCCTCATaga > 1:923056/1‑90 (MQ=255)
|
CGTTCCACGATTTCTACCGGGCATATATTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCATCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGCAATATGAATGGCCTCATAGA > NZ_CP009273/1854046‑1854209
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 23 ≤ 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
AAACCCGACTTGACCACGTTCCACGATTTCTACCGGGCATATATTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCATCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGCAATATGAATGGCCTCATAGAGGATGAACGCATTTCT > NZ_CP009273/1854030‑1854225
|
AAACCCGACTTGACCACGTTCCACGATTTCTACCGGGCATATATTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCAC < SRR3722078.1056040/100‑1 (MQ=60)
GACTTGACCACGTTCCACGATTTCTACCGGGCATATATTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACG > SRR3722078.1076679/1‑100 (MQ=60)
GACTTGACCACGTTCCACGATTTCTACCGGGCATATATTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACG > SRR3722078.1172092/1‑100 (MQ=60)
ACCACGTTCCACGATTTCTACCGGGCATATATTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGC > SRR3722078.796440/1‑100 (MQ=60)
TTCCACGATTTCTACCGGGCATATATTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAG < SRR3722078.339378/100‑1 (MQ=60)
CCACGATTTCTACCGGGCATATATTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGA > SRR3722078.987790/1‑100 (MQ=60)
CCACGATTTCTACCGGGCATATATTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGA < SRR3722078.1350967/100‑1 (MQ=60)
CTACCGGGCATATATTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATAT > SRR3722078.527729/1‑100 (MQ=60)
GGCATATATTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTG > SRR3722078.1007987/1‑100 (MQ=60)
GGCATATATTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTG > SRR3722078.358025/1‑100 (MQ=60)
TCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCCGCCCAACTCCCACCCCAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCAC < SRR3722078.1198684/100‑1 (MQ=60)
CAGCGTAACCAGTAAAGCTCCCGGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGCA > SRR3722078.744345/1‑100 (MQ=60)
CGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGCAATA < SRR3722078.1102885/100‑1 (MQ=60)
gatgtgtataagagacagGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGCAATATG < SRR3722078.377871/82‑1 (MQ=60)
TAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGCAATATG < SRR3722078.1357229/100‑1 (MQ=60)
ACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGCAATATGAA > SRR3722078.666537/1‑100 (MQ=60)
AGTAAAGCTCCCAGCCCAACTCCCCCCCCAAAACGGAAGGCAATAACGAAATCCATGTTCGGTGAGAAAGCACCGCCAACCATCGAGGCAATATGAATGG < SRR3722078.888555/100‑1 (MQ=60)
TCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGCAATATGAATGGCCTCATAG < SRR3722078.976966/100‑1 (MQ=60)
TCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGCAATATGAATGGCCTCATAG < SRR3722078.821443/100‑1 (MQ=60)
CCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGCAATATGAATGGCCTCATAGA > SRR3722078.935693/1‑100 (MQ=60)
CCAGACCAAATCCCACCAAAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGCAATATGAATGGCCTCATAGAG < SRR3722078.529593/100‑1 (MQ=60)
GCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGCAATATGAATGGCCTCATAGAGGAT > SRR3722078.195519/1‑100 (MQ=60)
GCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGCAATATGAATGGCCTCATAGAGGAT > SRR3722078.219155/1‑100 (MQ=60)
CCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGCAATATGAATGGCCTCATAGAGGATG < SRR3722078.1582821/100‑1 (MQ=60)
CAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGCAATATGAATGGCCTCATAGAGGATGAA > SRR3722078.1371062/1‑100 (MQ=60)
TCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGCAATATGAATGGCCTCATAGAGGATGAACGCATTTCT > SRR3722078.344407/1‑100 (MQ=60)
CCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGCAATATGAATGGCCTCATAGAGGATGAACGCATTTCT > SRR3722078.1041379/1‑100 (MQ=60)
CCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGCAATATGAATGGCCTCATAGAGGATGAACGCATTTCT > SRR3722078.34517/1‑100 (MQ=60)
CCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGCAATATGAATGGCCTCATAGAGGATGAACGCATTTCT > SRR3722078.1338507/1‑100 (MQ=60)
|
AAACCCGACTTGACCACGTTCCACGATTTCTACCGGGCATATATTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCATCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGCAATATGAATGGCCTCATAGAGGATGAACGCATTTCT > NZ_CP009273/1854030‑1854225
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
