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 |
4,057,873 |
C→G |
W418C (TGG→TGC) |
yihO ← |
MFS transporter |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 4,057,873 | 0 | C | G | 100.0%
| 138.4
/ NA
| 39 | W418C (TGG→TGC) | yihO | MFS transporter |
| Reads supporting (aligned to +/- strand): ref base C (0/0); new base G (23/16); total (23/16) |
TCAATAATCAATGCAAACCGTTTTTCATTGAGTGTGTAAAAGAATCCCATCGTCAATGCAGCAATAATTGCCAGTGCACAAGGCCAGATAAAAATGAGCTGACGCAAACCCTGTAATGTCGCATCGCTTTGCGCGATGTTGGGAACATAACCAATTTGCGTCA > NZ_CP009273/4057790‑4057952
|
tCAATAATCAATGCAAACCGTTTTTCATTGAGTGTGTAAAAGAATCCCATCGTCAATGCAGCAATAATTGCCAGTGCACAAGGGCAGATa < 2:443010/90‑1 (MQ=255)
aatCAATGCAAACCGTTTTTCATTGAGTGTGTAAAAGAATCCCATCGTCAATGCAGCAATAATTGCCAGTGCACAAGGGCAGATAAAAAt > 2:658780/1‑90 (MQ=255)
aaTGCAAACCGTTTTTCATTGAGTGTGTAAAAGAATCCCATCGTCAATGCAGCAATAATTGCCAGTGCACAAGGGCAGATAAAAATGAGc > 2:636886/1‑90 (MQ=255)
tGCAAACCGTTTTTCATTGAGTGTGTAAAAGAATCCCATCGTCAATGCAGCAATAATTGCCAGTGCACAAGGGCAGATAAAAATGAGCTg < 1:620358/90‑1 (MQ=255)
aaaCCGTTTTTCATTGAGTGTGTAAAAGAATCCCATCGTCAATGCAGCAATAATTGCCAGTGCACAAGGGCAGATAAAAATGAGCTGACg > 1:210733/1‑90 (MQ=255)
aaCCGTTTTTCATTGAGTGTGTAAAAGAATCCCATCGTCAATGCAGCAATAATTGCCAGTGCACAAGGGCAGATAAAAATGAGCTGACGc > 2:749762/1‑90 (MQ=255)
ccGTTTTTCATTGAGTGTGTAAAAGAATCCCATCGTCAATGCAGCAATAATTGCCAGTGCACAAGGGCAGATAAAAATGAGCTGACGCaa < 2:367533/90‑1 (MQ=255)
gTTTTTCATTGAGTGTGTAAAAGAATCCCATCGTCAATGCAGCAATAATTGCCAGTGCACAAGGGCAGATAAAAATGAGCTGACGCAAAc < 2:628060/90‑1 (MQ=255)
tttttCATTGAGTGTGTAAAAGAATCCCATCGTCAATGCAGCAATAATTGCCAGTGCACAAGGGCAGATAAAAATGAGCTGACGCAAAcc > 1:725956/1‑90 (MQ=255)
gAGTGTGTAAAAGAATCCCATCGTCAATGCAGCAATAATTGCCAGTGCACAAGGGCAGATAAAAATGAGCTGACGCAAACCCTGTAATGt > 2:558391/1‑90 (MQ=255)
gtgtAAAAGAATCCCATCGTCAATGCAGCAATAATTGCCAGTGCACAAGGGCAGATAAAAATGAGCTGACGCAAACCCTGTAATGTCGCa > 1:368019/1‑90 (MQ=255)
gtgtAAAAGAATCCCATCGTCAATGCAGCAATAATTGCCAGTGCACAAGGGCAGATAAAAATGAGCTGACGCAAACCCTGTAATGTCGCa > 1:241359/1‑90 (MQ=255)
gtgtAAAAGAATCCCATCGTCAATGCAGCAATAATTGCCAGTGCACAAGGGCAGATAAAAATGAGCTGACGCAAACCCTGTAATGTCGCa > 2:130617/1‑90 (MQ=255)
tgtAAAAGAATCCCATCGTCAATGCAGCAATAATTGCCAGTGCACAAGGGCAGATAAAAATGAGCTGACGCAAACCCTGTAATGTCGCAt < 2:663399/90‑1 (MQ=255)
gtAAAAGAATCCCATCGTCAATGCAGCAATAATTGCCAGTGCACAAGGGCAGATAAAAATGAGCTGACGCAAACCCTGTAATGTCGCATc < 1:177019/90‑1 (MQ=255)
