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 F4 I88 R1
|
217 |
30.5 |
1742422 |
95.9% |
1670982 |
87.3 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
635,449 |
T→C |
S81P (TCC→CCC) |
ahpF → |
alkyl hydroperoxide reductase subunit F |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 635,449 | 0 | T | C | 100.0%
| 113.2
/ NA
| 31 | S81P (TCC→CCC) | ahpF | alkyl hydroperoxide reductase subunit F |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (22/9); total (22/9) |
AGAAGATAACAGCTTGCCGGTGCGTAAGCCGTCTTTCCTGATCACCAACCCAGGTTCCAACCAGGGGCCACGTTTTGCAGGCTCCCCGCTGGGCCACGAGTTCACCTCGCTGGTACTGGCGTTGCTGTGGACCGGTGGTCATCCGTCGAAAGAAGCGCAGTC > NZ_CP009273/635367‑635528
|
agaagaTAACAGCTTGCCGGTGCGTAAGCCGTCTTTCCTGATCACCAACCCAGGTTCCAACCAGGGGCCACGTTTTGCAGGCCCCCCGCTg < 1:699064/91‑1 (MQ=255)
agaTAACAGCTTGCCGGTGCGTAAGCCGTCTTTCCTGATCACCAACCCAGGTTCCAACCAGGGGCCACGTTTTGCAGGCCCCCCGCTGGGc > 2:53979/1‑91 (MQ=255)
agaTAACAGCTTGCCGGTGCGTAAGCCGTCTTTCCTGATCACCAACCCAGGTTCCAACCAGGGGCCACGTTTTGCAGGCCCCCCGCTGGGc > 2:374407/1‑91 (MQ=255)
agaTAACAGCTTGCCGGTGCGTAAGCCGTCTTTCCTGATCACCAACCCAGGTTCCAACCAGGGGCCACGTTTTGCAGGCCCCCCGCTGGGc > 2:744471/1‑91 (MQ=255)
tAACAGCTTGCCGGTGCGTAAGCCGTCTTTCCTGATCACCAACCCAGGTTCCAACCAGGGGCCACGTTTTGCAGGCCCCCCGCTGGGCCAc > 2:934/1‑91 (MQ=255)
gTAAGCCGTCTTTCCTGATCACCAACCCAGGTTCCAACCAGGGGCCACGTTTTGCAGGCCCCCCGCTGGGCCACGAGTTCACCTCGCTGGt > 2:673496/1‑91 (MQ=255)
aGCCGTCTTTCCTGATCACCAACCCAGGTTCCAACCAGGGGCCACGTTTTGCAGGCCCCCCGCTGGGCCACGAGTTCACCTCGCTGGTACt < 2:26016/91‑1 (MQ=255)
cTTTCCTGATCACCAACCCAGGTTCCAACCAGGGGCCACGTTTTGCAGGCCCCCCGCTGGGCCACGAGTTCACCTCGCTGGTACTGGCGtt > 1:201387/1‑91 (MQ=255)
ttCCTGATCACCAACCCAGGTTCCAACCAGGGGCCACGTTTTGCAGGCCCCCCGCTGGGCCACGAGTTCACCTCGCTGGTACTGGCGTTGc > 2:194114/1‑91 (MQ=255)
ccTGATCACCAACCCAGGTTCCAACCAGGGGCCACGTTTTGCAGGCCCCCCGCTGGGCCACGAGTTCACCTCGCTGGTACTGGCGTTGCtg < 1:53979/91‑1 (MQ=255)
cTGATCACCAACCCAGGTTCCAACCAGGGGCCACGTTTTGCAGGCCCCCCGCTGGGCCACGAGTTCACCTCGCTGGTACTGGCGTTGCtgt > 2:354267/1‑91 (MQ=255)
cACCAACCCAGGTTCCAACCAGGGGCCACGTTTTGCAGGCCCCCCGCTGGGCCACGAGTTCACCTCGCTGGTACTGGCGTTGCTGTGGAcc < 2:522109/91‑1 (MQ=255)
cACCAACCCAGGTTCCAACCAGGGGCCACGTTTTGCAGGCCCCCCGCTGGGCCACGAGTTCACCTCGCTGGTACTGGCGTTGCTGTGGAcc > 1:537671/1‑91 (MQ=255)
cACCAACCCAGGTTCCAACCAGGGGCCACGTTTTGCAGGCCCCCCGCTGGGCCACGAGTTCACCTCGCTGGTACTGGCGTTGCTGTGGAcc < 1:404232/91‑1 (MQ=255)
