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 I205 R1
|
220 |
17.5 |
961422 |
97.1% |
933540 |
86.5 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
1,155,022 |
G→T |
T662T (ACC→ACA) |
fhuE ← |
ferric‑rhodotorulic acid/ferric‑coprogen receptor FhuE |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,155,022 | 0 | G | T | 100.0%
| 30.0
/ NA
| 9 | T662T (ACC→ACA) | fhuE | ferric‑rhodotorulic acid/ferric‑coprogen receptor FhuE |
| Reads supporting (aligned to +/- strand): ref base G (0/0); new base T (3/6); total (3/6) |
GAAGTTTTTCGTCACCTGGTAGCGGGTGAAGAGATCCACCAGCGCGTAGCTACCTTGCTCGGCGCGGAAGGTGCCATACGGCGTCACGGTGTCGGTATACACGCGATTTTGCCAGTTAACACCACCGCCGACCGTCAACTCTGGCATGACAGGC > NZ_CP009273/1154935‑1155088
|
gaAGTTTTTCGTCACCTGGTAGCGGGTGAAGAGATCCACCAGCGCGTAGCTACCTTGCTCGGCGCGGAAGGTGCCATACGGCGTCACTgt < 1:155651/90‑1 (MQ=255)
ttttCGTCACCTGGTAGCGGGTGAAGAGATCCACCAGCGCGTAGCTACCTTGCTCGGCGCGGAAGGTGCCATACGGCGTCACTGTGTCgg < 2:245239/90‑1 (MQ=255)
aCCTGGTAGCGGGTGAAGAGATCCACCAGCGCGTAGCTACCTTGCTCGGCGCGGAAGGTGCCATACGGCGTCACTGTGTCGGTATACAcg < 1:263884/90‑1 (MQ=255)
aCCTGGTAGCGGGTGAAGAGATCCACCAGCGCGTAGCTACCTTGCTCGGCGCGGAAGGTGCCATACGGCGTCACTGTGTCGGTATACAcg < 1:279601/90‑1 (MQ=255)
gaTCCACCAGCGCGTAGCTACCTTGCTCGGCGCGGAAGGTGCCATACGGCGTCACTGTGTCGGTATACACGCGATTTTGCCAGTTAacac > 1:314935/1‑90 (MQ=255)
aGCGCGTAGCTACCTTGCTCGGCGCGGAAGGTGCCATACGGCGTCACTGTGTCGGTATACACGCGATTTTGCCAGTTAACACCAccgccg < 1:104229/90‑1 (MQ=255)
gCTCGGCGCGGAAGGTGCCATACGGCGTCACTGTGTCGGTATACACGCGATTTTGCCAGTTAACACCACCGCCGACCGTCAACTCTGGCa > 1:271380/1‑90 (MQ=255)
gcgcGGAAGGTGCCATACGGCGTCACTGTGTCGGTATACACGCGATTTTGCCAGTTAACACCACCGCCGACCGTCAACTCTGGCATGACa > 1:39657/1‑90 (MQ=255)
cgGAAGGTGCCATACGGCGTCACTGTGTCGGTATACACGCGATTTTGCCAGTTAACACCACCGCCGACCGTCAACTCTGGCATGACAGGc < 1:179466/90‑1 (MQ=255)
|
GAAGTTTTTCGTCACCTGGTAGCGGGTGAAGAGATCCACCAGCGCGTAGCTACCTTGCTCGGCGCGGAAGGTGCCATACGGCGTCACGGTGTCGGTATACACGCGATTTTGCCAGTTAACACCACCGCCGACCGTCAACTCTGGCATGACAGGC > NZ_CP009273/1154935‑1155088
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ 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