gtAAAAGAATCCCATCGTCAATGCAGCAATAATTGCCAGCGCACAAGGGCAGATAAAAATGAGCTGACGCAAACCCTGTAATGTCGCATc > 2:145102/1‑90 (MQ=255)
gAATCCCATCGTCAATGCAGCAATAATTGCCAGTGCACAAGGGCAGATAAAAATGAGCTGACGCAAACCCTGTAAt < 2:618914/76‑1 (MQ=255)
gAATCCCATCGTCAATGCAGCAATAATTGCCAGTGCACAAGGGCAGATAAAAATGAGCTGACGCAAACCCTGTAAt > 1:618914/1‑76 (MQ=255)
aTCCCATCGTCAATGCAGCAATAATTGCCAGTGCACAAGGGCAGATAAAAATGAGCTGACGCAAACCCTGTAATGTCGCATCGCTTTgcg > 1:199105/1‑90 (MQ=255)
aTCCCATCGTCAATGCAGCAATAATTGCCAGTGCACAAGGGCAGATAAAAATGAGCTGACGCAAACCCTGTAATGTCGCATCGCTTTgcg > 2:607231/1‑90 (MQ=255)
aTCCCATCGTCAATGCAGCAATAATTGCCAGTGCACAAGGGCAGATAAAAATGAGCTGACGCAAACCCTGTAATGTCGCATCGCTTTgcg > 2:550569/1‑90 (MQ=255)
aTCCCATCGTCAATGCAGCAATAATTGCCAGTGCACAAGGGCAGATAAAAATGAGCTGACGCAAACCCTGTAATGTCGCATCGCTTTgcg > 1:638996/1‑90 (MQ=255)
tCCCATCGTCAATGCAGCAATAATTGCCAGTGCACAAGGGCAGATAAAAATGAGCTGACGCAAACCCTGTAATGTCGCATCGCTTTgcgc < 2:241359/90‑1 (MQ=255)
tCCCATCGTCAATGCAGCAATAATTGCCAGTGCACAAGGGCAGATAAAAATGAGCTGACGCAAACCCTGTAATGTCGCATCGCTTTgcgc < 2:641977/90‑1 (MQ=255)
tCCCATCGTCAATGCAGCAATAATTGCCAGTGCACAAGGGCAGATAAAAATGAGCTGACGCAAACCCTGTAATGTCGCATCGCTTTgcgc < 2:638996/90‑1 (MQ=255)
ccATCGTCAATGCAGCAATAATTGCCAGTGCACAAGGGCAGATAAAAATGAGCTGACGCAAACCCTGTAATGTCGCATCGCTTTGCGCGa < 1:648140/90‑1 (MQ=255)
tCGTCAATGCAGCAATAATTGCCAGTGCACAAGGGCAGATAAAAATGAGCTGACGCAAACCCTGTAATGTCGCATCGCTTTGCGCGATGt > 1:557357/1‑90 (MQ=255)
tCGTCAATGCAGCAATAATTGCCAGTGCACAAGGGCAGATAAAAATGAGCTGACGCAAACCCTGTAATGTCGCATCGCTTTGCGCGATGt > 1:532826/1‑90 (MQ=255)
gTCAATGCAGCAATAATTGCCAGTGCACAAGGGCAGATAAAAATGAGCTGACGCAAACCCTGTAATGTCGCATCGCTTTGCGCGATGTTg < 1:658780/90‑1 (MQ=255)
gTCAATGCAGCAATAATTGCCAGTGCACAAGGGCAGATAAAAATGAGCTGACGCAAACCCTGTAATGTCGCATCGCTTTGCGCGATGTTg > 1:469644/1‑90 (MQ=255)
tCAATGCAGCAATAATTGCCAGTGCACAAGGGCAGATAAAAATGAGCTGACGCAAACCCTGTAATGTCGCATCGCTTTGCGCGATGTTgg < 2:307689/90‑1 (MQ=255)
aaTGCAGCAATAATTGCCAGTGCACAAGGGCAGATAAAAATGAGCTGACGCAAACCCTGTAATGTCGCATCGCTTTGCGCGATGTTGGGa < 1:282607/90‑1 (MQ=255)
gcaATAATTGCCAGTGCACAAGGGCAGATAAAAATGAGCTGACGCAAACCCTGTAATGTCGCATCGCTTTgcg < 2:132465/73‑1 (MQ=255)
gcaATAATTGCCAGTGCACAAGGGCAGATAAAAATGAGCTGACGCAAACCCTGTAATGTCGCATCGCTTTgcg > 1:132465/1‑73 (MQ=255)
gcaATAATTGCCAGTGCACAAGGGCAGATAAAAATGAGCTGACGCAAACCCTGTAATGTCGCATCGCTTTGCGCGATGTTGGGAACATaa > 1:607010/1‑90 (MQ=255)
gcaATAATTGCCAGTACACAAGGGCAGATAAAAATGAGCTGACGCAAACCCTGTAATGTCGCATCGCTTTGCGCGATGTTGGGAACATaa > 2:711027/1‑90 (MQ=255)