ccAACCCAGGTTCCAACCAGGGGCCACGTTTTGCAGGCCCCCCGCTGGGCCACGAGTTCACCTCGCTGGTACTGGCGTTGCTGTGGACCgg > 1:708457/1‑91 (MQ=255)
ccAACCCAGGTTCCAACCAGGGGCCACGTTTTGCAGGCCCCCCGCTGGGCCACGAGTTCACCTCGCTGGTACTGGCGTTGCTGTGGACCgg > 2:849215/1‑91 (MQ=255)
ccAACCCAGGTTCCAACCAGGGGCCACGTTTTGCAGGCCCCCCGCTGGGCCACGAGTTCACCTCGCTGGTACTGGCGTTGCTGTGGACCgg > 2:585841/1‑91 (MQ=255)
aaCCCAGGTTCCAACCAGGGGCCACGTTTTGCAGGCCCCCCGCTGGGCCACGAGTTCACCTCGCTGGTACTGGCGTTGCTGTGGACCggtg > 2:125580/1‑91 (MQ=255)
aGGTTCCAACCAGGGGCCACGTTTTGCAGGCCCCCCGCTGGGCCACGAGTTCACCTCGCTg > 1:634681/1‑61 (MQ=255)
aGGTTCCAACCAGGGGCCACGTTTTGCAGGCCCCCCGCTGGGCCACGAGTTCACCTCGCTg < 2:634681/61‑1 (MQ=255)
cAACCAGGGGCCACGTTTTGCAGGCCCCCCGCTGGGCCACGAGTTCACCTCGCTGGTACTGGCGTTGCTGTGGACCGGTGGTCATCCGTCg > 1:184064/1‑91 (MQ=255)
cAACCAGGGGCCACGTTTTGCAGGCCCCCCGCTGGGCCACGAGTTCACCTCGCTGGTACTGGCGTTGCTGTGGACCGGTGGTCATCCGTCg > 2:502807/1‑91 (MQ=255)
aaCCAGGGGCCACGTTTTGCAGGCCCCCCGCTGGGCCACGAGTTTACCTCGCTGGTACTGGCGTTGCTGTGGACCGGTGGTCATCCGTCGa > 1:119475/1‑91 (MQ=255)
aaCCAGGGGCCACGTTTTGCAGGCCCCCCGCTGGGCCACGAGTTCACCTCGCTGGTACTGGCGTTGCTGTGGACCGGTGGTCATCCGTCGa > 2:396414/1‑91 (MQ=255)
ggggCCACGTTTTGCAGGCCCCCCGCTGGGCCACGAGTTCACCTCGCTGGTACTGGCGTTGCTGTGGACCGGTGGTCATCCGTCGAaagaa > 2:482898/1‑91 (MQ=255)
ggggCCACGTTTTGCAGGCCCCCCGCTGGGCCACGAGTTCACCTCGCTGGTACTGGCGTTGCTGTGGACCGGTGGTCATCCGTCGAaagaa > 2:741524/1‑91 (MQ=255)
ccACGTTTTGCAGGCCCCCCGCTGGGCCACGAGTTCACCTCGCTGGTACTGGCGTTGCTGTGGACCGGTGGTCATCCGTCGAAAGAAgcgc > 2:190314/1‑91 (MQ=255)
ccACGTTTTGCAGGCCCCCCGCTGGGCCACGAGTTCACCTCGCTGGTACTGGCGTTGCTGTGGACCGGTGGTCATCCGTCGAAAGAAgcgc < 2:148693/91‑1 (MQ=255)
ccACGTTTTGCAGGCCCCCCGCTGGGCCACGAGTGCACCTCGCTGGTACTGGCGGTGCTGTGGACCGGTGGTCATCCGTCGAAAGAAgcgc < 2:347944/91‑1 (MQ=255)
aCGTTTTGCAGGCCCCCCGCTGGGCCACGAGTTCACCTCGCTGGTACTGGCGTTGCTGTGGACCGGTGGTCATCCGTCGAAAGAAGCGCAg > 1:620216/1‑91 (MQ=255)
gTTTTGCAGGCCCCCCGCTGGGCCACGAGTTCACCTCGCTGGTACTGGCGTTGCTGTGGACCGGTGGTCATCCGTCGAAAGAAGCGCAGtc < 2:445753/91‑1 (MQ=255)
|
AGAAGATAACAGCTTGCCGGTGCGTAAGCCGTCTTTCCTGATCACCAACCCAGGTTCCAACCAGGGGCCACGTTTTGCAGGCTCCCCGCTGGGCCACGAGTTCACCTCGCTGGTACTGGCGTTGCTGTGGACCGGTGGTCATCCGTCGAAAGAAGCGCAGTC > NZ_CP009273/635367‑635528
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ 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
