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 I207 R1
|
218 |
45.0 |
2482936 |
97.1% |
2410930 |
86.1 |
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%
| 119.0
/ NA
| 36 | E389D (GAA→GAC) | tar | methyl‑accepting chemotaxis protein II |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base G (15/21); total (15/21) |
AGGGCTTTGATCTCTTTTGCCGCCTGGGCGCTGCGACTGGCAAGATTACGCACTTCACCCGCCACCACGGCAAAACCACGGCCCTGTTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAGTCTGGAAGGCAATACCGTCGATAAC > NZ_CP009273/1965696‑1965856
|
aGGGCTTTGATCTCTTTTGCCGCCTGGGCGCTGCGACTGGCAAGATTACGCACTTCACCCGCCACCACGGCAAAACCACGGCCCTGGTCa > 1:805843/1‑90 (MQ=255)
ggCTTTGATCTCTTTTGCCGCCTGGGCGCTGCGACTGGCAAGATTACGCACTTCACCCGCCACCACGGCAAAACCACGGCCCTGGTCAcc > 2:1082182/1‑90 (MQ=255)
ctctTTTGCCGCCTGGGCGCTGCGACTGGCAAGATTACGCACTTCACCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCAcgcgc > 1:332040/1‑90 (MQ=255)
ctctTTTGCCGCCTGGGCGCTGCAACTGGCAAGATTACGCACTTCACCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCAcgcgc > 1:969015/1‑90 (MQ=255)
ctctTTGGCCGCCTGGGCGCGGCGACGGGCAAGATTCCCCCCTCCCCCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCAcgcgc < 1:732606/90‑1 (MQ=21)
tctTTTGCCGCCGGGGCGCTGCGACTGGCAAGATTCCGCCCTTCCCCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCAcgcgcg < 1:559190/90‑1 (MQ=255)
ctTTTGCCGCCTGGGCGCTGCGACTGGCAAGATTACGCACTTCACCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCgg > 1:1005156/1‑90 (MQ=255)
ctTTTGCCGCCTGGGCGCTGCGACTGGCAAGATTACGCACTTCACCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCgg > 1:1221066/1‑90 (MQ=255)
ttcccgccgGGGCGCTGCGCCTGGCAAGATTCCGCCCTTCCCCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCtt < 1:546035/87‑1 (MQ=18)
gccgccTGGGCGCTGCGACTGGCAAGATTACGCACTTCACCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCa > 1:721970/1‑90 (MQ=255)
cTGGGCGCTGCGCCTGGCAAGATTACGCACTTCCCCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACcgc < 2:21027/90‑1 (MQ=21)
cTGGGCGCTGCGACTGGCAAGATTACGCACTTCCCCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACcgc < 2:490820/90‑1 (MQ=255)
cTGCGACTGGCAAGATTACGCACTTCACCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTc < 2:805843/90‑1 (MQ=255)
tGCGACTGGCAAGATTACGCACTTCACCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCa > 2:208902/1‑90 (MQ=255)
gCGACTGGCAAGATTACGCACTTCACCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCAcgcgc < 2:954003/69‑1 (MQ=255)
gCGACTGGCAAGATTACGCACTTCACCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCAcgcgc > 1:954003/1‑69 (MQ=255)
aCTGGCAAGATTACGCACTTCCCCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAgcgc < 2:958861/90‑1 (MQ=255)
cTGGCAAGATTACGCCCTTCCCCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGcgcg < 1:636894/90‑1 (MQ=255)
cTGGCAAGATTACGCACTTCCCCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGcgcg < 2:323532/90‑1 (MQ=255)
cTGGCAAGATTACGCACTTCACCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGcgcg < 2:1005156/90‑1 (MQ=255)
tGGCAAGATTCCCCCCTCCACCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGa < 1:331256/90‑1 (MQ=37)
aCGCACTTCACCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAGt > 1:101048/1‑90 (MQ=255)
cccgcACCCGCCCCCACGGCAAAACCACGGCCCTGGTCACCCGCCCGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAGTCTgg < 1:847755/86‑1 (MQ=255)
aCTTCACCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAGTCTgg < 2:1221066/90‑1 (MQ=255)
ttCACCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAGTCTGGaa > 1:648157/1‑90 (MQ=255)
ttCACCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAGTCTGGaa < 1:228893/90‑1 (MQ=255)
ccccGCCACCACGGCGAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAGTCTGGAAGGc < 2:500547/89‑1 (MQ=255)
ccGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAGTCTGGAAGGCaa < 2:519569/90‑1 (MQ=255)
ccGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAGTCTGGAAGGCaa < 1:801532/90‑1 (MQ=255)
caccacGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAg > 1:657833/1‑66 (MQ=255)
caccacGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAg < 2:657833/66‑1 (MQ=255)
caccacGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATAtt > 1:611227/1‑72 (MQ=255)
caccacGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATAtt < 2:611227/72‑1 (MQ=255)
caccacGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAGTCTGGAAGGCAATAcc > 2:470523/1‑90 (MQ=255)
cacGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAGTCTGGAAGGCAATACCGTc > 1:899778/1‑90 (MQ=255)
aaaaCCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAGTCTGGAAGGCAATACCGTCGATAAc < 2:912152/90‑1 (MQ=255)
|
AGGGCTTTGATCTCTTTTGCCGCCTGGGCGCTGCGACTGGCAAGATTACGCACTTCACCCGCCACCACGGCAAAACCACGGCCCTGTTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAGTCTGGAAGGCAATACCGTCGATAAC > NZ_CP009273/1965696‑1965856
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 24 ≤ 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
AGTCTTCAATGAGGGCTTTGATCTCTTTTGCCGCCTGGGCGCTGCGACTGGCAAGATTACGCACTTCACCCGCCACCACGGCAAAACCACGGCCCTGTTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAGTCTGGAAGGCAATACCGTCGATAACGCTGATAATGTC > NZ_CP009273/1965685‑1965868
|
AGTCTTCAATGAGGGCTTTGATCTCTTTTGCCGCCTGGGCGCTGCGACTGGAAAGATTACGCACTTCACCCGCCACCACGGCAAAACCACGGCCCTGGTC < SRR3722089.1254751/100‑1 (MQ=60)
GTCTTCAATGAGGGCTTTGATCTCTTTTGCCGCCTGGGCGCTGCGACTGGCAAGATTACGCACTTCACCCGCCACCACGGCAAAACCACGGCCCTGGTCA > SRR3722089.817054/1‑100 (MQ=60)
TCAATGAGGGCTTTGATCTCTTTTGCCGCCTGGGCGCTGCGACTGGCAAGATTACGCACTTCACCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCG < SRR3722089.516789/100‑1 (MQ=60)
GGGCTTTGATCTCTTTTGCCGCCTGGGCGCTGCGACTGGCAAGATTACGCACTTCACCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGC > SRR3722089.336194/1‑100 (MQ=60)
GGGCTTTGATCTCTTTTGCCGCCTGGGCGCTGCAACTGGCAAGATTACGCACTTCACCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGC > SRR3722089.983322/1‑100 (MQ=60)
GCTTTGATCTCTTTTGCCGCCTGGGCGCTGCGACTGGCAAGATTACGCACTTCACCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGG > SRR3722089.1020123/1‑100 (MQ=60)
GCTTTGATCTCTTTTGCCGCCTGGGCGCTGCGACTGGCAAGATTACGCACTTCACCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGG > SRR3722089.1239631/1‑100 (MQ=60)
GATCTCTTTTGCCGCCTGGGCGCTGCGACTGGCAAGATTACGCACTTCACCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCA > SRR3722089.731365/1‑100 (MQ=60)
CTCTTTGGCCGCCTGGGCGCGGCGACGGGCAAGATTCCCCCCTCCCCCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACC < SRR3722089.742150/100‑1 (MQ=60)
TCTTTTGCCGCCGGGGCGCTGCGACTGGCAAGATTCCGCCCTTCCCCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCG < SRR3722089.565702/100‑1 (MQ=60)
TTCCCGCCGGGGCGCTGCGCCTGGCAAGATTCCGCCCTTCCCCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGC < SRR3722089.552387/100‑1 (MQ=60)
CCTGGGCGCTGCGACTGGCAAGATTACGCACTTCACCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCctgtctcttat > SRR3722089.968022/1‑89 (MQ=60)
CTGGCAAGATTACGCCCTTCCCCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAG < SRR3722089.645011/100‑1 (MQ=60)
TGGCAAGATTCCCCCCTCCACCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAGT < SRR3722089.335399/100‑1 (MQ=60)
TGGCAAGATTACGCACTTCACCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAGT > SRR3722089.102308/1‑100 (MQ=60)
gatcccgccctcccCCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAGTCTGGAA < SRR3722089.646399/86‑1 (MQ=60)
GATTACGCACTTCACCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAGTCTGGAA > SRR3722089.656469/1‑100 (MQ=60)
cctcccCCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAGTCTGGAAGGCAATAC < SRR3722089.290859/94‑1 (MQ=60)
cctcccCCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAGTCTGGAAGGCAATAC < SRR3722089.1098485/94‑1 (MQ=60)
cccgCACCCGCCCCCACGGCAAAACCACGGCCCTGGTCACCCGCCCGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAGTCTGGAAGGCAATAC < SRR3722089.859815/96‑1 (MQ=60)
CTTCACCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAGTCctgtctcttataca > SRR3722089.666308/1‑86 (MQ=60)
CTTCACCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAGTCTGGAAGctgtctct > SRR3722089.618842/1‑92 (MQ=60)
TTCACCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAGTCTGGAAGGCAATACCG < SRR3722089.231799/100‑1 (MQ=60)
CACCCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAGTCTGGAAGGCAATACCGTC > SRR3722089.912832/1‑100 (MQ=60)
CCGCCACCACGGCAAAACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAGTCTGGAAGGCAATACCGTCGAT < SRR3722089.812643/100‑1 (MQ=60)
agatgtgtataagagacaGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAGTCTGGAAGGCAATACCGTCGATAAC < SRR3722089.730495/82‑1 (MQ=60)
AACCACGGCCCTGGTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAGTCTGGAAGGCAATACCGTCGATAACGCTGATAATGTC > SRR3722089.36036/1‑100 (MQ=60)
|
AGTCTTCAATGAGGGCTTTGATCTCTTTTGCCGCCTGGGCGCTGCGACTGGCAAGATTACGCACTTCACCCGCCACCACGGCAAAACCACGGCCCTGTTCACCCGCACGCGCGGCTTCAACCGCGGCATTCAGCGCGAGGATATTAGTCTGGAAGGCAATACCGTCGATAACGCTGATAATGTC > NZ_CP009273/1965685‑1965868
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