tGCCAGTGCACAAGGGCAGATAAAAATGAGCTGACGCAAACCCTGTAATGTCGCATCGCTTTGCGCGATGTTGGGAACATAACCAATTTg > 2:247753/1‑90 (MQ=255)
aGTGCACAAGGGCAGATAAAAATGAGCTGACGCAAACCCTGTAATGTCGCATCGCTTTGCGCGATGTTGGGAACATAACCAATTTGCGTc < 1:130617/90‑1 (MQ=255)
gTGCACAAGGGCAGATAAAAATGAGCTGACGCAAACCCTGTAATGTCGCATCGCTTTGCGCGATGTTGGGAACATAACCAATTTGCGTCa > 2:329055/1‑90 (MQ=255)
|
TCAATAATCAATGCAAACCGTTTTTCATTGAGTGTGTAAAAGAATCCCATCGTCAATGCAGCAATAATTGCCAGTGCACAAGGCCAGATAAAAATGAGCTGACGCAAACCCTGTAATGTCGCATCGCTTTGCGCGATGTTGGGAACATAACCAATTTGCGTCA > NZ_CP009273/4057790‑4057952
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ 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
GCGTTGGTTGATTTCCTCAATAATCAATGCAAACCGTTTTTCATTGAGTGTGTAAAAGAATCCCATCGTCAATGCAGCAATAATTGCCAGTGCACAAGGCCAGATAAAAATGAGCTGACGCAAACCCTGTAATGTCGCATCGCTTTGCGCGATGTTGGGAACATAACCAATTTGCGTCAGCATAATGCCTG > NZ_CP009273/4057774‑4057964
|
GCGTTGGTTGATTTCCTCAATAATCAATGCAAACCGTTTTTCATTGAGTGTGTAAAAGAATCCCATCGTCAATGCAGCAATAATTGCCAGTGCACAAGGG < SRR3722073.419694/100‑1 (MQ=60)
GCGTTGGTTGATTTCCTCAATAATCAATGCAAACCGTTTTTCATTGAGTGTGTAAAAGAATCCCATCGTCAATGCAGCAATAATTGCCAGTGCACAAGGG < SRR3722073.403735/100‑1 (MQ=60)
cagCCTCAATAATCAATGCAAACCGTTTTTCATTGAGTGTGTAAAAGAATCCCATCGTCAATGCAGCAATAATTGCCAGTGCACAAGGGCAGATAAAAAT < SRR3722073.591829/97‑1 (MQ=60)
TTTCCTCAATAATCAATGCAAACCGTTTTTCATTGAGTGTGTAAAAGAATCCCATCGTCAATGCAGCAATAATTGCCAGTGCACAAGGGCAGATAAAAAT < SRR3722073.471639/100‑1 (MQ=60)
TAATCAATGCAAACCGTTTTTCATTGAGTGTGTAAAAGAATCCCATCGTCAATGCAGCAATAATTGCCAGTGCACAAGGGCAGATAAAAATGAGCTGACG > SRR3722073.215071/1‑100 (MQ=60)
ATGCAAACCGTTTTTCATTGAGTGTGTAAAAGAATCCCATCGTCAATGCAGCAATAATTGCCAGTGCACAAGGGCAGATAAAAATGAGCTGACGCAAACC > SRR3722073.740606/1‑100 (MQ=60)
TGCAAACCGTTTTTCATTGAGTGTGTAAAAGAATCCCATCGTCAATGCAGCAATAATTGCCAGTGCACAAGGGCAGATAAAAATGAGCTGACGCAAACCC < SRR3722073.633252/100‑1 (MQ=60)
TTCATTGAGTGTGTAAAAGAATCCCATCGTCAATGCAGCAATAATTGCCAGTGCACAAGGGCAGATAAAAATGAGCTGACGCAAACCCTGTAATGTCGCA > SRR3722073.246425/1‑100 (MQ=60)
TTCATTGAGTGTGTAAAAGAATCCCATCGTCAATGCAGCAATAATTGCCAGTGCACAAGGGCAGATAAAAATGAGCTGACGCAAACCCTGTAATGTCGCA > SRR3722073.375829/1‑100 (MQ=60)
GTGTGTAAAAGAATCCCATCGTCAATGCAGCAATAATTGCCAGTGCACAAGGGCAGATAAAAATGAGCTGACGCAAACCCTGTAATGTCGCATCGCctgt > SRR3722073.631777/1‑96 (MQ=60)
GTGTAAAAGAATCCCATCGTCAATGCAGCAATAATTGCCAGTGCACAAGGGCAGATAAAAATGAGCTGACGCAAACCCTGTAATGTCGCATCGCTTTGCG > SRR3722073.203107/1‑100 (MQ=60)
