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 I200 R1
|
216 |
30.8 |
1683622 |
97.2% |
1636480 |
87.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
2,434,529 |
A→C |
F186V (TTT→GTT) |
fabB ← |
beta‑ketoacyl‑ACP synthase I |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 2,434,529 | 0 | A | C | 79.3%
| 70.7
/ 13.1
| 29 | F186V (TTT→GTT) | fabB | beta‑ketoacyl‑ACP synthase I |
| Reads supporting (aligned to +/- strand): ref base A (3/3); new base C (9/14); total (12/17) |
| Fisher's exact test for biased strand distribution p-value = 6.69e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.82e-01 |
CGGGGTGTCGTTGTATTTAGTAGACAGCGCACCCATTGCGTCGAATTCGCAAGCCATTTCCCAGCACAGCTCTTCGCCGCCGCCAGCAAACACGATGTCCTGTTTGCCCAGTTGGATCTGCTCTACTGCGTTACCGATACAGTGTGCGGAAGTCGCACACGCGGAGCTGAT > NZ_CP009273/2434440‑2434610
|
cGGGGTGTCGTTGTATTTAGTAGACAGCGCACCCATTGCGTCGAATTCGCAAGCCATTTCCCAGCACAGCTCTTCGCCGCCGCCAGCaaa < 1:135722/90‑1 (MQ=255)
tgtCGTTGTATTTAGTAGACAGCGCACCCATTGCGTCGAATTCGCAAGCCATTTCCCAGCACAGCTCTTCGCCGCCGCCAGCAACCACGa < 1:173934/90‑1 (MQ=255)
gtCGTTGTATTTAGTAGACAGCGCACCCATTGCGTCGAATTCGCAAGCCATTTCCCAGCACAGCTCTTCGCCGCCGCCAGCAACCACGAt > 2:201804/1‑90 (MQ=255)
tCGTTGTATTTAGTAGACAGCGCACCCATTGCGTCGAATTCGCAAGCCATTTCCCAGCACAGCTCTTCGCCGCCGCCAGCAACCACGATg < 1:42546/90‑1 (MQ=255)
cAGCGCACCCATTGCGTCGAATTCGCAAGCCATTTCCCAGCACAGCTCTTCGCCGCCGCCAGCAACCACGATGTCCTGTTTGCCCAGTTg > 2:652076/1‑90 (MQ=255)
gcgcACCCATTGCGTCGAATTCGCAAGCCATTTCCCAGCACAGCTCTTCGCCGCCGCCAGCAACCACGATGTCCTGTTTGCCCAGTTGGa > 2:98278/1‑90 (MQ=255)
gcgcACCCATTGCGTCGAATTCGCAAGCCATTTCCCAGCACAGCTCTTCGCCGCCGCCAGCAACCACGATGTCCTGTTTGCCCAGTTGGa > 2:202767/1‑90 (MQ=255)
gcgcACCCATTGCGTCGAATTCGCAAGCCATTTCCCAGCACAGCTCTTCGCCGCCGCCAGCAACCACGATGTCCTGTTTGCCCAGTTGGa < 1:812895/90‑1 (MQ=255)
gcgcACCCATTGCGTCGAATTCGCAAGCCATTTCCCAGCACAGCTCTTCGCCGCCGCCAGCAACCACGATGTCCTGTTTGCCCAGTTGGa > 1:464313/1‑90 (MQ=255)
gcgcACCCATTGCGTCGAATTCGCAAGCCATTTCCCAGCACAGCTCTTCGCCGCCGCCAGCAAACACGATGTCCTGTTTGCCCAGTTGGa > 2:189259/1‑90 (MQ=255)
gcACCCATTGCGTCGAATTCGCAAGCCATTTCCCAGCACAGCTCTTCGCCGCCGCCAGCAACCACGATGTCCTGTTTGCCCAGTTGGATc < 1:201804/90‑1 (MQ=255)
tGCGTCGAATTCGCAAGCCATTTCCCAGCACAGCTCTTCGCCGCCGCCAGCAACCACGATGTCCTGTTTGCCCAGTTGGATCTGCTCTAc < 2:97763/90‑1 (MQ=255)
tGCGTCGAATTCGCAAGCCATTTCCCAGCACAGCTCTTCGCCGCCGCCAGCAACCACGATGTCCTGTTTGCCCAGTTGGATCTGCTCTAc > 2:557735/1‑90 (MQ=255)
