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 I231 R1
|
218 |
12.8 |
703680 |
97.2% |
683976 |
86.9 |
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%
| 42.0
/ NA
| 14 | A167T (GCC→ACC) | ygiL | fimbrial‑like protein |
| Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (5/9); total (5/9) |
GTTCAACAATACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATGCCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGATTGCTTACGAGTAATCGCATTTGGCCGGGTTCGCCCGGCCACAT > NZ_CP009273/3179204‑3179354
|
gTTCAACAATACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGc < 2:115028/90‑1 (MQ=255)
tCAACAATACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTc < 2:289455/90‑1 (MQ=255)
caacaaTACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCa > 1:254542/1‑90 (MQ=255)
caacaaTACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCa < 2:254542/90‑1 (MQ=255)
aTACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGCTg < 1:241921/90‑1 (MQ=255)
aTACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGCTg > 2:244959/1‑90 (MQ=255)
aaCAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGCTGACTAc > 2:273514/1‑90 (MQ=255)
tttCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGATTGCTTACGAGTAATc < 1:293602/90‑1 (MQ=255)
ttCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGATTGCTTACGAGTAATCg > 1:22364/1‑90 (MQ=255)
aaTCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGAt > 1:281067/1‑58 (MQ=255)
aaTCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGAt < 2:281067/58‑1 (MQ=255)
aGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGATTGCTTACGAGTAATCGCATTTGGCCGGGTTCGCCCGGCca < 1:57807/90‑1 (MQ=255)
aGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGATTGCTTACGAGTAATCGCATTTGGCCGGGTTCGCCCGGCca < 2:296467/90‑1 (MQ=255)
aaaGAAACCACCCCGGGCAACGTTTACGCTCAGGCTGACTCCAAGATTGCTTACGAGTAATCGCATTTGGCCGGGTTCGCCCGGCCAcat < 1:336051/90‑1 (MQ=255)
|
GTTCAACAATACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATGCCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGATTGCTTACGAGTAATCGCATTTGGCCGGGTTCGCCCGGCCACAT > NZ_CP009273/3179204‑3179354
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 23 ≤ ATCG/ATCG < 31 ≤ 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
AAGTAACTTTAGGTACTCCGGTAGTAATTACGTTCAACAATACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATGCCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGATTGCTTACGAGTAATCGCATTTGGCCGGGTTCGCCCGGCCACATCATTAACGGA > NZ_CP009273/3179173‑3179364
|
AAGTAACTTTAGGTACTCCGGTAGTAATTACGTTCAACAATACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATAC > SRR3722116.135238/1‑100 (MQ=60)
ACTTTAGGTACTCCGGTAGTAATTACGTTCAACAATACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCC < SRR3722116.274117/100‑1 (MQ=60)
ACTTTAGGTACTCCGGTAGTAATTACGTTCAACAATACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCC < SRR3722116.312209/100‑1 (MQ=60)
TAATTACGTTCAACAATACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCA > SRR3722116.258153/1‑100 (MQ=60)
ATACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGAT < SRR3722116.245272/100‑1 (MQ=60)
GGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGATTGCTTACGAGTAATCG > SRR3722116.22661/1‑100 (MQ=60)
TTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGATTGCTTACGAGTAATCGCATTTGGCC < SRR3722116.297897/100‑1 (MQ=60)
GCTCGTATGGAATCCCCAAGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGATTGCTTACGAGctgtctcttatacacatctgac > SRR3722116.285147/1‑78 (MQ=60)
AGCAAAGATACCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGATTGCTTACGAGTAATCGCATTTGGCCGGGTTCGCCCGGCCACATCATTAAC < SRR3722116.58514/100‑1 (MQ=60)
AAAGAAACCACCCCGGGCAACGTTTACGCTCAGGCTGACTCCAAGATTGCTTACGAGTAATCGCATTTGGCCGGGTTCGCCCGGCCACATCATTAACGGA < SRR3722116.341058/100‑1 (MQ=60)
|
AAGTAACTTTAGGTACTCCGGTAGTAATTACGTTCAACAATACCAACAGCTATCAGGAACTGAATTTCAAAGCTCGTATGGAATCCCCAAGCAAAGATGCCACCCCGGGCAACGTTTACGCTCAGGCTGACTACAAGATTGCTTACGAGTAATCGCATTTGGCCGGGTTCGCCCGGCCACATCATTAACGGA > NZ_CP009273/3179173‑3179364
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
