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 I205 R1
|
220 |
17.5 |
961422 |
97.1% |
933540 |
86.5 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
1,965,782 |
T→G |
E389D (GAA→GAC) |
tar ← |
methyl‑accepting chemotaxis protein II |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,965,782 | 0 | T | G | 100.0%
| 39.6
/ NA
| 13 | E389D (GAA→GAC) | tar | methyl‑accepting chemotaxis protein II |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base G (7/6); total (7/6) |
CTCTTTTGCCGCCTGGGCGCTGCGACTGGCAAGATTACGCACTTCACCCGCCACCACGGCAAAACCACGGCCCTGTTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAGTCTGGAAGGCAATACCGTCGATAACGCTGAT > NZ_CP009273/1965707‑1965862
|
ctctTTTGCCGCCTGGGCGCTGCGACTGGCAAGATTACGCACTTCACCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCAcgcgc < 1:142080/90‑1 (MQ=255)
gCGACTGGCAAGATTACGCACTTCACCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAg > 1:171732/1‑90 (MQ=255)
ggCAAGATTACGCACTTCACCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAg < 1:43836/90‑1 (MQ=255)
gatACGCACTTCCCCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATAtt < 1:125648/88‑1 (MQ=255)
cTTCACCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAGTCTGGa > 2:193388/1‑90 (MQ=255)
tcccccGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAGTCTGGAAg < 2:152553/87‑1 (MQ=255)
ccGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAGTCTGGAAGGCaa < 1:50883/90‑1 (MQ=255)
gCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAGTCTGGAAGGCAATa > 1:22856/1‑90 (MQ=255)
ccaccaCGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAGTCTGGAAGGCAATAc < 2:162233/90‑1 (MQ=255)
caccacGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAGTCTGGAAGGCAATAcc > 2:167640/1‑90 (MQ=255)
acGGCAAAACCACGGCCCTGGTCACCCGCCCCGGCGGCTTCAACCGCGGCTTTCAGCCCGGGGATATTGGTCTGGAAGGCAATAccgccg > 1:37819/1‑90 (MQ=25)
acGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAGTCTGGAAGGCAATACCGTCg > 1:384542/1‑90 (MQ=255)
aCGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAGTCTGGAAGGCAATACCGTCGATAACGCTGAt > 1:361338/1‑90 (MQ=255)
|
CTCTTTTGCCGCCTGGGCGCTGCGACTGGCAAGATTACGCACTTCACCCGCCACCACGGCAAAACCACGGCCCTGTTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAGTCTGGAAGGCAATACCGTCGATAACGCTGAT > NZ_CP009273/1965707‑1965862
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 10 ≤ ATCG/ATCG < 26 ≤ 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
GGAGTCTTCAATGAGGGCTTTGATCTCTTTTGCCGCCTGGGCGCTGCGACTGGCAAGATTACGCACTTCACCCGCCACCACGGCAAAACCACGGCCCTGTTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAGTCTGGAAGGCAATACCGTCGATAACGCTGAT > NZ_CP009273/1965683‑1965862
|
GGAGTCTTCAATGAGGGCTTTGATCTCTTTTGCCGCCTGGGCGCTGCGACTGGCAAGATTACGCACTTCACCCGCCACCACGGTAAAACCACGGCCCTGG > SRR3722087.53956/1‑100 (MQ=60)
AGTCTTCAATGAGGGCTTTGATCTCTTTTGCCGCCTGGGCGCTGCGACTGGCAAGATTACGCACTTCACCCGCCACCACGGCAAAACCACGGCCCTGGTC < SRR3722087.91155/100‑1 (MQ=60)
AGTCTTCAATGAGGGCTTTGATCTCTTTTGCCGCCTGGGCGCTGCGACTGCCAAGATTACGCACTTCACCCGCCACCACGGCAAAACCACGGCCCTGGTC < SRR3722087.144214/100‑1 (MQ=60)
CTCTTTTGCCGCCTGGGCGCTGCGACTGGCAAGATTACGCACTTCACCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACC < SRR3722087.143396/100‑1 (MQ=60)
CCTGGGCGCTGCGACTGGCAAGATTACGCACTTCACCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAG > SRR3722087.173286/1‑100 (MQ=60)
GGCAAGATTACGCACTTCACCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAGTC < SRR3722087.44188/100‑1 (MQ=60)
gaTACGCACTTCCCCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAGTCTGGAAG < SRR3722087.126832/98‑1 (MQ=60)
CACTTCACCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAGTCTGGAAGGCAATA > SRR3722087.23027/1‑100 (MQ=60)
ACCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCCCCGGCGGCTTCAACCGCGGCTTTCAGCCCGGGGATATTGGTCTGGAAGGCAATACCGCCG > SRR3722087.38125/1‑100 (MQ=60)
ACCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAGTCTGGAAGGCAATACCGTCG > SRR3722087.388974/1‑100 (MQ=60)
CCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAGTCTGGAAGGCAATACCGTCGAT < SRR3722087.51306/100‑1 (MQ=60)
CGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAGTCTGGAAGGCAATACCGTCGATAACGCTGAT > SRR3722087.365428/1‑100 (MQ=60)
|
GGAGTCTTCAATGAGGGCTTTGATCTCTTTTGCCGCCTGGGCGCTGCGACTGGCAAGATTACGCACTTCACCCGCCACCACGGCAAAACCACGGCCCTGTTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAGTCTGGAAGGCAATACCGTCGATAACGCTGAT > NZ_CP009273/1965683‑1965862
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 10 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
