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 |
3,103,871 |
(A)7→6 |
intergenic (+71/+78) |
BW25113_RS15410 → / ← yghD |
tRNA‑Phe/GspM family type II secretion system protein YghD |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 3,103,865 | 0 | A | . | 100.0%
| 60.1
/ NA
| 15 | intergenic (+65/+84) | BW25113_RS15410/yghD | tRNA‑Phe/GspM family type II secretion system protein YghD |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base . (4/11); total (4/11) |
TCCGAGTCCGGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACGAAAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAATCTCCTG > NZ_CP009273/3103784‑3103943
|
tCCGAGTCCGGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACGaaaaaatta < 1:130631/90‑4 (MQ=255)
cGGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATaa < 2:236239/90‑1 (MQ=255)
cGGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATaa < 1:82773/90‑1 (MQ=255)
ttAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACGaaaaaat < 2:338674/64‑2 (MQ=255)
ttAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACGaaaaaat > 1:338674/1‑63 (MQ=255)
ttAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTAc > 1:234894/1‑90 (MQ=255)
aCCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGc < 1:74595/90‑1 (MQ=255)
cGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCAc > 2:103546/1‑90 (MQ=255)
aaGGCGGGTTTTTGCTTTTTGAACTGACAATAACCTTTCCG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACg < 2:227891/90‑1 (MQ=255)
aGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACga > 2:187629/1‑90 (MQ=255)
gggTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGt < 1:59481/90‑1 (MQ=255)
gggTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGt < 2:199039/90‑1 (MQ=255)
cTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAAt < 1:343248/90‑1 (MQ=255)
tGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAAtc < 1:41565/90‑1 (MQ=255)
aaTAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAATCTCCt < 2:281722/90‑1 (MQ=255)
aTAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAATCTCCTg < 2:248901/90‑1 (MQ=255)
ttCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACg < 2:33122/55‑1 (MQ=255)
ttCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACg > 1:33122/1‑55 (MQ=255)
|
TCCGAGTCCGGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACGAAAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAATCTCCTG > NZ_CP009273/3103784‑3103943
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 34 ≤ 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
TCCGAGTCCGGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACGAAAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAATCTCCTGATACTT > NZ_CP009273/3103784‑3103949
|
TCCGAGTCCGGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAG < SRR3722116.132169/100‑1 (MQ=60)
CGGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGG < SRR3722116.83805/100‑1 (MQ=60)
CCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAActgtctcttatacaca > SRR3722116.343714/1‑84 (MQ=60)
CCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTAC > SRR3722116.238116/1‑100 (MQ=60)
ACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACG < SRR3722116.75536/100‑1 (MQ=60)
GGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTG < SRR3722116.60205/100‑1 (MQ=60)
CTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAATCTCCTGATAC < SRR3722116.348360/100‑1 (MQ=60)
TGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAATCTCCTGATACT < SRR3722116.42057/100‑1 (MQ=60)
GACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTctgtctcttatacacatctgacgct > SRR3722116.33507/1‑75 (MQ=60)
|
TCCGAGTCCGGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACGAAAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAATCTCCTGATACTT > NZ_CP009273/3103784‑3103949
|
| 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: ‑ |