cGTCGAATTCGCAAGCCATTTCCCAGCCCAGCTCTTCGCCGCCGCCAGCAACCACGATGTCCTGTTTGCCCAGTTGGATCTGCTCTACTg < 2:532415/90‑1 (MQ=255)
cGTCGAATTCGCAAGCCATTTCCCAGCACAGCTCTTCGCCGCCGCCAGCAAACACGATGTCCTGTTTGCCCAGTTGGATCTGCTCTACTg < 1:189259/90‑1 (MQ=255)
gTCGAATTCGCAAGCCATTTCCCAGCACAGCTCTTCGCCGCCGCCAGCAAACACGATGTCCTGTTTGCCCAGTTGGATCTGCTCTACTGc > 2:729202/1‑90 (MQ=255)
gAATTCGCAAGCCATTTCCCAGCACAGCTCTTCGCCGCCGCCAGCAACCACGATGTCCTGTTTGCCCAGTTGGATCTGCTCTACTGCGtt < 1:557735/90‑1 (MQ=255)
gAATTCGCAAGCCATTTCCCAGCACAGCTCTTCCCCGCCGCCAGCAACCACGATGTCCTGTTTGCCCAGTTGGATCTGCTCTACTGCGtt < 2:614075/90‑1 (MQ=255)
aaGCCATTTCCCAGCACAGCTCTTCGCCGCCGCCAGCAACCACGATGTCCTGTTTGCCCAGTTGGATCTGCTCTACTGCGTTACCGATAc < 2:774997/90‑1 (MQ=255)
gCCATTTCCCAGCACAGCTCTTCGCCGCCGCCAGCAACCACGATGTCCTGTTTGCCCAGTTGGATCTGCTCTACTGCGTTACCGATACAg < 2:400290/90‑1 (MQ=255)
ttCCCAGCACAGCTCTTCGCCGCCGCCAGCAACCACGATGTCCTGTTTGCCCAGTTGGATCTGCTCTACTGCGTTACCGATACAGTGTGc < 1:331881/90‑1 (MQ=255)
ttCCCAGCACAGCTCTTCGCCGCCGCCAGCAAACACGATGTCCTGTTTGCCCAGTTGGATCTGCTCTACTGCGTTACCGATACAGTGTGc < 1:729202/90‑1 (MQ=255)
cAGCACAGCTCTTCGCCGCCGCCAGCAAACACGATGTCCTGTTTGCCCAGTTGGATCTGCTCTACTGCGTTACCGATACAGTGTGCGGaa > 2:37974/1‑90 (MQ=255)
gCTCTTCGCCGCCGCCAGCAACCACGATGTCCTGTTTGCCCAGTTGGATCTGctct < 1:814811/56‑1 (MQ=255)
gCTCTTCGCCGCCGCCAGCAACCACGATGTCCTGTTTGCCCAGTTGGATCTGctct > 2:814811/1‑56 (MQ=255)
gCTCTTCGCCGCCGCCAGCAACCACGATGTCCTGTTTGCCCAGTTGGATCTGCTCTACTGCGTTAc < 2:64897/66‑1 (MQ=255)
gCTCTTCGCCGCCGCCAGCAACCACGATGTCCTGTTTGCCCAGTTGGATCTGCTCTACTGCGTTAc > 1:64897/1‑66 (MQ=255)
gCTCTTCGCCGCCGCCAGCAACCACGATGTCCTGTTTGCCCAGTTGGATCTGCTCTACTGCGTTACCGATACAGTGTGCGGAAGTCGcac > 1:330449/1‑90 (MQ=255)
ccgccgccAGCAACCACGATGTCCTGTTTGCCCAGTTGGATCTGCTCTACTGCGTTACCGATACAGTGTGCGGAAGTCGTACACGCGGAg < 1:635531/90‑1 (MQ=255)
gccAGCAAACACGATGTCCTGTTTGCCCAGTTGGATCTGCTCTACTGCGTTACCGATACAGTGTGCGGAAGTCGCACACGCGGAGCTGAt < 1:37974/90‑1 (MQ=255)
|
CGGGGTGTCGTTGTATTTAGTAGACAGCGCACCCATTGCGTCGAATTCGCAAGCCATTTCCCAGCACAGCTCTTCGCCGCCGCCAGCAAACACGATGTCCTGTTTGCCCAGTTGGATCTGCTCTACTGCGTTACCGATACAGTGTGCGGAAGTCGCACACGCGGAGCTGAT > NZ_CP009273/2434440‑2434610
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 33 ≤ 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
CGGGGTGTCGTTGTATTTAGTAGACAGCGCACCCATTGCGTCGAATTCGCAAGCCATTTCCCAGCACAGCTCTTCGCCGCCGCCAGCAAACACGATGTCCTGTTTGCCCAGTTGGATCTGCTCTACTGCGTTACCGATACAGTGTGCGGAAGTCGCACACGCGGAGCTGATGGAGTAGTTA > NZ_CP009273/2434440‑2434620
|