GTGTAAAAGAATCCCATCGTCAATGCAGCAATAATTGCCAGTGCACAAGGGCAGATAAAAATGAGCTGACGCAAACCCTGTAATGTCGCATCGCTTTGCG > SRR3722073.652183/1‑100 (MQ=60)
GTAAAAGAATCCCATCGTCAATGCAGCAATAATTGCCAGTGCACAAGGGCAGATAAAAATGAGCTGACGCAAACCCTGTAATGTCGCATCGCTTTGCGCG < SRR3722073.180465/100‑1 (MQ=60)
AAGAATCCCATCGTCAATGCAGCAATAATTGCCAGTGCACAAGGGCAGATAAAAATGAGCTGACGCAAACCCTGTAATGTCGCATCGCTTTGCGCGATGT > SRR3722073.543953/1‑100 (MQ=60)
AAGAATCCCATCGTCAATGCAGCAATAATTGCCAGTGCACAAGGGCAGATAAAAATGAGCTGACGCAAACCCTGTAATGTCGCATCGCTTTGCGCGATGT > SRR3722073.568994/1‑100 (MQ=60)
GAATCCCATCGTCAATGCAGCAATAATTGCCAGTGCACAAGGGCAGATAAAAATGAGCTGACGCAAACCCTGTAATGTCGCATCGCTTTGCGCGATGTTG > SRR3722073.479649/1‑100 (MQ=60)
cggcagcgtcagatgtgtataagagacagGCACAAGGGCAGATAAAAATGAGCTGACGCAAACCCTGTAATGTCGCATCGCTTTGCGCGATGTTGGGAAC < SRR3722073.772182/71‑1 (MQ=60)
CCATCGTCAATGCAGCAATAATTGCCAGTGCACAAGGGCAGATAAAAATGAGCTGACGCAAACCCTGTAATGTCGCATCGCTTTGCGCGATGTTGGGAAC < SRR3722073.661484/100‑1 (MQ=60)
CGTCAATGCAGCAATAATTGCCAGTGCACAAGGGCAGATAAAAATGAGCTGACGCAAACCCTGTAATGTCGCATCGCTTTGCGCGATGTTGGGctgtctc > SRR3722073.135233/1‑93 (MQ=60)
CGTCAATGCAGCAATAATTGCCAGTGCACAAGGGCAGATAAAAATGAGCTGACGCAAACCCTGTAATGTCGCATCGCTTTGCGCGATGTTGGGAACATAA > SRR3722073.619653/1‑100 (MQ=60)
GTCAATGCAGCAATAATTGCCAGTGCACAAGGGCAGATAAAAATGAGCTGACGCAAACCCTGTAATGTCGCATCGCTTTGCGCGATGTTGGGAACATAAC < SRR3722073.672279/100‑1 (MQ=60)
AATGCAGCAATAATTGCCAGTGCACAAGGGCAGATAAAAATGAGCTGACGCAAACCCTGTAATGTCGCATCGCTTTGCGCGATGTTGGGAACATAACCAA < SRR3722073.288590/100‑1 (MQ=60)
CCAGTGCACAAGGGCAGATAAAAATGAGCTGACGCAAACCCTGTAATGTCGCATCGCTTTGCGCGATGTTGGGAACATAACCAATTTGCGTCAGCATAAT > SRR3722073.528049/1‑100 (MQ=60)
AGTGCACAAGGGCAGATAAAAATGAGCTGACGCAAACCCTGTAATGTCGCATCGCTTTGCGCGATGTTGGGAACATAACCAATTTGCGTCAGCATAATGC < SRR3722073.133347/100‑1 (MQ=60)
GCACAAGGGCAGATAAAAATGAGCTGACGCAAACCCTGTAATGTCGCATCGCTTTGCGCGATGTTGGGAACATAACCAATTTGCGTCAGCATAATGCCTG > SRR3722073.6264/1‑100 (MQ=60)
GCACAAGGGCAGATAAAAATGAGCTGACGCAAACCCTGTAATGTCGCATCGCTTTGCGCGATGTTGGGAACATAACCAATTTGCGTCAGCATAATGCCTG > SRR3722073.400658/1‑100 (MQ=60)
|
GCGTTGGTTGATTTCCTCAATAATCAATGCAAACCGTTTTTCATTGAGTGTGTAAAAGAATCCCATCGTCAATGCAGCAATAATTGCCAGTGCACAAGGCCAGATAAAAATGAGCTGACGCAAACCCTGTAATGTCGCATCGCTTTGCGCGATGTTGGGAACATAACCAATTTGCGTCAGCATAATGCCTG > NZ_CP009273/4057774‑4057964
|
| 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: ‑ |
