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 I195 R1
|
222 |
27.1 |
1551108 |
96.0% |
1489063 |
86.0 |
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%
| 89.1
/ NA
| 26 | M121V (ATG→GTG) | ydjK | MFS transporter |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (7/19); total (7/19) |
TCCACGATTTCTACCGGGCATATATTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCATCACAAAACGGCAGGCAATAAGGAAATCCATATT‑CGGTGAGAAAGCACCGACAACCATCGAGGCAATATGAATGGCC > NZ_CP009273/1854049‑1854202
|
tCCACGATTTCTACCGGGCATATATTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACggca < 1:468206/90‑1 (MQ=255)
aCCGGGCATATATTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGaa < 1:754416/90‑1 (MQ=255)
aCCGGGCATATATTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGaa < 2:415250/90‑1 (MQ=255)
aCCGGGCATATATTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGaa < 2:18155/90‑1 (MQ=255)
ccGGGCATATATTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGaaa > 1:55765/1‑90 (MQ=255)
gggCATATATTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATc > 2:214182/1‑90 (MQ=255)
ggCATATATTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATcc > 1:546465/1‑90 (MQ=255)
gTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATT‑CGGTgag > 2:193637/1‑90 (MQ=255)
aaCCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATT‑CGGTGAGAAAg < 2:560518/90‑1 (MQ=255)
aCAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATT‑CGGTGAGAAAGCACCGACaa < 2:142661/90‑1 (MQ=255)
tAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATT‑CGGTGAGAAAGCACCGACAACCATCg < 2:367004/90‑1 (MQ=255)
aCCAGTAAAGCCCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATT‑CGGTGAGAAAGCACCGACAACCATCGAg < 2:625450/90‑1 (MQ=255)
ccAGTAAAGCTCCCAGCCCAACCCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATT‑CGGTGAGAAAGCACCGACAACCATCGAgg < 1:579733/90‑1 (MQ=255)
aGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATT‑CGGTGAGAAAGCACCGACaa < 2:571114/79‑1 (MQ=255)
aGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATT‑CGGTGAGAAAGCACCGACaa < 2:31737/79‑1 (MQ=255)
aGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATT‑CGGTGAGAAAGCACCGACaa > 1:571114/1‑79 (MQ=255)
aGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATT‑CGGTGAGAAAGCACCGACaa > 1:31737/1‑79 (MQ=255)
tCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATT‑CGGTGAGAAAGCACCGACAACCATCGAGGCAATATGAAt < 2:78217/90‑1 (MQ=255)
tCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATT‑CGGTGAGAAAGCACCGACAACCATCGAGGCAATATGAAt < 2:66862/90‑1 (MQ=255)
tCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATT‑CGGTGAGAAAGCACCGACAACCATCGAGGCAATATGAAt < 1:686174/90‑1 (MQ=255)
tCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATT‑CGGTGAGAAAGCACCGACAACCATCGAGGCAATATGAAt < 1:655725/90‑1 (MQ=255)
tCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATT‑CGGTGAGAAAGCACCGACAACCATCGAGGCAATATGAAt < 1:515888/90‑1 (MQ=255)
cccAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATT‑CGGTGAGAAAGCACCGACAACCATCGAGGCAATATGAATg > 1:523525/1‑90 (MQ=255)
aGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATT‑CGGTGAGAAAGCACCGACAACCATCGAGGCAATATGAATGGcc < 2:532891/90‑1 (MQ=255)
aGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATT‑CGGTGAGAAAGCACCGACAACCATCGAGGCAATATGAATGGcc < 1:401524/90‑1 (MQ=255)
gCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCCGGTGAGAAAGCACCGACAACCATCGAGGCAATATGAATGGcc < 2:103482/90‑1 (MQ=255)
|
TCCACGATTTCTACCGGGCATATATTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCATCACAAAACGGCAGGCAATAAGGAAATCCATATT‑CGGTGAGAAAGCACCGACAACCATCGAGGCAATATGAATGGCC > NZ_CP009273/1854049‑1854202
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 28 ≤ 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
AGGAAACCCGACTTGACCACGTTCCACGATTTCTACCGGGCATATATTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCATCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGCAATATGAATGGCCTCATAGAGGATGAACGCATTTCT > NZ_CP009273/1854027‑1854225
|
AGGAAACCCGACTTGACCACGTTCCACGATTTCTACCGGGCATATATTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCAC < SRR3722073.633089/100‑1 (MQ=60)
AGGAAACCCGACTTGACCACGTTCCACGATTTCTACCGGGCATATATTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACACCCAC < SRR3722073.673910/100‑1 (MQ=60)
AAACCCGACTTGACCACGTTCCACGATTTCTACCGGGCATATATTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCAC < SRR3722073.655648/100‑1 (MQ=60)
TCCACGATTTCTACCGGGCATATATTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGG < SRR3722073.478186/100‑1 (MQ=60)
ACGATTTCTACCGGGCATATATTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAA > SRR3722073.57080/1‑100 (MQ=60)
ATTTCTACCGGGCATATATTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCC > SRR3722073.557879/1‑100 (MQ=60)
ACCGGGCATATATTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTC < SRR3722073.769679/100‑1 (MQ=60)
aacaacCGTAACCAGTAAA‑CCCCCAGCCCAACCCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGG < SRR3722073.148987/94‑1 (MQ=60)
CAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGCC > SRR3722073.583042/1‑100 (MQ=60)
CAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGCC > SRR3722073.32538/1‑100 (MQ=60)
CCAGTAAAGCTCCCAGCCCAACCCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGCAATATGAAT < SRR3722073.591840/100‑1 (MQ=60)
CAGTAAAGCTCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGCAATATGAATG > SRR3722073.534511/1‑100 (MQ=60)
TCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGCAATATGAATGGCCTCATAG < SRR3722073.526758/100‑1 (MQ=60)
TCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGCAATATGAATGGCCTCATAG < SRR3722073.669174/100‑1 (MQ=60)
TCCCAGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGCAATATGAATGGCCTCATAG < SRR3722073.700156/100‑1 (MQ=60)
AGCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGCAATATGAATGGCCTCATAGAGGA < SRR3722073.410074/100‑1 (MQ=60)
GCCCAACTCCCACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGCAATATGAATGctgtctcttataca > SRR3722073.751261/1‑86 (MQ=60)
ACCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGCAATATGAATGGCCTCATAGAGGATGAACGCATTTC < SRR3722073.129601/100‑1 (MQ=60)
CCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGCAATATGAATGGCCTCtgtctcttatacacatctgac > SRR3722073.214438/1‑79 (MQ=60)
|
AGGAAACCCGACTTGACCACGTTCCACGATTTCTACCGGGCATATATTCGGTGAAACCAGCAAACAGCGTAACCAGTAAAGCTCCCAGCCCAACTCCCATCACAAAACGGCAGGCAATAAGGAAATCCATATTCGGTGAGAAAGCACCGACAACCATCGAGGCAATATGAATGGCCTCATAGAGGATGAACGCATTTCT > NZ_CP009273/1854027‑1854225
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 23 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