CGGGGTGTCGTTGTATTTAGTAGACAGCGCACCCATTGCGTCGAATTCGCAAGCCATTTCCCAGCACAGCTCTTCGCCGCCGCCAGCAAACACGATGTCC < SRR3722079.136867/100‑1 (MQ=60)
TGTCGTTGTATTTAGTAGACAGCGCACCCATTGCGTCGAATTCGCAAGCCATTTCCCAGCACAGCTCTTCGCCGCCGCCAGCAACCACGATGTCCTGTTT < SRR3722079.175444/100‑1 (MQ=60)
TCGTTGTATTTAGTAGACAGCGCACCCATTGCGTCGAATTCGCAAGCCATTTCCCAGCACAGCTCTTCGCCGCCGCCAGCAACCACGATGTCCTGTTTGC < SRR3722079.42869/100‑1 (MQ=60)
TTAGTAGACAGCGCACCCATTGCGTCGAATTCGCAAGCCATTTCCCAGCACAGCTCTTCGCCGCCGCCAGCAACCACGATGTCCTGTTTGCCCAGTTGGA > SRR3722079.468374/1‑100 (MQ=60)
GCGCACCCATTGCGTCGAATTCGCAAGCCATTTCCCAGCACAGCTCTTCGCCGCCGCCAGCAACCACGATGTCCTGTTTGCCCAGTTGGATCTGCTCTAC < SRR3722079.821612/100‑1 (MQ=60)
GCACCCATTGCGTCGAATTCGCAAGCCATTTCCCAGCACAGCTCTTCGCCGCCGCCAGCAACCACGATGTCCTGTTTGCCCAGTTGGATCTGCTCTACTG < SRR3722079.203546/100‑1 (MQ=60)
ctcggagatgtgtataagagacagTCCCAGCACAGCTCTTCGCCGCCGCCAGCAACCACGATGTCCTGTTTGCCCAGTTGGATCTGCTCTACTGCGTTAC < SRR3722079.823544/76‑1 (MQ=60)
CGTCGAATTCGCAAGCCATTTCCCAGCACAGCTCTTCGCCGCCGCCAGCAAACACGATGTCCTGTTTGCCCAGTTGGATCTGCTCTACTGCGTTACCGAT < SRR3722079.190904/100‑1 (MQ=60)
GAATTCGCAAGCCATTTCCCAGCACAGCTCTTCGCCGCCGCCAGCAACCACGATGTCCTGTTTGCCCAGTTGGATCTGCTCTACTGCGTTACCGATACAG < SRR3722079.563133/100‑1 (MQ=60)
TTCCCAGCACAGCTCTTCGCCGCCGCCAGCAACCACGATGTCCTGTTTGCCCAGTTGGATCTGCTCTACTGCGTTACCGATACAGTGTGCGGAAGTCGCA < SRR3722079.334525/100‑1 (MQ=60)
TTCCCAGCACAGCTCTTCGCCGCCGCCAGCAAACACGATGTCCTGTTTGCCCAGTTGGATCTGCTCTACTGCGTTACCGATACAGTGTGCGGAAGTCGCA < SRR3722079.736994/100‑1 (MQ=60)
TCCCAGCACAGCTCTTCGCCGCCGCCAGCAACCACGATGTCCTGTTTGCCCAGTTGGATCTGCTCTACTGCGTTACCGATACAGTGctgtctcttataca > SRR3722079.65430/1‑86 (MQ=60)
TCCCAGCACAGCTCTTCGCCGCCGCCAGCAACCACGATGTCCTGTTTGCCCAGTTGGATCTGCTCTACTGCGTTACCGATACAGTGTGCGGAAGTCGCAC > SRR3722079.333086/1‑100 (MQ=60)
CCGCCGCCAGCAACCACGATGTCCTGTTTGCCCAGTTGGATCTGCTCTACTGCGTTACCGATACAGTGTGCGGAAGTCGTACACGCGGAGCTGATGGAGT < SRR3722079.642054/100‑1 (MQ=60)
CCGCCAGCAACCACGATGTCCTGTTTGCCCAGTTGGATCTGCTCTACTGCGTTACCGATACAGTGTGCGGAAGTCGCACACGCGGAGCTGATGGAGTAGT > SRR3722079.14949/1‑100 (MQ=60)
GCCAGCAAACACGATGTCCTGTTTGCCCAGTTGGATCTGCTCTACTGCGTTACCGATACAGTGTGCGGAAGTCGCACACGCGGAGCTGATGGAGTAGTTA < SRR3722079.38253/100‑1 (MQ=60)
|
CGGGGTGTCGTTGTATTTAGTAGACAGCGCACCCATTGCGTCGAATTCGCAAGCCATTTCCCAGCACAGCTCTTCGCCGCCGCCAGCAAACACGATGTCCTGTTTGCCCAGTTGGATCTGCTCTACTGCGTTACCGATACAGTGTGCGGAAGTCGCACACGCGGAGCTGATGGAGTAGTTA > NZ_CP009273/2434440‑2434620
|
| 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: ‑ |
