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 |
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 | 96.9%
| 105.6
/ NA
| 33 | A167T (GCC→ACC) | ygiL | fimbrial‑like protein |
| Reads supporting (aligned to +/- strand): ref base G (0/0); major base A (12/19); minor base C (0/1); total (13/20) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
CTCCGGTAGTAATTACGTTCAACAATACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATGCCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGATTGCTTACGAGTAATCGCATTTGGCCGGGTTCGCCCGGCCA > NZ_CP009273/3179188‑3179351
|
cTCCGGTAGTAATTACGTTCAACAATACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCAccc > 2:385255/1‑90 (MQ=255)
tagtaATTACGTTCAACAATACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCa < 1:55085/90‑1 (MQ=255)
tagtaATTACGTTCAACAATACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCa < 1:561309/90‑1 (MQ=255)
agtaATTACGTTCAACAATACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCGCGGGCaa > 1:431672/1‑90 (MQ=255)
gtaATTACGTTCAACAATACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAAc < 2:261511/90‑1 (MQ=255)
ttACGTTCAACAATACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGttt < 1:285493/90‑1 (MQ=255)
ttACGTTCAACAATACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGttt < 1:425020/90‑1 (MQ=255)
tCAACAATACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTc < 2:48995/90‑1 (MQ=255)
caacaaTACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCa < 1:385255/90‑1 (MQ=255)
caaTACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGc < 1:9399/90‑1 (MQ=255)
aTACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATCCCACCCCGGGCAACGTTTACGCTCAGGCTg < 1:411000/90‑1 (MQ=255)
aTACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGCTg < 1:185371/90‑1 (MQ=255)
aTACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGCTg < 2:412994/90‑1 (MQ=255)
ccAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGCTGACt < 1:604225/90‑1 (MQ=255)
ccAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGCTGACt > 1:53287/1‑90 (MQ=255)
aaCAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGCTGACTAc > 2:532586/1‑90 (MQ=255)
cAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGCTGACTACaa > 1:484777/1‑90 (MQ=255)
aTCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGATTg > 1:586013/1‑90 (MQ=255)
aTCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGATTg > 1:417591/1‑90 (MQ=255)
aCTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATTCCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGATTGCTTACGa > 2:520449/1‑90 (MQ=255)
aCTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGATTGCTTACGa > 1:493888/1‑90 (MQ=255)
aCTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGATTGCTTACGa > 2:152655/1‑90 (MQ=255)
tttCAAAGCTTGTATGGAATCCCCAAGCAAAGGTACCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGATTGCTTACGAGTAATc < 2:110395/90‑1 (MQ=255)
tttCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGATTGCTTACGAGTAATc < 2:390026/90‑1 (MQ=255)
aaGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGATTGCTTACGAGTAATCGCAtt < 1:532586/90‑1 (MQ=255)
aaGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGATTGCTTACGAGTAATCGCAtt > 1:371861/1‑90 (MQ=255)
tCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGATTGCTTACGAGTAATCGCATTTGGc < 1:72664/90‑1 (MQ=255)
aTCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGc > 2:103162/1‑45 (MQ=255)
aTCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGc < 1:103162/45‑1 (MQ=255)
tCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGATTGCTTACGAGTAATCGCATTTGGCCGGGTTCGcc < 2:553366/90‑1 (MQ=255)
ccccAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGCTg < 1:172521/45‑1 (MQ=255)
ccccAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGCTg > 2:172521/1‑45 (MQ=255)
aGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGATTGCTTACGAGTAATCGCATTTGGCCGGGTTCACCCGGCca < 2:605937/90‑1 (MQ=255)
|
CTCCGGTAGTAATTACGTTCAACAATACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATGCCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGATTGCTTACGAGTAATCGCATTTGGCCGGGTTCGCCCGGCCA > NZ_CP009273/3179188‑3179351
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ 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
AGGTACTCCGGTAGTAATTACGTTCAACAATACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATGCCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGATTGCTTACGAGTAATCGCATTTGGCCGGGTTCGCCCGGCCACATCATTAACGGATTAA > NZ_CP009273/3179183‑3179368
|
AGGTACTCCGGTAGTAATTACGTTCAACAATACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGC < SRR3722088.185439/100‑1 (MQ=60)
GTACTCCGGTAGTAATTACGTTCAACAATACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCGCGGGCAA > SRR3722088.436589/1‑100 (MQ=60)
TAGTAATTACGTTCAACAATACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGC < SRR3722088.568211/100‑1 (MQ=60)
TAGTAATTACGTTCAACAATACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGC < SRR3722088.55673/100‑1 (MQ=60)
TTACGTTCAACAATACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGC < SRR3722088.288241/100‑1 (MQ=60)
TTACGTTCAACAATACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGC < SRR3722088.429791/100‑1 (MQ=60)
TTCAACAATACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGCTGACT > SRR3722088.53853/1‑100 (MQ=60)
CAACAATACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGCTGACTAC < SRR3722088.389335/100‑1 (MQ=60)
ACAATACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAA > SRR3722088.490546/1‑100 (MQ=60)
ggtctcgtgggctcggagatgtgtataagagacAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAG < SRR3722088.104221/67‑1 (MQ=60)
CAATACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAG < SRR3722088.9515/100‑1 (MQ=60)
ggtctcgtgggctcggagatgtgtataagagacagCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGAT < SRR3722088.174257/65‑1 (MQ=60)
ATACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATCCCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGAT < SRR3722088.415532/100‑1 (MQ=60)
ATACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGAT < SRR3722088.187226/100‑1 (MQ=60)
ACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGATTG > SRR3722088.422225/1‑100 (MQ=60)
ACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGATTG > SRR3722088.593197/1‑100 (MQ=60)
CCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGATTGC < SRR3722088.611665/100‑1 (MQ=60)
GCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGATTGCTTACGA > SRR3722088.499789/1‑100 (MQ=60)
CTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGATTGCTTACGAGTAATCGCATT > SRR3722088.375809/1‑100 (MQ=60)
AAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGATTGCTTACGAGTAATCGCATTTGGCCGGGTT < SRR3722088.539046/100‑1 (MQ=60)
TCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGATTGCTTACGAGTAATCGCATTTGGCCGGGTTCGCC < SRR3722088.73407/100‑1 (MQ=60)
AAGATACCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGATTGCTTACGAGTAATCGCATTTGGCCGGGTTCGCCCGGCCACATCATTAACGGAT > SRR3722088.84283/1‑100 (MQ=60)
ATACCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGATTGCTTACGAGTAATCGCATTTGGCCGGGTTCGCCCGGCCACATCATTAACGGATTAA > SRR3722088.119419/1‑100 (MQ=60)
|
AGGTACTCCGGTAGTAATTACGTTCAACAATACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATGCCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGATTGCTTACGAGTAATCGCATTTGGCCGGGTTCGCCCGGCCACATCATTAACGGATTAA > NZ_CP009273/3179183‑3179368
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
