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 I231 R1
|
218 |
12.8 |
703680 |
97.2% |
683976 |
86.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
3,369,157 |
T→C |
G310G (GGT→GGC) |
dcuC → |
anaerobic C4‑dicarboxylate transporter DcuC |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 3,369,157 | 0 | T | C | 100.0%
| 46.9
/ NA
| 16 | G310G (GGT→GGC) | dcuC | anaerobic C4‑dicarboxylate transporter DcuC |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (12/4); total (12/4) |
GTTCTTCCGCAAGCATAACTTGCGCGAAACAATGGACGATGTGCAGGCGTTTTTTGACGGCATGGGTACGCAGTTTGCCAACGTGGTAACGCTGGTGGTCGCGGGTGAAATATTTGCGAAAGGCTTAACGACGATTGGCACTGTCGATGCGG > NZ_CP009273/3369091‑3369242
|
gTTCTTCCGCAAGCATAACTTGCGCGAAACAATGGACGATGTGCAGGCGTTTTTTGACGGCATGGGCACGCAGTTTGCCAACGTGGTAAc > 2:29647/1‑90 (MQ=255)
gCAAGCATAACTTGCGCGAAACAATGGACGATGTGCAGGCGTTTTTTGACGGCATGGGCACGCAGTTTGCCAACGTGGTAACGCtggtgg > 2:183523/1‑90 (MQ=255)
cATAACTTGCGCGAAACAATGGACGATGTGCAGGCGTTTTTTGACGGCATGGGCACGCAGTTTGCCAACGTGGTAACGCTGGTGGTcgcg > 2:14477/1‑90 (MQ=255)
cATAACTTGCGCGAAACAATGGACGATGTGCAGGCGTTTTTTGACGGCATGGGCACGCAGTTTGCCAACGTGGTAACGCTGGTGGTcgcg > 2:224185/1‑90 (MQ=255)
cGATGTGCAGGCGTTTTTTGACGGCATGGGCACGCAGTTTGCCAACGTGGTAACGCTGGTGGTCGCGGGTGAAATATTTGCGAAAGGCtt > 1:93456/1‑90 (MQ=255)
cGATGTGCAGGCGTTTTTTGACGGCATGGGCACGCAGTTTGCCAACGTGGTAACGCTGGTGGTCGCGGGTGAAATATTTGCGAAAGGCtt > 2:284366/1‑90 (MQ=255)
aTGTGCAGGCGTTTTTTGACGGCATGGGCACGCAGTTTGCCAACGTGGTAACGCTGGTGGTCGCGGGTGAAATATTTGCGAAAGGCTTaa > 1:9537/1‑90 (MQ=255)
aTGTGCAGGCGTTTTTTGACGGCATGGGCACGCAGTTTGCCAACGTGGTAACGCTGGTGGTCGCGGGTGAAATATTTGCGAAAGGCTTaa > 2:180363/1‑90 (MQ=255)
aTGTGCAGGCGTTTTTTGACGGCATGGGCACGCAGTTTGCCAACGTGGTAACGCTGGTGGTCGCGGGTGAAATATTTGCGAAAGGCTTaa > 2:198357/1‑90 (MQ=255)
cAGGCGTTTTATGACGGCATGGGCACGCAGTTTGCCAACGTGGTAACGCTGGTGGTCGCGGGTGAAATATTTGCGAAAGGCTTAacgacg > 1:312124/1‑90 (MQ=255)
gTTTTTTGACGGCATGGGCACGCAGTTTGCCAACGTGGTAACGCTGGTGGTCGCGGGTGAAATATTTGCGAAAGGCTTAACGACGATTgg > 1:299727/1‑90 (MQ=255)
gTTTTTTGACGGCATGGGCACGCAGTTTGCCAACGTGGTAACGCTGGTGGTCGCGGGTGAAATATTTGCGAAAGGCTTAACGACGATTgg > 2:306336/1‑90 (MQ=255)
tttGACGGCATGGGCACGCAGTTTGCCAACGTGGTAACGCTGGTGGTCGCGGGTGAAATATTTGCGAAAGGCTTAACGACGATTGGCACt < 1:148876/90‑1 (MQ=255)
