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 |
1,761,086 |
A→C |
R619R (CGT→CGG) |
ydiJ ← |
FAD‑binding and (Fe‑S)‑binding domain‑containing protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,761,086 | 0 | A | C | 100.0%
| 41.6
/ NA
| 13 | R619R (CGT→CGG) | ydiJ | FAD‑binding and (Fe‑S)‑binding domain‑containing protein |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base C (3/10); total (3/10) |
GGCAATTAACGTCCGCAAACTGACGCCGGATTCAGGCAGTTCTTGTTCCAGTTTGAGTGGATCAACGCCGCGATCCGCCAACAAACGCAGCCATTCACGCACCAGCGTTGCGCGCCCTTTCGGTGAATGAATCCGGTTCTGGGTGATCTTCATCGACGGACACATCGGAC > NZ_CP009273/1761002‑1761171
|
ggCAATTAACGTCCGCAAACTGACGCCGGATTCAGGCAGTTCTTGTTCCAGTTTGAGTGGATCAACGCCGCGATCCGCCAACAACCGCAg < 2:197712/90‑1 (MQ=255)
aCGTCCGCAAACTGACGCCGGATTCAGGCAGTTCTTGTTCCAGTTTGAGTGGATCAACGCCGCGATCCGCCAACAACCGCAGCCATTCAc < 2:514254/90‑1 (MQ=255)
gCAAACTGACGCCGGATTCAGGCAGTTCTTGTTCCAGTTTGAGTGGATCAACGCCGCGATCCGCCAACAACCGCAGCCATTCACGCACCa > 2:754753/1‑90 (MQ=255)
ccGGATTCAGGCAGTTCTTGTTCCAGTTTGAGTGGATCAACGCCGCGATCCGCCAACAACCGCAGCCATTCACGCACCAGCGTTgcgcgc < 1:491766/90‑1 (MQ=255)
ccGGATTCAGGCAGTTCTTGTTCCAGTTTGAGTGGATCAACGCCGCGATCCGCCAACAACCGCAGCCATTCACGCACCAGCGTTgcgcgc < 2:394354/90‑1 (MQ=255)
ggCAGTTCTTGTTCCAGTTTGAGTGGATCAACGCCGCGATCCGCCAACAACCGCAGCCATTCACGCACCAGCGTTGCGCGCCCTTTCGGt < 1:623145/90‑1 (MQ=255)
gTTCTTGTTCCAGTTTGAGTGGATCAACGCCGCGATCCGCCAACAACCGCAGCCATTCACGCACCAGCGTTGCGCGCCCTTTCGGtgaat > 1:190874/1‑90 (MQ=255)
ttCTTGTTCCAGTTTGAGTGGATCAACGCCGCGATCCGCCAACAACCGCAGCCATTCACGCACCAGCGTTGCGCGCCCTTTCGGtgaatg < 2:156705/90‑1 (MQ=255)
ttCTTGTTCCAGTTTGAGTGGATCAACGCCGCGATCCGCCAACAACCGCAGCCATTCACGCACCAGCGTTGCGCGCCCTTTCGGtgaatg < 2:433202/90‑1 (MQ=255)
ttCTTGTTCCAGTTTGAGTGGATCAACGCCGCGATCCGCCAACAACCGCAGCCATTCACGCACCAGCGTTGCGCGCCCTTTCGGtgaacg < 2:142847/90‑3 (MQ=255)
gATCAACGCCGCGATCCGCCAACAACCGCAGCCATTCACGCACCAGCGTTGCGCGCCCTTTCGGTGAATGAATCCGGTTCTGGGTGATCt > 2:631704/1‑90 (MQ=255)
gATCCGCCAACAACCGCAGCCATTCACGCACCAGCGTTGCGCGCCCTTTCGGTGAATGAATCCGGTTCTGGGTGATCTTCATCGACGGac < 1:754753/90‑1 (MQ=255)
