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 |
874,237 |
C→T |
L14F (CTT→TTT) |
yliI → |
aldose sugar dehydrogenase YliI |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 874,237 | 0 | C | T | 93.8%
| 50.3
/ ‑3.7
| 16 | L14F (CTT→TTT) | yliI | aldose sugar dehydrogenase YliI |
| Reads supporting (aligned to +/- strand): ref base C (1/0); new base T (5/10); total (6/10) |
| Fisher's exact test for biased strand distribution p-value = 3.75e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.35e-01 |
ACTGACTACGCTTTAAGCCAGAGTCAATCCGGAGGCGTTATGCATCGACAATCCTTTTTCCTTGTGCCCCTTATTTGTCTTTCTTCCGCTCTCTGGGCGGCTCCTGCAACGGTAAATGTCGAAGTACTGCAAGACAAACTCGACCAT > NZ_CP009273/874159‑874305
|
aCTGACTACGCTTTAAGCCAGAGTCAATCCGGAGGCGTTATGCATCGACAATCCTTTTTCCTTGTGCCCCTTATTTGTTTTTCTTCCGct < 1:570749/90‑1 (MQ=255)
aCTGACTACGCTTTAAGCCAGAGTCAATCCGGAGGCGTTATGCATCGACAATCCTTTTTCCTTGTGCCCCTTATTTGTTTTTCTTCCGct < 2:36572/90‑1 (MQ=255)
gACTACGCTTTAAGCCAGAGTCAATCCGGAGGCGTTATGCATCGACAATCCTTTTTCCTTGTGCTCCTTATTTGTTTTTCTTCCGctctc > 2:416854/1‑90 (MQ=255)
gACTACGCTTTAAGCCAGAGTCAATCCGGAGGCGTTATGCATCGACAATCCTTTTTCCTTGTGCCCCTTATTTGTTTTTCTTCCGctctc > 1:420856/1‑90 (MQ=255)
gCTTTAAGCCAGAGTCAATCCGGAGGCGTTATGCATCGACAATCCTTTTTCCTTGTGCCCCTTATTTGTTTTTCTTCCGCTCTCTGggcg < 1:387379/90‑1 (MQ=255)
ttAAGCCAGAGTCAATCCGGAGGCGTTATGCATCGACAATCCTTTTTCCTTGTGCCCCTTATTTGTTTTTCTTCCGCTCTCTGGGCGGCt < 1:73848/90‑1 (MQ=255)
gagTCAATCCGGAGGCGTTATGCATCGACAATCCTTTTTCCTTGTGCCCCTTATTTGTTTTTCTTCCGCTCTCTGGGCGGCTCCTGCAAc > 1:244768/1‑90 (MQ=255)
cGTTATGCATCGACAATCCTTTTTCCTTGTGCCCCTTATTTGTTTTTCTTCCGCTCTCTGGGCGGCTCCTGCAACGGTAAATGTCGAAGt < 1:107939/90‑1 (MQ=255)
tCGACAATCCTTTTTCCTTGTGCCCCTTATTTGTCTTTCTTCCGCTCTCTGGGCGGCTCCTGCAACGGTAAATGTCGAAGTACTGCAAGa > 2:278666/1‑90 (MQ=255)
cGACAATCCTTTTTCCTTGTGCCCCTTATTTGTTTTTCTTCCGCTCTCTGGGCGGCTCCTGCAACGGTAAATGTCGAAGTACTGCAAGAc < 2:542314/90‑1 (MQ=255)
gACAATCCTTTTTCCTTGTGCCCCTTATTTGTTTTTCTTCCGCTCTCTGGGCGGCTCCTGCAACGGTAAATGTCGAAGTACTGCAAGACa > 2:479598/1‑90 (MQ=255)
aaTCCTTTTTCCTTGTGCCCCTTATTTGTTTTTCTTCCGCTCTCTGGGCGGCTCCTGCAACGGTAAATGTCGAAGTACTGCAAGACAAAc > 2:264665/1‑90 (MQ=255)
ttttCCTTGTGCCCCTTATTTGTTTTTCTTCCGCTCTCTGGGCGGCTCCTGCAACGGTAAATGTCGAAGTACTGCAAGACAAACTCGAcc < 1:269003/90‑1 (MQ=255)
ttttCCTTGTGCCCCTTATTTGTTTTTCTTCCGCTCTCTGGGCGGCTCCTGCAACGGTAAATGTCGAAGTACTGCAAGACAAACTCGAcc < 2:244768/90‑1 (MQ=255)
