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 I230 R1
|
226 |
18.8 |
1048726 |
96.7% |
1014118 |
86.4 |
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%
| 86.2
/ NA
| 21 | 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 . (4/17); total (4/17) |
TTAGATTCCGAGTCCGGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACGAAAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAATCTCCTGATACTT > NZ_CP009273/3103778‑3103949
|
ttAGATTCCGAGTCCGGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACGa < 1:103453/88‑1 (MQ=255)
ttAGATTCCGAGTCCGGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACGa > 2:103453/1‑88 (MQ=255)
aGATTCCGAGTCCGGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACGaaaaa > 2:466790/1‑90 (MQ=255)
cGAGTCCGGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGc < 1:87258/90‑1 (MQ=255)
aaGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTActc < 1:375904/90‑1 (MQ=255)
aCCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGc < 2:467101/90‑1 (MQ=255)
cccGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGcc > 2:97793/1‑90 (MQ=255)
cccACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGt < 1:280789/90‑1 (MQ=255)
gggTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGt > 1:274210/1‑90 (MQ=255)
cTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTAtt < 1:97793/90‑1 (MQ=255)
cTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTAtt < 2:233900/90‑1 (MQ=255)
cTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTAtt < 1:16284/90‑1 (MQ=255)
cTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTAtt < 2:490501/90‑1 (MQ=255)
ttGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGat < 1:337294/90‑1 (MQ=255)
cTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAAt < 1:425610/90‑1 (MQ=255)
cTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAAt < 2:454319/90‑1 (MQ=255)
tGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGt > 1:516872/1‑71 (MQ=255)
tGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGt < 2:516872/71‑1 (MQ=255)
tGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAAtc < 2:94586/90‑1 (MQ=255)
tGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAAtc < 1:90528/90‑1 (MQ=255)
tAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAATCTCCTGa < 1:189297/90‑1 (MQ=255)
aaCCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAATCTCCTGAt < 1:287542/90‑1 (MQ=255)
aaCCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAATCTCCTGAt < 1:389477/90‑1 (MQ=255)
ttCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAATCTCCTGATACtt > 1:145179/1‑90 (MQ=255)
|
TTAGATTCCGAGTCCGGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACGAAAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAATCTCCTGATACTT > NZ_CP009273/3103778‑3103949
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ 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
GGTTAGATTCCGAGTCCGGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACGAAAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAATCTCCTGATACTTTACCCCCGTCCAAACTC > NZ_CP009273/3103776‑3103966
|
GGTTAGATTCCGAGTCCGGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGC < SRR3722114.104543/100‑1 (MQ=60)
CGAGTCCGGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTC < SRR3722114.88182/100‑1 (MQ=60)
AAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTT < SRR3722114.380424/100‑1 (MQ=60)
CCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGT > SRR3722114.277065/1‑100 (MQ=60)
CCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGT < SRR3722114.283734/100‑1 (MQ=60)
CTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGctgtctctt > SRR3722114.523355/1‑91 (MQ=60)
CTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAATC < SRR3722114.16441/100‑1 (MQ=60)
CTTTTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAATC < SRR3722114.98826/100‑1 (MQ=60)
TTGGATCTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAATCTCC < SRR3722114.341088/100‑1 (MQ=60)
CTGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAATCTCCTGATAC < SRR3722114.430847/100‑1 (MQ=60)
TGACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAATCTCCTGATACT < SRR3722114.91483/100‑1 (MQ=60)
GACAATAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAATCTCCTGATACTT > SRR3722114.146664/1‑100 (MQ=60)
TAACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAATCTCCTGATACTTTACCC < SRR3722114.191143/100‑1 (MQ=60)
AACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAATCTCCTGATACTTTACCCC < SRR3722114.290585/100‑1 (MQ=60)
AACCTTCACG‑AAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAATCTCCTGATACTTTACCCC < SRR3722114.394197/100‑1 (MQ=60)
AAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAATCTCCTGATACTTTACCCCCGTCCAAACTC < SRR3722114.222676/100‑1 (MQ=60)
|
GGTTAGATTCCGAGTCCGGGCACCACTAATTCTTAAGAACCCGCCCACAAGGCGGGTTTTTGCTTTTGGATCTGACAATAACCTTCACGAAAAAAATTAGCTTATAAAGTCTGGGGGAATTACTCTCGCCACGTTAACGAGAGTAATTTTATTGATATTAATCTCCTGATACTTTACCCCCGTCCAAACTC > NZ_CP009273/3103776‑3103966
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
