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 I206 R1
|
206 |
23.7 |
1314362 |
96.8% |
1272302 |
86.2 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
1,840,928 |
T→C |
E97G (GAA→GGA) |
topB ← |
DNA topoisomerase III |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,840,928 | 0 | T | C | 100.0%
| 55.3
/ NA
| 18 | E97G (GAA→GGA) | topB | DNA topoisomerase III |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (10/8); total (10/8) |
GTCCAGCACTTCATCCACCAGCAATTGCCCTTCACGATCCGGGTCCCCGGCGTGAACGATTTCGCTGGCTTCATGCAGGAACCGTTTGATGACGTTAAGTTGTTTGGTCACGGAGGGTCGGGGCTGTAATTGCCACTTTTCCGGG > NZ_CP009273/1840867‑1841011
|
gTCCAGCACTTCATCCACCAGCAATTGCCCTTCACGATCCGGGTCCCCGGCGTGAACGATTCCGCTGGCTTCATGCAGGAACCGTTtgat < 1:170216/90‑1 (MQ=255)
gTCCAGCACTTCATCCACCAGCAATTGCCCTTCACGATCCGGGTCCCCGGCGTGAACGATTCCGCTGGCTTCATGCAGGAACCGTTtgat > 2:157908/1‑90 (MQ=255)
gTCCAGCACTCCATCCACCAGCAATTGCCCTTCACGATCCGGGTCCCCGGCGTGAACGATTCCGCTGGCTTCATGCAGGAACCGTTtgat > 2:318491/1‑90 (MQ=255)
tCATCCACCAGCAATTGCCCTTCACGATCCGGGTCCCCGGCGTGAACGATTCCGCTGGCTTCATGCAGGAACCGTTTGATGACGTTAAgt > 1:394956/1‑90 (MQ=255)
tCATCCACCAGCAATTGCCCTTCACGATCCGGGTCCCCGGCGTGAACGATTCCGCTGGCTTCATGCAGGAACCGTTTGATGACGTTAAgt > 2:24550/1‑90 (MQ=255)
tCATCCACCAGCAATTGCCCTTCACGATCCGGGTCCCCGGCGTGAACGATTCCGCTGGCTTCATGCAGGAACCGTTTGATGACGTTAAgt > 2:243400/1‑90 (MQ=255)
caccaGCAATTGCCCTTCACGATCCGGGTCCCCGGCGTGAACGATTCCGCTGGCTTCATGCAGGAACCGTTTGATGACGTTAAGTTGttt < 1:12858/90‑1 (MQ=255)
ttGCCNTTNANGATACGGGTCCCCGGCGTGAACGATTCCGCTGGCTTCATGCAGGAACCGTTTGATGACGTTAAGTTGTTTGGTCACGGa < 2:305491/90‑1 (MQ=255)
ttGCCCTTCACGATCCGGGTCCCCGGCGTGAACGATTCCGCTGGCTTCATGCAGGAACCGTTTGATGACGTTAAGTTGTTTGGTCACGGa < 1:189662/90‑1 (MQ=255)
tCACGATCCGGTTCCCCGGCGTGAACGATTCCGCTGGCTTCATGCAGGAACCGTTTGATGACGTTAAGTTGTTTGGTCACGGAGGGTCgg > 2:240550/1‑90 (MQ=255)
aTCCGGGTCCCCGGCGTGAACGATTCCGCTGGCTTc < 1:390469/36‑1 (MQ=39)
aTCCGGGTCCCCGGCGTGAACGATTCCGCTGGCTTc > 2:390469/1‑36 (MQ=255)
ggTCCCCGGCGTGAACGATTCCGCTGGCTTCATGCAGGAACCGTTTGATGACGTTAAGTTGTTTGGTCACGGAGGGTc > 2:568062/1‑78 (MQ=255)
ggTCCCCGGCGTGAACGATTCCGCTGGCTTCATGCAGGAACCGTTTGATGACGTTAAGTTGTTTGGTCACGGAGGGTc < 1:568062/78‑1 (MQ=255)
gTCCCCGGCGTGAACGATTCCGCTGGCTTCATGCAGGAACCGTTTGATGACGTTAAGTTGTTTGGTCACGGAGGGTCGGGGCTGTAATTg > 1:611698/1‑90 (MQ=255)
ccGGCGTGAACGATTCCGCTGGCTTCATGCAGGAACCGTTTGATGACGTTAAGTTGTTTGGTCACGGAGGGTCGGGGCTGTAATTGCCAc > 2:120467/1‑90 (MQ=255)