ttCCTTGTGCCCCTTATTTGTTTTTCTTCCGCTCTCTGGGCGGCTCCTGCAACGGTAAATGTCGAAGTACTGCAAGACAAACTCGACCAt < 1:160665/90‑1 (MQ=255)
ttCCTTGTGCCCCTTATTTGTTTTTCTTCCGCTCTCTGGGCGGCTCCTGCAACGGTAAATGTCGAAGTACTGCAAGACAAACTCGACCAt < 1:332024/90‑1 (MQ=255)
|
ACTGACTACGCTTTAAGCCAGAGTCAATCCGGAGGCGTTATGCATCGACAATCCTTTTTCCTTGTGCCCCTTATTTGTCTTTCTTCCGCTCTCTGGGCGGCTCCTGCAACGGTAAATGTCGAAGTACTGCAAGACAAACTCGACCAT > NZ_CP009273/874159‑874305
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ 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: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
CTCCTCCACTGACTACGCTTTAAGCCAGAGTCAATCCGGAGGCGTTATGCATCGACAATCCTTTTTCCTTGTGCCCCTTATTTGTCTTTCTTCCGCTCTCTGGGCGGCTCCTGCAACGGTAAATGTCGAAGTACTGCAAGACAAACTCGACCATCCCTGGGCAC > NZ_CP009273/874152‑874315
|
CTCCTCCACTGACTACGCTTTAAGCCAGAGTCAATCCGGAGGCGTTATGCATCGACAATCCTTTTTCCTTGTGCCCCTTATTTGTTTTTCTTCCGCTCTC > SRR3722111.427074/1‑100 (MQ=60)
ACTGACTACGCTTTAAGCCAGAGTCAATCCGGAGGCGTTATGCATCGACAATCCTTTTTCCTTGTGCCCCTTATTTGTTTTTCTTCCGCTCTCTGGGCGG < SRR3722111.579718/100‑1 (MQ=60)
GCTTTAAGCCAGAGTCAATCCGGAGGCGTTATGCATCGACAATCCTTTTTCCTTGTGCCCCTTATTTGTTTTTCTTCCGCTCTCTGGGCGGCTCCTGCAA < SRR3722111.392971/100‑1 (MQ=60)
CTTTAAGCCAGAGTCAATCCGGAGGCGTTATGCATCGACAATCCTTTTTCCTTGTGCCCCTTATTTGTTTTTCTTCCGCTCTCTGGGCGGCTCCTGCAAC > SRR3722111.247665/1‑100 (MQ=60)
TTAAGCCAGAGTCAATCCGGAGGCGTTATGCATCGACAATCCTTTTTCCTTGTGCCCCTTATTTGTTTTTCTTCCGCTCTCTGGGCGGCTCCTGCAACGG < SRR3722111.74738/100‑1 (MQ=60)
CGTTATGCATCGACAATCCTTTTTCCTTGTGCCCCTTATTTGTTTTTCTTCCGCTCTCTGGGCGGCTCCTGCAACGGTAAATGTCGAAGTACTGCAAGAC < SRR3722111.109295/100‑1 (MQ=60)
TTTTCCTTGTGCCCCTTATTTGTTTTTCTTCCGCTCTCTGGGCGGCTCCTGCAACGGTAAATGTCGAAGTACTGCAAGACAAACTCGACCATCCCTGGGC < SRR3722111.272258/100‑1 (MQ=60)
TTCCTTGTGCCCCTTATTTGTTTTTCTTCCGCTCTCTGGGCGGCTCCTGCAACGGTAAATGTCGAAGTACTGCAAGACAAACTCGACCATCCCTGGGCAC < SRR3722111.162690/100‑1 (MQ=60)
TTCCTTGTGCCCCTTATTTGTTTTTCTTCCGCTCTCTGGGCGGCTCCTGCAACGGTAAATGTCGAAGTACTGCAAGACAAACTCGACCATCCCTGGGCAC < SRR3722111.336470/100‑1 (MQ=60)
|
CTCCTCCACTGACTACGCTTTAAGCCAGAGTCAATCCGGAGGCGTTATGCATCGACAATCCTTTTTCCTTGTGCCCCTTATTTGTCTTTCTTCCGCTCTCTGGGCGGCTCCTGCAACGGTAAATGTCGAAGTACTGCAAGACAAACTCGACCATCCCTGGGCAC > NZ_CP009273/874152‑874315
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ 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: ‑ |