ACGAGAAGTTTTTCGTCACCTGGTAGCGGGTGAAGAGATCCACCAGCGCGTAGCTACCTTGCTCGGCGCGGAAGGTGCCATACGGCGTCACGGTGTCGGTATACACGCGATTTTGCCAGTTAACACCACCGCCGACCGTCAACTCTGGCATGACAGGCAACCGATAGCTGGTGAACATTTTAACCGTGGT > NZ_CP009273/1154931‑1155120
|
ACGAGAAGTTTTTCGTCACCTGGTAGCGGGTGAAGAGATCCACCAGCGCGTAGCTACCTTGCTCGGCGCGGAAGGTGCCATACGGCGTCACTGTGTCGGT < SRR3722087.8953/100‑1 (MQ=60)
AGAAGTTTTTCGTCACCTGGTAGCGGGTGAAGAGATCCACCAGCGCGTAGCTACCTTGCTCGGCGCGGAAGGTGCCATACGGCGTCACTGTGTCGGTATA < SRR3722087.126535/100‑1 (MQ=60)
GAAGTTTTTCGTCACCTGGTAGCGGGTGAAGAGATCCACCAGCGCGTAGCTACCTTGCTCGGCGCGGAAGGTGCCATACGGCGTCACTGTGTCGGTATAC < SRR3722087.157082/100‑1 (MQ=60)
ACCTGGTAGCGGGTGAAGAGATCCACCAGCGCGTAGCTACCTTGCTCGGCGCGGAAGGTGCCATACGGCGTCACTGTGTCGGTATACACGCGATTTTGCC < SRR3722087.266477/100‑1 (MQ=60)
ACCTGGTAGCGGGTGAAGAGATCCACCAGCGCGTAGCTACCTTGCTCGGCGCGGAAGGTGCCATACGGCGTCACTGTGTCGGTATACACGCGATTTTGCC < SRR3722087.282375/100‑1 (MQ=60)
CGGGTGAAGAGATCCACCAGCGCGTAGCTACCTTGCTCGGCGCGGAAGGTGCCATACGGCGTCACTGTGTCGGTATACACGCGATTTTGCCAGTTAACAC > SRR3722087.318288/1‑100 (MQ=60)
AGCGCGTAGCTACCTTGCTCGGCGCGGAAGGTGCCATACGGCGTCACTGTGTCGGTATACACGCGATTTTGCCAGTTAACACCACCGCCGACCGTCAACT < SRR3722087.105230/100‑1 (MQ=60)
TAGCTACCTTGCTCGGCGCGGAAGGTGCCATACGGCGTCACTGTGTCtgtctcttatacacatctccgagcccacgagactaaggcgaatctcgtatgcc > SRR3722087.340676/1‑47 (MQ=60)
TAGCTACCTTGCTCGGCGCGGAAGGTGCCATACGGCGTCACTGTGTCGGTATACACGCGATTTTGCCAGTTAACACCACCGCCGACCGTCAACTCTGGCA > SRR3722087.274049/1‑100 (MQ=60)
ACCTTGCTCGGCGCGGAAGGTGCCATACGGCGTCACTGTGTCGGTATACACGCGATTTTGCCAGTTAACACCACCGCCGACCGTCAACTCTGGCATGACA > SRR3722087.39977/1‑100 (MQ=60)
CGGAAGGTGCCATACGGCGTCACTGTGTCGGTATACACGCGATTTTGCCAGTTAACACCACCGCCGACCGTCAACTCTGGCATGACAGGCAACCGATAGC < SRR3722087.181068/100‑1 (MQ=60)
GTCACTGTGTCGGTATACACGCGATTTTGCCAGTTAACACCACCGCCGACCGTCAACTCTGGCATGACAGGCAACCGATAGCTGGTGAACATTTTAACCG > SRR3722087.235991/1‑100 (MQ=60)
CTGTGTCGGTATACACGCGATTTTGCCAGTTAACACCACCGCCGACCGTCAACTCTGGCATGACAGGCAACCGATAGCTGGTGAACATTTTAACCGctgt > SRR3722087.173998/1‑96 (MQ=60)
|
ACGAGAAGTTTTTCGTCACCTGGTAGCGGGTGAAGAGATCCACCAGCGCGTAGCTACCTTGCTCGGCGCGGAAGGTGCCATACGGCGTCACGGTGTCGGTATACACGCGATTTTGCCAGTTAACACCACCGCCGACCGTCAACTCTGGCATGACAGGCAACCGATAGCTGGTGAACATTTTAACCGTGGT > NZ_CP009273/1154931‑1155120
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
