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 F3 I122 R1
|
193 |
20.9 |
1228102 |
94.7% |
1163012 |
84.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
3,650,010 |
(T)6→5 |
coding (91/333 nt) |
hdeA ← |
acid‑activated periplasmic chaperone HdeA |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 3,650,005 | 0 | T | . | 100.0%
| 136.6
/ NA
| 32 | coding (96/333 nt) | hdeA | acid‑activated periplasmic chaperone HdeA |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base . (14/18); total (14/18) |
GCGCTTCAGCAAAACCAACTGCAGTTGGCTGGAAGGATTCGTCCACAGCCAGGAAATCTTCACAGGTCCAGGAGTTGACCGGTTTTTTGTTATCAGCTGCTTTTTGCGCATCCGCTGCATTGCTCACAACTGGCAGAAGAAGCAGACCACCAAGAATAACGCCTAA > NZ_CP009273/3649923‑3650088
|
gcgcTTCAGCAAAACCAACTGCAGTTGGCTGGAAGGATTCGTCCACAGCCAGGAAATCTTCACAGGTCCAGGAGTTGACCGGtttttgtt > 1:121129/1‑87 (MQ=255)
cgcTTCAGCAAAACCAACTGCAGTTGGCTGGAAGGATTCGTCCACAGCCAGGAAATCTTCACAGGTCCAGGAGTTGACCGGtttttgtta < 2:179329/90‑5 (MQ=255)
tCAGCAAAACCAACTGCAGTTGGCTGGAAGGATTCGTCCACAGCCAGGAAATCTTCACAGGTCCAGGAGTTGACCGG‑TTTTTGTTATCAg > 1:270369/1‑90 (MQ=255)
tCAGCAAAACCAACTGCAGTTGGCTGGAAGGATTCGTCCACAGCCAGGAAATCTTCACAGGTCCAGGAGTTGACCGG‑TTTTTGTTATCAg < 2:509930/90‑1 (MQ=255)
aGCAAAACCAACTGCAGTTGGCTGGAAGGATTCGTCCACAGCCAGGAAATCTTCACAGGTCCAGGAGTTGACCGG‑TTTTTGTTATCAgct < 1:422332/90‑1 (MQ=255)
cTGCAGTTGGCTGGAAGGATTCGTCCACAGCCAGGAAATCTTCACAGGTCCAGGAGTTGACCGG‑TTTTTGTTATCAGCTGCTTTTTgcgc > 1:210563/1‑90 (MQ=255)
tGCAGTTGGCTGGAAGGATTCGTCCACAGCCAGGAAATCTTCACAGGTCCAGGAGTTGACCGG‑TTTTTGTTATCAGCTGCTTTTTGCGCa < 2:210563/90‑1 (MQ=255)
aGTTGGCTGGAAGGATTCGTCCACAGCCAGGAAATCTTCACAGGTCCAGGAGTTGACCGG‑TTTTTGTTATCAGCTGCTTTTTGCGCATcc < 2:162969/90‑1 (MQ=255)
cTGGAAGGATTCGTCCACAGCCAGGAAATCTTCACAGGTCCAGGAGTTGACCGG‑TTTTTGTTATCAGCTGCTTTTTGCGCATCCGCTGCa > 2:254908/1‑90 (MQ=255)
tGGAAGGATTCGTCCACAGCCAGGAAATCTTCACAGGTCCAGGAGTTGACCGG‑TTTTTGTTATCAGCTGCTTTTTGCGCATCCGCTGCAt < 2:547155/90‑1 (MQ=255)