ccGGCGTGAACGATTCCGCTGGCTTCATGCAGGAACCGTTTGATGACGTTAAGTTGTTTGGTCACGGAGGGTCGGGGCTGTAATTGCCAc < 1:254923/90‑1 (MQ=255)
aCGATTCCGCTGGCTTCATGCAGGAACCGTTTGATGACGTTAAGTTGTTTGGTCACGGAGGGTCGGGGCTGTAATTGCCACTTTTCCggg < 1:633905/90‑1 (MQ=255)
|
GTCCAGCACTTCATCCACCAGCAATTGCCCTTCACGATCCGGGTCCCCGGCGTGAACGATTTCGCTGGCTTCATGCAGGAACCGTTTGATGACGTTAAGTTGTTTGGTCACGGAGGGTCGGGGCTGTAATTGCCACTTTTCCGGG > NZ_CP009273/1840867‑1841011
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ 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
CGGTGCCAGTTGCAGATAGTCCAGCACTTCATCCACCAGCAATTGCCCTTCACGATCCGGGTCCCCGGCGTGAACGATTTCGCTGGCTTCATGCAGGAACCGTTTGATGACGTTAAGTTGTTTGGTCACGGAGGGTCGGGGCTGTAATTGCCACTTTTCCGGGACAATCGGCA > NZ_CP009273/1840849‑1841021
|
atctagtacggtctcgtgggctcggagatgtgtataagagacagGCCCTTCACGATCCGGGTCCCCGGCGTGAACGATTCCGCTGGCTTCATGCAGGAAC < SRR3722088.394646/56‑1 (MQ=60)
GTCCAGCACTTCATCCACCAGCAATTGCCCTTCACGATCCGGGTCCCCGGCGTGAACGATTCCGCTGGCTTCATGCAGGAACCGTTTGATGACGTTAAGT < SRR3722088.171935/100‑1 (MQ=60)
GTCCAGCACTTCATCCACCAGCAATTGCCCTTCACGATCCGGGTCCCCGGCGTGAACGATTCCGCTGGCTTCATGCAGGAACCGTTTGATGACGTTAAGT > SRR3722088.399207/1‑100 (MQ=60)
CACCAGCAATTGCCCTTCACGATCCGGGTCCCCGGCGTGAACGATTCCGCTGGCTTCATGCAGGAACCGTTTGATGACGTTAAGTTGTTTGGTCACGGAG < SRR3722088.13000/100‑1 (MQ=60)
TTGCCCTTCACGATCCGGGTCCCCGGCGTGAACGATTCCGCTGGCTTCATGCAGGAACCGTTTGATGACGTTAAGTTGTTTGGTCACGGAGGGTCGGGGC < SRR3722088.191560/100‑1 (MQ=60)
gagatgtgtataagagacaGGCGTGAACGATTCCGCTGGCTTCATGCAGGAACCGTTTGATGACGTTAAGTTGTTTGGTCACGGAGGGTCGGGGCTGTAA < SRR3722088.416681/81‑1 (MQ=60)
agTCACGATCCGGGTCCCCGGCGTGAACGATTCCGCTGGCTTCATGCAGGAACCGTTTGATGACGTTAAGTTGTTTGGTCACGGAGGGTCGGGGCTGTAA < SRR3722088.575028/98‑1 (MQ=60)
CACGATCCGGGTCCCCGGCGTGAACGATTCCGCTGGCTTCATGCAGGAACCGTTTGATGACGTTAAGTTGTTTGGTCACGGAGGGTCGGGGCTGTAATTG > SRR3722088.619236/1‑100 (MQ=60)
CCGGCGTGAACGATTCCGCTGGCTTCATGCAGGAACCGTTTGATGACGTTAAGTTGTTTGGTCACGGAGGGTCGGGGCTGTAATTGCCACTTTTCCGGGA < SRR3722088.257405/100‑1 (MQ=60)
ACGATTCCGCTGGCTTCATGCAGGAACCGTTTGATGACGTTAAGTTGTTTGGTCACGGAGGGTCGGGGCTGTAATTGCCACTTTTCCGGGACAATCGGCA < SRR3722088.641743/100‑1 (MQ=60)
|
CGGTGCCAGTTGCAGATAGTCCAGCACTTCATCCACCAGCAATTGCCCTTCACGATCCGGGTCCCCGGCGTGAACGATTTCGCTGGCTTCATGCAGGAACCGTTTGATGACGTTAAGTTGTTTGGTCACGGAGGGTCGGGGCTGTAATTGCCACTTTTCCGGGACAATCGGCA > NZ_CP009273/1840849‑1841021
|
| 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: ‑ |
