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 I199 R1
|
220 |
57.5 |
3163680 |
97.0% |
3068769 |
86.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
554,427 |
A→G |
intergenic (+217/‑3) |
fimA → / → fimC |
type 1 fimbrial major subunit FimA/type 1 fimbria chaperone FimC |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 554,427 | 0 | A | G | 100.0%
| 138.9
/ NA
| 42 | intergenic (+217/‑3) | fimA/fimC | type 1 fimbrial major subunit FimA/type 1 fimbria chaperone FimC |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (20/22); total (20/22) |
TGATGTGTTGTAAGAAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAACTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCATGCTGCCGGAGGGATCGC > NZ_CP009273/554349‑554512
|
tgatgTGTTGTAAGAAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACt < 2:244839/90‑1 (MQ=255)
tgttgtAAGAAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAAt < 2:846912/90‑1 (MQ=255)
tgttgtAAGAAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAAt > 1:1265656/1‑90 (MQ=255)
tgttgtAAGAAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAAt > 1:1529664/1‑90 (MQ=255)
tgttgtAAGAAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAAt > 1:217101/1‑90 (MQ=255)
gttgtAAGAAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAGTACACAAGGCGTATTAGCTATGATGACTAAAATa < 2:264371/90‑1 (MQ=255)
gttgtAAGAAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATa < 1:58637/90‑1 (MQ=255)
gtAAGAAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTatgatg > 1:53803/1‑78 (MQ=255)
gtAAGAAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTatgatg < 2:53803/78‑1 (MQ=255)
aaaCCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGAc > 2:871763/1‑75 (MQ=255)
aaaCCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGAc < 1:871763/75‑1 (MQ=255)
aaCCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAGAATAAAGTTATTg > 1:1372335/1‑90 (MQ=255)
aaaGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGc < 1:551145/90‑1 (MQ=255)
aaaGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGc < 1:609723/90‑1 (MQ=255)
aTCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATta < 2:1509209/90‑1 (MQ=255)
ttCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTAtattt < 2:730381/90‑1 (MQ=255)
ttCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTAtattt < 1:1198731/90‑1 (MQ=255)
ttCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTAtattt < 2:1419041/90‑1 (MQ=255)
cTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATg > 2:37633/1‑76 (MQ=255)
cTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATg < 1:37633/76‑1 (MQ=255)
ccTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCAt > 2:1429314/1‑90 (MQ=255)
cTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCAtt > 1:1339210/1‑90 (MQ=255)
tttGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGcc < 1:670820/90‑1 (MQ=255)
tGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAg > 1:1185409/1‑90 (MQ=255)
cAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCa > 1:565404/1‑90 (MQ=255)
gAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCAtgc < 1:906443/90‑1 (MQ=255)
gAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCAtgc < 1:1050093/90‑1 (MQ=255)
tACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCAtgctgc < 1:944292/90‑1 (MQ=255)
aGGCGTATTAGTTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCa > 2:253032/1‑71 (MQ=255)
aGGCGTATTAGTTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCa < 1:253032/71‑1 (MQ=255)
aGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCATGCTGCCGGAgg > 1:146917/1‑90 (MQ=255)
aGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCATGCTGCCGGAgg > 1:1504774/1‑90 (MQ=255)
aGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCATGCTGCCGGAgg > 2:447799/1‑90 (MQ=255)
ggCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCATGCTGCCGGAggg > 2:1087073/1‑90 (MQ=255)
cGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCATGCTGCCGGAGGGAt < 1:722914/90‑1 (MQ=255)
cGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCATGCTGCCGGAGGGAt < 2:344383/90‑1 (MQ=255)
gTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCATGCTGCCGGAGGGATc < 2:146917/90‑1 (MQ=255)
tATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCATGCTGCCGGAGGGATCg > 1:419476/1‑90 (MQ=255)
tATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCATGCTGCCGGAGGGATCg > 1:655786/1‑90 (MQ=255)
aTTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCATGCTGCCGGAGGGa > 2:1079336/1‑86 (MQ=255)
aTTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCATGCTGCCGGAGGGa < 1:1079336/86‑1 (MQ=255)
aTTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCATGCTGCCGGAGGGATCGc > 1:365259/1‑90 (MQ=255)