tGGAAGGATTCGTCCACAGCCAGGAAATCTTCACAGGTCCAGGAGTTGACCGG‑TTTTTGTTATCAGCTGCTTTTTGCGCATCCGCTGCAt < 2:287170/90‑1 (MQ=255)
tGGAAGGACTCGTCCACAGCCAGGAAATCTTCACAGGTCCAGGAGTTGACCGG‑TTTTTGTTATCAGCTGCTTTTTGCGCATCCGCTGCAt < 1:24357/90‑1 (MQ=255)
ggATTCGTCCACAGCCAGGAAATCTTCACAGGTCCAGGAGTTGACCGG‑TTTTTGTTATCAGCTGCTTTTTGCGCATCCGCTGCATTGCTc < 2:533521/90‑1 (MQ=255)
ggATTCGTCCACAGCCAGGAAATCTTCACAGGTCCAGGAGTTGACCGG‑TTTTTGTTATCAGCTGCTTTTTGCGCATCCGCTGCATTGCTc < 2:270369/90‑1 (MQ=255)
aTTCGTCCACAGCCAGGAAATCTTCACAGGTCCAGGAGTTGACCGG‑TTTTTGTTATCAGCTGCTTTTTGCGCATCCGCTGCATTGCTcac < 2:85550/90‑1 (MQ=255)
caGCCAGGAAATCTTCACAGGTCCAGGAGTTGACCGG‑TTTTTGTTATCAGCTGCTTTTTGCGCATCCGCTGCATTGCTCACAACTGGCag > 1:338905/1‑90 (MQ=255)
aGGAAATCTTCACAGGTCCAGGAGTTGACCGG‑TTTTTGTTATCAGCTGCTTTTTGCGCATCCGCTGCAt < 2:557956/69‑1 (MQ=255)
aGGAAATCTTCACAGGTCCAGGAGTTGACCGG‑TTTTTGTTATCAGCTGCTTTTTGCGCATCCGCTGCAt > 1:557956/1‑69 (MQ=255)
aGGAAATCTTCACAGGTCCAGGAGTTGACCGG‑TTTTTGTTATCAGCTGCTTTTTGCGCATCCGCTGCATTGCTCACAACTGGCAgaagaa > 2:117601/1‑90 (MQ=255)
tCTTCACAGGTCCAGGAGTTGACCGG‑TTTTTGTTATCAGCTGCTTTTTGCGCATCCGCTGCATTGCTCACAACTGGCAGAAGAAGCAGac < 2:282203/90‑1 (MQ=255)
acaGGTCCAGGAGTTGACCGG‑TTTTTGTTATCAGCTGCTTTTTGCGCATCCGCTGCATTGCTCACAACTGGCAGAAGAAGCAGAccacca < 1:89275/90‑1 (MQ=255)
acaGGTCCAGGAGTTGACCGG‑TTTTTGTTATCAGCTGCTTTTTGCGCATCCGCTGCATTGCTCACAACTGGCAGAAGAAGCAGAccacca < 2:192802/90‑1 (MQ=255)
ggAGTTGACCGG‑TTTTTGTTATCAGCTGCTTTTTGCGCATCCGCTGCATTGCTCACAACTGGCAGAAGAAGCAGACCACCAAGAATAACg < 2:338905/90‑1 (MQ=255)
aGTTGACCGG‑TTTTTGTTATCAGCTGCTTTTTGCGCATCCGCTGCATTGCTCACAACTGGCAGAAGAAGCAGACCACCAAGAATAACGcc > 1:491911/1‑90 (MQ=255)
ttGACCGG‑TTTTTGTTATCAGCTGCTTTTTGCGCATCCGCTGCATTGCTca < 2:267354/51‑1 (MQ=255)
ttGACCGG‑TTTTTGTTATCAGCTGCTTTTTGCGCATCCGCTGCATTGCTca > 1:267354/1‑51 (MQ=255)
tGACCGG‑TTTTTGTTATCAGCTGCTTTTTGCGCATCCGCTGCATTGCTCACAACTgg > 1:76032/1‑57 (MQ=255)
