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 I228 R1
|
214 |
26.5 |
1448192 |
97.1% |
1406194 |
86.4 |
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%
| 46.3
/ NA
| 16 | E389D (GAA→GAC) | tar | methyl‑accepting chemotaxis protein II |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base G (8/8); total (8/8) |
AGGGCTTTGATCTCTTTTGCCGCCTGGGCGCTGCGACTGGCAAGATTACGCACTTCACCCGCCACCACGGCAAAACCACGGCCCTGTTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAGTCTGGAAGGCAATACCGTCGATAACGCTGAT > NZ_CP009273/1965696‑1965862
|
aGGGCTTTGATCTCTTTTGCCGCCTGGGCGCTGCGACTGGCAAGATTGCGCACTTCACCCGCCACCACGGCAAAACCACGGCCCTGGTCa > 1:506881/1‑90 (MQ=255)
ctctTTTGCCGCCTGGGCGCTGCGACTGGCAAGATTACGCACTTCACCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCAcgcgc > 1:633712/1‑90 (MQ=255)
ctctTTTGCCCCCTGGGCGCGGCGACTGGCAAGATTACGCACTTCCCCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCAcgcgc < 1:704517/90‑1 (MQ=25)
tctTTTGCCGCCTGGGCGCTGCGACTGGCAAGATTACGCACTTCACCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCAcgcgcg > 1:599245/1‑90 (MQ=255)
gCGACTGGCAAGATTACGCACTTCACCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAg > 2:330382/1‑90 (MQ=255)
cTGGCAAGATTCCCCCCTTCCCCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGcgcg < 1:101137/90‑1 (MQ=255)
cTGGCAAGATTACGCACTTCCCCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGcgcg < 2:617273/90‑1 (MQ=255)
tGGCAAGTTTCCGCACTTCCCCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGcgcgg < 1:261486/90‑2 (MQ=37)
ggCAAGATTACGCACTTCACCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAg < 2:633712/90‑1 (MQ=255)
ggCAAGATTACGCACTCCCCCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAg < 1:688533/90‑1 (MQ=37)
tACGCACTTCCCCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAg < 2:488799/90‑1 (MQ=255)
cGCACTTCACCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAGTc > 1:461997/1‑90 (MQ=255)
ttCACCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAGTCTGGaa > 2:68504/1‑90 (MQ=255)
accacGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAGTCTGGAAGGCAATACCg < 1:311516/90‑1 (MQ=255)
ccacGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCG‑GGATATTAGTCTGGAAGGCAATACCGTc > 1:632382/1‑90 (MQ=37)
aCGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAGTCTGGAAGGCAATACCGTCGATAACGCTGAt > 1:236620/1‑90 (MQ=255)
|
AGGGCTTTGATCTCTTTTGCCGCCTGGGCGCTGCGACTGGCAAGATTACGCACTTCACCCGCCACCACGGCAAAACCACGGCCCTGTTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAGTCTGGAAGGCAATACCGTCGATAACGCTGAT > NZ_CP009273/1965696‑1965862
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
GTCTTCAATGAGGGCTTTGATCTCTTTTGCCGCCTGGGCGCTGCGACTGGCAAGATTACGCACTTCACCCGCCACCACGGCAAAACCACGGCCCTGTTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAGTCTGGAAGGCAATACCGTCGATAACGCTGAT > NZ_CP009273/1965686‑1965862
|
GTCTTCAATGAGGGCTTTGATCTCTTTTGCCGCCTGGGCGCTGCGACTGGCAAGATTGCGCACTTCACCCGCCACCACGGCAAAACCACGGCCCTGGTCA > SRR3722112.514263/1‑100 (MQ=60)
GGGCTTTGATCTCTTTTGCCGCCTGGGCGCTGCGACTGGCAAGATTACGCACTTCACCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGC > SRR3722112.643528/1‑100 (MQ=60)
GGCTTTGATCTCTTTTGCCGCCTGGGCGCTGCGACTGGCAAGATTACGCACTTCACCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCG > SRR3722112.608422/1‑100 (MQ=60)
CTCTTTTGCCCCCTGGGCGCGGCGACTGGCAAGATTACGCACTTCCCCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACC < SRR3722112.715517/100‑1 (MQ=60)
CTGGCAAGATTCCCCCCTTCCCCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAG < SRR3722112.102396/100‑1 (MQ=60)
TGGCAAGTTTCCGCACTTCCCCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCG‑GGATATTAGTC < SRR3722112.264560/100‑1 (MQ=60)
GGCAAGATTACGCACTTCACCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAGTC > SRR3722112.468537/1‑100 (MQ=60)
GGCAAGATTACGCACTCCCCCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAGTC < SRR3722112.699286/100‑1 (MQ=60)
TCACCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCG‑GGATATTAGTCTGGAAGGCAATACCGTC > SRR3722112.642175/1‑100 (MQ=60)
ACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAGTCTGGAAGGCAATACCGTCGATAACGC < SRR3722112.315085/100‑1 (MQ=60)
CGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAGTCTGGAAGGCAATACCGTCGATAACGCTGAT > SRR3722112.239445/1‑100 (MQ=60)
|
GTCTTCAATGAGGGCTTTGATCTCTTTTGCCGCCTGGGCGCTGCGACTGGCAAGATTACGCACTTCACCCGCCACCACGGCAAAACCACGGCCCTGTTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAGTCTGGAAGGCAATACCGTCGATAACGCTGAT > NZ_CP009273/1965686‑1965862
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