acaaCCGCAGCCATTCACGCACCAGCGTTGCGCGCCCTTTCGGTGAATGAATCCGGTTCTGGGTGATCTTCATCGACGGACACATCGGAc < 2:95415/90‑1 (MQ=255)
|
GGCAATTAACGTCCGCAAACTGACGCCGGATTCAGGCAGTTCTTGTTCCAGTTTGAGTGGATCAACGCCGCGATCCGCCAACAAACGCAGCCATTCACGCACCAGCGTTGCGCGCCCTTTCGGTGAATGAATCCGGTTCTGGGTGATCTTCATCGACGGACACATCGGAC > NZ_CP009273/1761002‑1761171
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ 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: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
GCTATTGCGCGTGCGGGCAATTAACGTCCGCAAACTGACGCCGGATTCAGGCAGTTCTTGTTCCAGTTTGAGTGGATCAACGCCGCGATCCGCCAACAAACGCAGCCATTCACGCACCAGCGTTGCGCGCCCTTTCGGTGAATGAATCCGGTTCTGGGTGATCTTCATCGACGGACACATCGGACT > NZ_CP009273/1760987‑1761172
|
GCTATTGCGCGTGCGGGCAATTAACGTCCGCAAACTGACGCCGGATTCAGGCAGTTCTTGTTCCAGTTTGAGTGGATCAACGCCGCGATCCGCCAACAAC > SRR3722073.442461/1‑100 (MQ=60)
CTATTGCGCGTGCGGGCAATTAACGTCCGCAAACTGACGCCGGATTCAGGCAGTTCTTGTTCCAGTTTGAGTGGATCAACGCCGCGATCCGCCAACAACC > SRR3722073.159877/1‑100 (MQ=60)
TGCGCGTGCGGGCAATTAACGTCCGCAAACTGACGCCGGATTCAGGCAGTTCTTGTTCCAGTTTGAGTGGATCAACGCCGCGATCCGCCAACAACCGCAG < SRR3722073.780154/100‑1 (MQ=60)
GCGTGCGGGCAATTAACGTCCGCAAACTGACGCCGGATTCAGGCAGTTCTTGTTCCAGTTTGAGTGGATCAACGCCGCGATCCGCCAACAACCGCAGCCA < SRR3722073.311345/100‑1 (MQ=60)
CCGGATTCAGGCAGTTCTTGTTCCAGTTTGAGTGGATCAACGCCGCGATCCGCCAACAACCGCAGCCATTCACGCACCAGCGTTGCGCGCCCTTTCGGTG < SRR3722073.502188/100‑1 (MQ=60)
GATTCAGGCAGTTCTTGTTCCAGTTTGAGTGGATCAACGCCGCGATCCGCCAACAACCGCAGCCATTCACGCACCAGCGTTGCGCGCCCTTTCGGTGAAT > SRR3722073.194666/1‑100 (MQ=60)
GGCAGTTCTTGTTCCAGTTTGAGTGGATCAACGCCGCGATCCGCCAACAACCGCAGCCATTCACGCACCAGCGTTGCGCGCCCTTTCGGTGAATGAATCC < SRR3722073.636088/100‑1 (MQ=60)
GATCCGCCAACAACCGCAGCCATTCACGCACCAGCGTTGCGCGCCCTTTCGGTGAATGAATCCGGTTCTGGGTGATCTTCATCGACGGACACATCGGACT < SRR3722073.770019/100‑1 (MQ=60)
|
GCTATTGCGCGTGCGGGCAATTAACGTCCGCAAACTGACGCCGGATTCAGGCAGTTCTTGTTCCAGTTTGAGTGGATCAACGCCGCGATCCGCCAACAAACGCAGCCATTCACGCACCAGCGTTGCGCGCCCTTTCGGTGAATGAATCCGGTTCTGGGTGATCTTCATCGACGGACACATCGGACT > NZ_CP009273/1760987‑1761172
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