tGACCGG‑TTTTTGTTATCAGCTGCTTTTTGCGCATCCGCTGCATTGCTCACAACTgg < 2:76032/57‑1 (MQ=255)
tGACCGG‑TTTTTGTTATCAGCTGCTTTTTGCGCATCCGCTGCATTGCTCACAACTGGCaga < 2:389168/61‑1 (MQ=255)
tGACCGG‑TTTTTGTTATCAGCTGCTTTTTGCGCATCCGCTGCATTGCTCACAACTGGCaga > 1:389168/1‑61 (MQ=255)
tGACCGG‑TTTTTGTTATCAGCTGCTTTTTGCGCATCCGCTGCATTGCTCACAACTGGCAGAAGAAGCAGACCACCAAGAATAACGCCTaa > 2:161655/1‑90 (MQ=255)
tGACCGG‑TTTTTGTTATCAGCTGCTTTTTGCGCATCCGCTGCATTGCTCACAACTGGCAGAAGAAGCAGACCACCAAGAATAACGCCTaa > 2:299869/1‑90 (MQ=255)
tGACCGG‑TTTTTGTTATCAGCTGCTTTTTGCGCATCCGCTGCATTGCTCACAACTGGCAGAAGAAGCAGACCACCAAGAATAACGCCTaa > 1:84212/1‑90 (MQ=255)
tGACCGG‑TTTTTGTTATCAGCTGCTTTTTGCGCATCCGCTGCATTGCTCACAACTGGCAGAAGAAGCAGACCACCAAGAATAACGCCTaa > 1:17592/1‑90 (MQ=255)
|
GCGCTTCAGCAAAACCAACTGCAGTTGGCTGGAAGGATTCGTCCACAGCCAGGAAATCTTCACAGGTCCAGGAGTTGACCGGTTTTTTGTTATCAGCTGCTTTTTGCGCATCCGCTGCATTGCTCACAACTGGCAGAAGAAGCAGACCACCAAGAATAACGCCTAA > NZ_CP009273/3649923‑3650088
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
TTGTTGTTCAGCGCTTCAGCAAAACCAACTGCAGTTGGCTGGAAGGATTCGTCCACAGCCAGGAAATCTTCACAGGTCCAGGAGTTGACCGGTTTTTTGTTATCAGCTGCTTTTTGCGCATCCGCTGCATTGCTCACAACTGGCAGAAGAAGCAGACCACCAAGAATAACGCCTAATACTTTTTTCATCGTAATAT > NZ_CP009273/3649913‑3650108
|
TTGTTGTTCAGCGCTTCAGCAAAACCAACTGCAGTTGGCTGGAAGGATTCGTCCACAGCCAGGAAATCTTCACAGGTCCAGGAGTTGACCGG‑TTTTTGTT > SRR3721989.123341/1‑100 (MQ=60)
GTTCAGCGCTTCAGCAAAACCAACTGCAGTTGGCTGGAAGGATTCGTCCACAGCCAGGAAATCTTCACAGGTCCAGGAGTTGACCGG‑TTTTTGTTATCAG > SRR3721989.275187/1‑100 (MQ=60)
ccaccgagatctacactccttacgtcgtcggcagcgtcagatgtgtataagagacagGGTCCAGGAGTTGACCGG‑TTTTTGTTATCAGCTGCTTTTTGCG < SRR3721989.581373/43‑1 (MQ=60)
AGCAAAACCAACTGCAGTTGGCTGGAAGGATTCGTCCACAGCCAGGAAATCTTCACAGGTCCAGGAGTTGACCGG‑TTTTTGTTATCAGCTGCTTTTTGCG < SRR3721989.431053/100‑1 (MQ=60)
GCAAAACCAACTGCAGTTGGCTGGAAGGATTCGTCCACAGCCAGGAAATCTTCACAGGTCCAGGAGTTGACCGG‑TTTTTGTTATCAGCTGCTTTTTGCGC > SRR3721989.214381/1‑100 (MQ=60)