cGGCATGGGCACGCAGTTTGCCAACGTGGTAACGCTGGTGGTCGCGGGTGAAATATTTGCGAAAGGCTTAACGACGATTGGCACTGTCGa < 2:221263/90‑1 (MQ=255)
gCATGGGCACGCAGTTTGCCACCGTGGTAACGCTGGTGGTCGCGGGTGAAATATTTGCGAAAGGCTTAACGCCGATTGGCACTGTCGATg < 1:284344/90‑1 (MQ=255)
tGGGCACGCAGTTTGCCAACGTGGTAACGCTGGTGGTCGCGGGTGAAATATTTGCGAAAGGCTTAACGACGATTGGCACTGTCGATGCgg < 2:247307/90‑1 (MQ=255)
|
GTTCTTCCGCAAGCATAACTTGCGCGAAACAATGGACGATGTGCAGGCGTTTTTTGACGGCATGGGTACGCAGTTTGCCAACGTGGTAACGCTGGTGGTCGCGGGTGAAATATTTGCGAAAGGCTTAACGACGATTGGCACTGTCGATGCGG > NZ_CP009273/3369091‑3369242
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 25 ≤ 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
TTACTGAGTTTGACTGTGACGATGTTTGTTGAGTTCTTCCGCAAGCATAACTTGCGCGAAACAATGGACGATGTGCAGGCGTTTTTTGACGGCATGGGTACGCAGTTTGCCAACGTGGTAACGCTGGTGGTCGCGGGTGAAATATTTGCGAAAGGCTTAACGACGATTGGCACTGTCGATGCGGTTATCAGGGGGGC > NZ_CP009273/3369059‑3369255
|
TTACTGAGTTTGACTGTGACGATGTTTGTTGAGTTCTTCCGCAAGCATAACTTGCGCGAAACAATGGACGATGTGCAGGCGTTTTTTGACGGCATGGGCA < SRR3722116.49642/100‑1 (MQ=60)
AAACAATGGACGATGTGCAGGCGTTTTTTGACGGCATGGGCACGCAGTTTGCCAACGTGGTAACGCTGGTGGTCGCGGGTGAAATATTTGCGAAAGGCTT > SRR3722116.94610/1‑100 (MQ=60)
ACAATGGACGATGTGCAGGCGTTTTTTGACGGCATGGGCACGCAGTTTGCCAACGTGGTAACGCTGGTGGTCGCGGGTGAAATATTTGCGAAAGGCTTAA > SRR3722116.9655/1‑100 (MQ=60)
GGACGATGTGCAGGCGTTTTATGACGGCATGGGCACGCAGTTTGCCAACGTGGTAACGCTGGTGGTCGCGGGTGAAATATTTGCGAAAGGCTTAACGACG > SRR3722116.316740/1‑100 (MQ=60)
ATGTGCAGGCGTTTTTTGACGGCATGGGCACGCAGTTTGCCAACGTGGTAACGCTGGTGGTCGCGGGTGAAATATTTGCGAAAGGCTTAACGACGATTGG > SRR3722116.304126/1‑100 (MQ=60)
TTTGACGGCATGGGCACGCAGTTTGCCAACGTGGTAACGCTGGTGGTCGCGGGTGAAATATTTGCGAAAGGCTTAACGACGATTGGCACTGTCGATGCGG < SRR3722116.150586/100‑1 (MQ=60)
GCATGGGCACGCAGTTTGCCACCGTGGTAACGCTGGTGGTCGCGGGTGAAATATTTGCGAAAGGCTTAACGCCGATTGGCACTGTCGATGCGGTTATCAG < SRR3722116.288483/100‑1 (MQ=60)
GCACGCAGTTTGCCAACGTGGTAACGCTGGTGGTCGCGGGTGAAATATTTGCGAAAGGCTTAACGACGATTGGCACTGTCGATGCGGTTATCAGGGGGGC < SRR3722116.14671/100‑1 (MQ=60)
|
TTACTGAGTTTGACTGTGACGATGTTTGTTGAGTTCTTCCGCAAGCATAACTTGCGCGAAACAATGGACGATGTGCAGGCGTTTTTTGACGGCATGGGTACGCAGTTTGCCAACGTGGTAACGCTGGTGGTCGCGGGTGAAATATTTGCGAAAGGCTTAACGACGATTGGCACTGTCGATGCGGTTATCAGGGGGGC > NZ_CP009273/3369059‑3369255
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
