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 I225 R1
|
227 |
21.4 |
1179702 |
97.1% |
1145490 |
86.5 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
1,855,234 |
Δ1 bp |
coding (356/1077 nt) |
ydjL ← |
zinc‑binding dehydrogenase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,855,231 | 0 | C | . | 100.0%
| 54.3
/ NA
| 14 | coding (359/1077 nt) | ydjL | zinc‑binding dehydrogenase |
| Reads supporting (aligned to +/- strand): ref base C (0/0); new base . (6/8); total (6/8) |
ATCAACACCATCAGGGATTTCCCACAACGCATGACGATGAATTTTGAGAATTTCACCAGGAACCAGACAATATTTGGAAAAACCACCGCCCCAGGTATTATTATCCAGACCAAGGTTTACTTTTTCTGTACAACACAGAAAATCACCTTGTTCACAGGCCGGACAAACAC > NZ_CP009273/1855143‑1855312
|
aTCAACACCATCAGGGATTTCCCACAACGCATGACGATGAATTTTGAGAATTTCACCAGGAACCAGACAATATTTGGAAAAACCACCGcc < 1:166370/90‑1 (MQ=255)
cAACACCATCAGGGATTTCCCACAACGCATGACGATGAATTTTGAGAATTTCACCAGGAACCAGACAATATTTGGAAAAACCACCGccca < 2:144351/90‑2 (MQ=255)
acacCATCAGGGATTTCCCACAACGCATGACGATGAATTTTGAGAATTTCACCAGGAACCAGACAATATTTGGAAAAACCACCGcccagg > 2:466404/1‑87 (MQ=255)
acacCATCAGGGATTTCCCACAACGCATGACGATGAATTTTGAGAATTTCACCAGGAACCAGACAATATTTGGAAAAACCACCGcccagg > 1:53461/1‑87 (MQ=255)
aTCAGGGATTTCCCACAACGCATGACTATGAATTTTGAGAATTTCACCAGGAACCAGACAATATTTGGAAAAACCACCG‑CCCAGGtatta > 1:277535/1‑90 (MQ=255)
ggATTTCCCACAACGCATGACGATGAATTTTGAGAATTTCACCAGGAACCAGACAATATTTGGAAAAACCACCG‑CCCAGGTATTATTATc > 1:571459/1‑90 (MQ=255)
ttCCCACAACGCATGACGATGAATTTTGAGAATTTCACCAGGAACCAGACAATATTTGGAAAAACCACCG‑CCCAGGTATTATTATCCAGa > 1:503896/1‑90 (MQ=255)
aCGCATGACGATGAATTTTGAGAATTTCACCAGGAACCAGACAATATTTGGAAAAACCACCG‑CCCAGGTATTATTATCCAGACCAAGGtt > 2:391713/1‑90 (MQ=255)
aTGACGATGAATTTTGAGAATTTCACCAGGAACCAGACAATATTTGGAAAAACCACCG‑CCCAGGTATTATTATCCAGACCAAGGTTTACt < 1:5284/90‑1 (MQ=255)
aTGAATTTTGAGAATTTCACCAGGAACCAGACAATATTTGGAAAAACCACCG‑CCCAGGTATTATTATCCAGACCAAGGTTTACTTTTTCt > 2:227959/1‑90 (MQ=255)
aTTTTGAGAATTTCACCAGGAACCAGACAATATTTGGAAAAACCACCG‑CCCAGGTATTATTATCCAGACCAAGGTTTACTTTTTCTGTac < 2:53461/90‑1 (MQ=255)
ttGAGAATTTCACCAGGAACCAGACAATATTTGGAAAAACCACCG‑CCCAGGTATTATTATCCAGACCAAGGTTTACTTTTTCTGTacaac < 2:33062/90‑1 (MQ=255)
aGACAATATTTGGAAAAACCACCG‑CCCAGGTATTATTATCCAGACCAAGGTTTACTTTTTCTGTACAACACAGAAAATCACCTTGTTcac < 1:192744/90‑1 (MQ=255)
atatTTGGAAAAACCACCG‑CCCAGGTATTATTATCCAGACCAAGGTTTACTTTTTCTGTACAACACAGAAAATCACCTTGTTCACAGGcc < 1:495286/90‑1 (MQ=255)
atatTTGGAAAAACCACCG‑CCCAGGTATTATTATCCAGACCAAGGTTTACTTTTTCTGTACAACACAGAAAATCACCTTGTTCACAGGcc < 1:245791/90‑1 (MQ=255)
aaaaaCCACCG‑CCCAGGTATTATTATCCAGACCAAGGTTTACTTTTTCTGTACAACACAGAAAATCACCTTGTTCACAGGCCGGACAAac < 2:241442/90‑1 (MQ=255)