TGGAAGGACTCGTCCACAGCCAGGAAATCTTCACAGGTCCAGGAGTTGACCGG‑TTTTTGTTATCAGCTGCTTTTTGCGCATCCGCTGCATTGCTCACAAC < SRR3721989.24776/100‑1 (MQ=60)
GATTCGTCCACAGCCAGGAAATCTTCACAGGTCCAGGAGTTGACCGG‑TTTTTGTTATCAGCTGCTTTTTGCGCATCCGCTGCATTGCTCACAACTGGCAG > SRR3721989.345386/1‑100 (MQ=60)
GTCCACAGCCAGGAAATCTTCACAGGTCCAGGAGTTGACCGG‑TTTTTGTTATCAGCTGCTTTTTGCGCATCCGCTGCATTGCTCACAACctgtctcttat > SRR3721989.570059/1‑89 (MQ=60)
ACAGGTCCAGGAGTTGACCGG‑TTTTTGTTATCAGCTGCTTTTTGCGCATCCGCTGCATTGCTCACAACTGGCAGAAGAAGCAGACCACCAAGAATAACGC < SRR3721989.90889/100‑1 (MQ=60)
CAGGTCCAGGAGTTGACCGG‑TTTTTGTTATCAGCTGCTTTTTGCGCATCCGCTGCATTGCTCACAACTGGCAGAAGAAGCAGACCACCAAGAATAACGCC > SRR3721989.502316/1‑100 (MQ=60)
GGTCCAGGAGTTGACCGG‑TTTTTGTTATCAGCTGCTTTTTGCGCATCCGCTGCATTGCTCACAACTGGCAGctgtctcttatacacatctgacgctgccg > SRR3721989.272099/1‑71 (MQ=60)
GTCCAGGAGTTGACCGG‑TTTTTGTTATCAGCTGCTTTTTGCGCATCCGCTGCATctgtctcttatacacatctgacgctgccgacgacgtaaggagtgta > SRR3721989.158078/1‑54 (MQ=60)
GTCCAGGAGTTGACCGG‑TTTTTGTTATCAGCTGCTTTTTGCGCATCCGCTGCATTGCTCACAACTGGCAGAAGAAGCctgtctcttatacacatctgacg > SRR3721989.77387/1‑77 (MQ=60)
GTCCAGGAGTTGACCGG‑TTTTTGTTATCAGCTGCTTTTTGCGCATCCGCTGCATTGCTCACAACTGGCAGAAGAAGCAGACCtgtctcttatacacatct > SRR3721989.397019/1‑82 (MQ=60)
GTCCAGGAGTTGACCGG‑TTTTTGTTATCAGCTGCTTTTTGCGCATCCGCTGCATTGCTCACAACTGGCAGAAGAAGCAGACCACCAAGAATAACGCCTAA > SRR3721989.17900/1‑100 (MQ=60)
GTCCAGGAGTTGACCGG‑TTTTTGTTATCAGCTGCTTTTTGCGCATCCGCTGCATTGCTCACAACTGGCAGAAGAAGCAGACCACCAAGAATAACGCCTAA > SRR3721989.85733/1‑100 (MQ=60)
TTGTTATCAGCTGCTTTTTGCGCATCCGCTGCATTGCTCACAACTGGCAGAAGAAGCAGACCACCAAGAATAACGCCTAATACTTTTTTCATCGTAATAT < SRR3721989.164592/100‑1 (MQ=60)
|
TTGTTGTTCAGCGCTTCAGCAAAACCAACTGCAGTTGGCTGGAAGGATTCGTCCACAGCCAGGAAATCTTCACAGGTCCAGGAGTTGACCGGTTTTTTGTTATCAGCTGCTTTTTGCGCATCCGCTGCATTGCTCACAACTGGCAGAAGAAGCAGACCACCAAGAATAACGCCTAATACTTTTTTCATCGTAATAT > NZ_CP009273/3649913‑3650108
|
| 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: ‑ |