AGAAGATAACAGCTTGCCGGTGCGTAAGCCGTCTTTCCTGATCACCAACCCAGGTTCCAACCAGGGGCCACGTTTTGCAGGCTCCCCGCTGGGCCACGAGTTCACCTCGCTGGTACTGGCGTTGCTGTGGACCGGTGGTCATCCGTCGAAAGAAGCGCAGTCTCTGCTGGAGCAGATTCG > NZ_CP009273/635367‑635546
|
AGAAGATAACAGCTTGCCGGTGCGTAAGCCGTCTTTCCTGATCACCAACCCAGGTTCCAACCAGGGGCCACGTTTTGCAGGCCCCCCGCTGGGCCACGAGT < SRR3722118.714316/101‑1 (MQ=60)
CGTAAGCCGTCTTTCCTGATCACCAACCCAGGTTCCAACCAGGGGCCACGTTTTGCAGGCCCCCCGCTGGGCCACGAGTTCACCTCGCTGGTACTGGCGTT > SRR3722118.205386/1‑101 (MQ=60)
CCGTCTTTCCTGATCACCAACCCAGGTTCCAACCAGGGGCCACGTTTTGCAGGCCCCCGGCTGGGCCACGAGTTCACCTCGCTGGTACTGGCGTTGCTGTG > SRR3722118.679559/1‑101 (MQ=60)
CTTTCCTGATCACCAACCCAGGTTCCAACCAGGGGCCACGTTTTGCAGGCCCCCCGCTGGGCCtgtctcttatacacatctccgagcccacgagacggact > SRR3722118.370094/1‑63 (MQ=60)
CTTTCCTGATCACCAACCCAGGTTCCAACCAGGGGCCACGTTTTGCAGGCCCCCCGCTGGGCCACGAGTTCACCTCGCTGGTACTGGCGTTGCTGTGGACC > SRR3722118.549079/1‑101 (MQ=60)
TTCCTGATCACCAACCCAGGTTCCAACCAGGGGCCACGTTTTGCAGGCCCCCCGCTGGGCCACGAGTTCACCTCGCTGGTACTGGCGTTGCTGTGGACCGG > SRR3722118.723973/1‑101 (MQ=60)
CCTGATCACCAACCCAGGTTCCAACCAGGGGCCACGTTTTGCAGGCCCCCCGCTGGGCCACGAGTTCACCTCGCTGGTACTGGCGTTGCTGTGGACCGGTG < SRR3722118.54983/101‑1 (MQ=60)
TCACCAACCCAGGTTCCAACCAGGGGCCACGTTTTGCAGGCCCCCCGCTGGGCCACGAGTTCACCTCGCTGGTACTGGCGTctgtctcttatacacatctc > SRR3722118.648363/1‑81 (MQ=60)
CACCAACCCAGGTTCCAACCAGGGGCCACGTTTTGCAGGCCCCCCGCTGGGCCACGAGTTCACCTCGCTGGTACTGGCGTTGCTGTGGACCGGTGGTCATC < SRR3722118.412713/101‑1 (MQ=60)
ACCCAGGTTCCAACCAGGGGCCACGTTTTGCAGGCCCCCCGCTGGGCCACGAGTTCACCTCGCTGGTACTGGCGTTGCTGTGGACCGGTGGTCATCCGTCG > SRR3722118.187692/1‑101 (MQ=60)
CCCAGGTTCCAACCAGGGGCCACGTTTTGCAGGCCCCCCGCTGGGCCACGAGTTTACCTCGCTGGTACTGGCGTTGCTGTGGACCGGTGGTCATCCGTCGA > SRR3722118.121707/1‑101 (MQ=60)
ACCAGGGGCCACGTTTTGCAGGCCCCCCGCTGGGCCACGAGTTCACCTCGCTGGTACTGGCGTTGCTGTGGACCGGTGGTCATCCGTCGAAAGAAGCGCAG > SRR3722118.633517/1‑101 (MQ=60)
CGTTTTGCAGGCCCCCCGCTGGGCCACGAGTTCACCTCGCTGGTACTGGCGTTGCTGTGGACCGGTGGTCATCCGTCGAAAGAAGCGCAGTCTCTGCTGGA > SRR3722118.660469/1‑101 (MQ=60)
GGCCCCCCGCTGGGCCACGAGTTCACCTCGCTGGTACTGGCGTTGCTGTGGACCGGTGGTCATCCGTCGAAAGAAGCGCAGTCTCTGCTGGAGCAGATTCG > SRR3722118.301849/1‑101 (MQ=60)
|
AGAAGATAACAGCTTGCCGGTGCGTAAGCCGTCTTTCCTGATCACCAACCCAGGTTCCAACCAGGGGCCACGTTTTGCAGGCTCCCCGCTGGGCCACGAGTTCACCTCGCTGGTACTGGCGTTGCTGTGGACCGGTGGTCATCCGTCGAAAGAAGCGCAGTCTCTGCTGGAGCAGATTCG > NZ_CP009273/635367‑635546
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