|
TGATGTGTTGTAAGAAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAACTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCATGCTGCCGGAGGGATCGC > NZ_CP009273/554349‑554512
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
TTTATTAAATGAAAAGGGAATGATGTGTTGTAAGAAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAACTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCATGCTGCCGGAGGGATCGCATTAGGTGCCACGC > NZ_CP009273/554329‑554526
|
TTTATTAAATGAAAAGGGAATGATGTGTTGTAAGAAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGC < SRR3722078.469452/100‑1 (MQ=60)
AATGAAAAGGGAATGATGTGTTGTAAGACACCAAAGCAATCAATTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATG < SRR3722078.1241987/100‑1 (MQ=60)
AATGAAAAGGGAATGATGTGTTGTAAGAAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATG < SRR3722078.825079/100‑1 (MQ=60)
GGGAATGATGTGTTGTAAGAAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAAT > SRR3722078.219732/1‑100 (MQ=60)
GGGAATGATGTGTTGTAAGAAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAAT > SRR3722078.1285741/1‑100 (MQ=60)
GGGAATGATGTGTTGTAAGAAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAAT > SRR3722078.1554587/1‑100 (MQ=60)
gacagGTGTTGTAAGAAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAG < SRR3722078.883444/95‑1 (MQ=60)
ATGATGTGTTGTAAGAAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAct > SRR3722078.54440/1‑98 (MQ=60)
GTGTTGTAAGAAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGActgtctcttatacacatct > SRR3722078.1347851/1‑81 (MQ=60)
TGTTGTAAGAAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAGAATAAAGTTATTG > SRR3722078.1394447/1‑100 (MQ=60)
GTTGTAAGAAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGA < SRR3722078.59331/100‑1 (MQ=60)
acagGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATAT < SRR3722078.38086/96‑1 (MQ=60)
AAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATT < SRR3722078.616763/100‑1 (MQ=60)
AAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATT < SRR3722078.557653/100‑1 (MQ=60)
TTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCA < SRR3722078.1217536/100‑1 (MQ=60)
CTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATT > SRR3722078.1360678/1‑100 (MQ=60)
TCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAG > SRR3722078.1203945/1‑100 (MQ=60)
TTTTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCA > SRR3722078.572032/1‑100 (MQ=60)
TTTGCCGTCAGGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCATG < SRR3722078.678484/100‑1 (MQ=60)
aagagacagGGAATACACAAGGCGTATTAGTTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCATGC < SRR3722078.256130/91‑1 (MQ=60)
GGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCATGCTGCCGGAGG > SRR3722078.1529321/1‑100 (MQ=60)
GGAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCATGCTGCCGGAGG > SRR3722078.148629/1‑100 (MQ=60)
gtataagagacagGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCATGCTGCCGGAGGG < SRR3722078.1029370/87‑1 (MQ=60)
GAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCATGCTGCCGGAGGG < SRR3722078.918635/100‑1 (MQ=60)
GAATACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCATGCTGCCGGAGGG < SRR3722078.1065833/100‑1 (MQ=60)
TACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCATGCTGCCGGAGGGATC < SRR3722078.957469/100‑1 (MQ=60)
ACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCATGCTGCCGGAGGGATCG > SRR3722078.663296/1‑100 (MQ=60)
ACACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCATGCTGCCGGAGGGATCG > SRR3722078.424543/1‑100 (MQ=60)
CACAAGGCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCATGCTGCCGGAGGGATCGC > SRR3722078.369721/1‑100 (MQ=60)
GCGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCATGCTGCCGGAGGGATCGCATTAGG < SRR3722078.1095668/100‑1 (MQ=60)
CGTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCATGCTGCCGGAGGGATCGCATTAGGT < SRR3722078.731888/100‑1 (MQ=60)
GTATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCATGCTGCCGGAGGGATCGCATTAGGTG > SRR3722078.882753/1‑100 (MQ=60)
TATTAGCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCATGCTGCCGGAGGGATCGCATTAGGTGC > SRR3722078.1577869/1‑100 (MQ=60)
GCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCATGCTGCCGGAGGGATCGCATTAGGTGCCACGC > SRR3722078.445044/1‑100 (MQ=60)
GCTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCATGCTGCCGGAGGGATCGCATTAGGTGCCACGC > SRR3722078.691193/1‑100 (MQ=60)
|
TTTATTAAATGAAAAGGGAATGATGTGTTGTAAGAAACCAAAGCAATCATTTCTTTATATTCCTTATTTTTGCCGTCAGGAATACACAAGGCGTATTAACTATGATGACTAAAATAAAGTTATTGATGCTCATTATATTTTATTTAATCATTTCGGCCAGCGCCCATGCTGCCGGAGGGATCGCATTAGGTGCCACGC > NZ_CP009273/554329‑554526
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