aaaaaCCACCG‑CCCAGGTATTATTATCCAGACCAAGGTTTACTTTTTCTGTACAACACAGAAAATCACCTTGTTCACAGGCCGGACAAac < 2:472133/90‑1 (MQ=255)
aaaCCACCG‑CCCAGGTATTATTATCCAGACCAAGGTTTACTTTTTCTGTACAACACAGAAAATCACCTTGTTCACAGGCCGGACAAacac > 1:535371/1‑90 (MQ=255)
|
ATCAACACCATCAGGGATTTCCCACAACGCATGACGATGAATTTTGAGAATTTCACCAGGAACCAGACAATATTTGGAAAAACCACCGCCCCAGGTATTATTATCCAGACCAAGGTTTACTTTTTCTGTACAACACAGAAAATCACCTTGTTCACAGGCCGGACAAACAC > NZ_CP009273/1855143‑1855312
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ 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
CTCATAATCAACACCATCAGGGATTTCCCACAACGCATGACGATGAATTTTGAGAATTTCACCAGGAACCAGACAATATTTGGAAAAACCACCGCCCCAGGTATTATTATCCAGACCAAGGTTTACTTTTTCTGTACAACACAGAAAATCACCTTGTTCACAGGCCGGACAAACACCGCAAACGTGACCGCTGTT > NZ_CP009273/1855137‑1855331
|
CTCATAATCAACACCATCAGGGATTTCCCACAACGCATGACGATGAATTTTGAGAATTTCACCAGGAACCAGACAATATTTGGAAAAACCACCG‑CCCAGG > SRR3722109.54098/1‑100 (MQ=60)
AATCAACACCATCAGGGATTTCCCACAACGCATGACTATGAATTTTGAGAATTTCACCAGGAACCAGACAATATTTGGAAAAACCACCG‑CCCAGGTATTA > SRR3722109.281029/1‑100 (MQ=60)
ATCAACACCATCAGGGATTTCCCACAACGCATGACGATGAATTTTGAGAATTTCACCAGGAACCAGACAATATTTGGAAAAACCACCG‑CCCAGGTATTAT < SRR3722109.168429/100‑1 (MQ=60)
ACACCATCAGGGATTTCCCACAACGCATGACGATGAATTTTGAGAATTTCACCAGGAACCAGACAATATTTGGAAAAACCACCG‑CCCAGGTATTATTATC > SRR3722109.580122/1‑100 (MQ=60)
CATCAGGGATTTCCCACAACGCATGACGATGAATTTTGAGAATTTCACCAGGAACCAGACAATATTTGGAAAAACCACCG‑CCCAGGTATTATTATCCAGA > SRR3722109.511515/1‑100 (MQ=60)
ATGACGATGAATTTTGAGAATTTCACCAGGAACCAGACAATATTTGGAAAAACCACCG‑CCCAGGTATTATTATCCAGACCAAGGTTTACTTTTTCTGTAC < SRR3722109.5367/100‑1 (MQ=60)
AGACAATATTTGGAAAAACCACCG‑CCCAGGTATTATTATCCAGACCAAGGTTTACTTTTTCTGTACAACACAGAAAATCACCTTGTTCACAGGCCGGACA < SRR3722109.195104/100‑1 (MQ=60)
ATATTTGGAAAAACCACCG‑CCCAGGTATTATTATCCAGACCAAGGTTTACTTTTTCTGTACAACACAGAAAATCACCTTGTTCACAGGCCGGACAAACAC < SRR3722109.248677/100‑1 (MQ=60)
ATATTTGGAAAAACCACCG‑CCCAGGTATTATTATCCAGACCAAGGTTTACTTTTTCTGTACAACACAGAAAATCACCTTGTTCACAGGCCGGACAAACAC < SRR3722109.502767/100‑1 (MQ=60)
ATATTTGGAAAAACCACCG‑CCCAGGTATTATTATCCAGACCAAGGTTTACTTTTTCTGTACAACACAGAAAATCACCTTGTTCACAGGCCGGACAAACAC > SRR3722109.543517/1‑100 (MQ=60)
CCCAGGTATTATTATCCAGACCAAGGTTTACTTTTTCTGTACAACACAGAAAATCACCTTGTTCACAGGCCGGACAAACACCGCAAACGTGACCGCTGTT > SRR3722109.487411/1‑100 (MQ=60)
|
CTCATAATCAACACCATCAGGGATTTCCCACAACGCATGACGATGAATTTTGAGAATTTCACCAGGAACCAGACAATATTTGGAAAAACCACCGCCCCAGGTATTATTATCCAGACCAAGGTTTACTTTTTCTGTACAACACAGAAAATCACCTTGTTCACAGGCCGGACAAACACCGCAAACGTGACCGCTGTT > NZ_CP009273/1855137‑1855331
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
