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 I227 R1
|
223 |
21.3 |
1167702 |
97.0% |
1132670 |
86.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
3,179,271 |
G→A |
A167T (GCC→ACC) |
ygiL → |
fimbrial‑like protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 3,179,271 | 0 | G | A | 100.0%
| 54.0
/ NA
| 17 | A167T (GCC→ACC) | ygiL | fimbrial‑like protein |
| Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (8/9); total (8/9) |
ACTCCGGTAGTAATTACGTTCAACAATACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATGCCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGATTGCTTACGAGTAATCGCATTTGGCCGGGTTCGCCCGGCCACA > NZ_CP009273/3179187‑3179353
|
aCTCCGGTAGTAATTACGTTCAACAATACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATaccacc > 2:425833/1‑90 (MQ=255)
tagtaATTACGTTCAACAATACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCa < 1:118778/90‑1 (MQ=255)
aaTTACGTTCAACAATACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGt > 1:97478/1‑90 (MQ=255)
gTTCAACAATACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGttt > 2:508404/1‑86 (MQ=255)
gTTCAACAATACCAACAGCTATCACGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGttt < 1:508404/86‑1 (MQ=255)
tCAACAATACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTc < 1:320710/90‑1 (MQ=255)
tCAACAATACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTc > 2:292153/1‑90 (MQ=255)
caaTACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGc < 1:266190/90‑1 (MQ=255)
caaTACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGc < 1:562922/90‑1 (MQ=255)
caaTACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGc < 1:427439/90‑1 (MQ=255)
aTACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGCTg > 1:462546/1‑90 (MQ=255)
aTACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGCTg < 1:418088/90‑1 (MQ=255)
aaCAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGCTGACTAc > 1:385007/1‑90 (MQ=255)
cTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGAt < 1:365969/90‑1 (MQ=255)
gAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGATTGCTTAc > 2:341963/1‑90 (MQ=255)
cTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGATTGCTTACGAg > 1:279999/1‑90 (MQ=255)
aTCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGATTGCTTACGAGTAATCGCATTTGGCCGGGTTCGc > 1:542388/1‑90 (MQ=255)
cAAAGATACCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGATTGCTTACGAGTAATCGCATTTGGCCGGGTTCGCCCGGCcaca < 1:425833/90‑1 (MQ=255)
|
ACTCCGGTAGTAATTACGTTCAACAATACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATGCCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGATTGCTTACGAGTAATCGCATTTGGCCGGGTTCGCCCGGCCACA > NZ_CP009273/3179187‑3179353
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 30 ≤ 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
TAACTTTAGGTACTCCGGTAGTAATTACGTTCAACAATACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATGCCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGATTGCTTACGAGTAATCGCATTTGGCCGGGTTCGCCCGGCCACATCATTAACGGATTAATG > NZ_CP009273/3179176‑3179370
|
TAACTTTAGGTACTCCGGTAGTAATTACGTTCAACAATACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCAC < SRR3722111.206914/100‑1 (MQ=60)
ACTTTAGGTACTCCGGTAGTAATTACGTTCAACAATACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCC < SRR3722111.272134/100‑1 (MQ=60)
CTCCGGTAGTAATTACGTTCAACAATACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGT > SRR3722111.98689/1‑100 (MQ=60)
TAGTAATTACGTTCAACAATACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGC < SRR3722111.120274/100‑1 (MQ=60)
TTACGTTCAACAATACCAACAGCTATCACGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGC < SRR3722111.516275/100‑1 (MQ=60)
ACGTTCAACAATACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGCTG > SRR3722111.469588/1‑100 (MQ=60)
TCAACAATACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGCTGACTA < SRR3722111.324955/100‑1 (MQ=60)
CAACAATACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGCTGACTAC > SRR3722111.390547/1‑100 (MQ=60)
CAATACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAG < SRR3722111.269390/100‑1 (MQ=60)
CAATACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAG < SRR3722111.433797/100‑1 (MQ=60)
CAATACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAG < SRR3722111.571773/100‑1 (MQ=60)
ATACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGAT < SRR3722111.424254/100‑1 (MQ=60)
CTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGATTGCTTACGAG > SRR3722111.283510/1‑100 (MQ=60)
CTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGATTGCTTACGAG < SRR3722111.371112/100‑1 (MQ=60)
CTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGATTGCTTACGAGTAATCGCATTTGGCCGGGTTCGC > SRR3722111.550918/1‑100 (MQ=60)
CAAAGATACCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGATTGCTTACGAGTAATCGCATTTGGCCGGGTTCGCCCGGCCACATCATTAACGG < SRR3722111.432157/100‑1 (MQ=60)
ACCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGATTGCTTACGAGTAATCGCATTTGGCCGGGTTCGCCCGGCCACATCATTAACGGATTAATG < SRR3722111.412262/100‑1 (MQ=60)
|
TAACTTTAGGTACTCCGGTAGTAATTACGTTCAACAATACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATGCCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGATTGCTTACGAGTAATCGCATTTGGCCGGGTTCGCCCGGCCACATCATTAACGGATTAATG > NZ_CP009273/3179176‑3179370
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
