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 |
1,230,259 |
C→T |
intergenic (‑86/‑135) |
nhaB ← / → fadR |
Na(+)/H(+) antiporter NhaB/fatty acid metabolism transcriptional regulator FadR |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,230,259 | 0 | C | T | 100.0%
| 39.8
/ NA
| 12 | intergenic (‑86/‑135) | nhaB/fadR | Na(+)/H(+) antiporter NhaB/fatty acid metabolism transcriptional regulator FadR |
| Reads supporting (aligned to +/- strand): ref base C (0/0); new base T (5/7); total (5/7) |
ATGGTTTCCCTTACCTTACAAATAATCAATGATGTTTTTATGTTTAAACGCAAAGCTTAACGGTCAGGCAGGAGTGAGGCAAGTCTTGATAGTCAAGGGGAAAGAGATGCGGAAAATGAAGCCTTGATCCCTTTTTCTTCTTTTTGTCTGCTATCAGCGTAGTTAGCCCTC > NZ_CP009273/1230175‑1230345
|
atgGTTTCCCTTACCTTACAAATAATCAATGATGTTTTTATGTTTAAACGCAAAGCTTAACGGTCAGGCAGGAGTGAGGCAAGTTTTGAt < 1:36008/90‑1 (MQ=255)
atgGTTTCCCTTACCTTACAAATAATCAATGATGTTTTTATGTTTAAACGCAAAGCTTAACGGTCAGGCAGGAGTGAGGCAAGTTTTGAt < 2:169812/90‑1 (MQ=255)
ttCCCTTACCTTACAAATAATCAATGATGTTTTTATGTTTAAACGCAAAGCTTAACGGTCAGGCAGGAGTGAGGCAAGTTTTGATAGTCa > 1:523700/1‑90 (MQ=255)
ccttacAAATAATCAATGATGTTTTTATGTTTAAACGCAAAGCTTAACGGTCAGGCAGGAGTGAGGCAAGTTTTGATAGTCAAGGGGaaa > 1:514820/1‑90 (MQ=255)
ccttacAAATAATCAATGATGTTTTTATGTTTAAACGCAAAGCTTAACGGTCAGGCAGGAGTGAGGCAAGTTTTGATAGTCAAGGGGaaa > 2:319504/1‑90 (MQ=255)
aaTGATGTTTTTATGTTTAAACGCAAAGCTTAACGGTCAGGCAGGAGTGAGGCAAGTTTTGATAGTCAAGGGGAAAGAGATGCGGAAAAt > 1:565477/1‑90 (MQ=255)
gatgTTTTTATGTTTAAACGCAAAGCTTAACGGTCAGGCAGGAGTGAGGCAAGTTTTGATAGTCAAGGGGAAAGAGATGCGGAAAATGaa < 2:330012/90‑1 (MQ=255)
gCAAAGCTTAACGGTCAGGCAGGAGTGAGGCAAGTTTTGATAGTCAAGGGGAAAGAGATGCGGAAAATGAAGCCTTGATCCCTTTttctt > 1:194702/1‑90 (MQ=255)
aggAGTGAGGCAAGTTTTGATAGTCAAGGGGAAAGAGATGCGGAAAATGAAGCCTTGATCCCTTTTTCTTCTTTTTGTCTGCTATCAGCg < 2:414467/90‑1 (MQ=255)
aGGCAAGTTTTGATAGTCAAGGGGAAAGAGATGCGGAAAATGAAGCCTTGATCCCTTTTTCTTCTTTTTGTCTGCTATCACCGTAGTTAg < 1:401452/90‑1 (MQ=255)
cAAGTTTTGATAGTCAAGGGGAAAGAGATGCGGAAAATGAAGCCTTGATCCCTTTTTCTTCTTTTTGTCTGCTATCAGCGTAGTTAGccc < 2:468832/90‑1 (MQ=255)
aGTTTTGATAGTCAAGGGGAAAGAGATGCGGAAAATGAAGCCTTGATCCCTTTTTCTTCTTTTTGTCTGCTATCAGCGTAGTTAGCCctc < 2:561168/90‑1 (MQ=255)
|
ATGGTTTCCCTTACCTTACAAATAATCAATGATGTTTTTATGTTTAAACGCAAAGCTTAACGGTCAGGCAGGAGTGAGGCAAGTCTTGATAGTCAAGGGGAAAGAGATGCGGAAAATGAAGCCTTGATCCCTTTTTCTTCTTTTTGTCTGCTATCAGCGTAGTTAGCCCTC > NZ_CP009273/1230175‑1230345
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 25 ≤ 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
GATCTCCATGATGGTTTCCCTTACCTTACAAATAATCAATGATGTTTTTATGTTTAAACGCAAAGCTTAACGGTCAGGCAGGAGTGAGGCAAGTCTTGATAGTCAAGGGGAAAGAGATGCGGAAAATGAAGCCTTGATCCCTTTTTCTTCTTTTTGTCTGCTATCAGCGTAGTTAGCCCTCTGGTAT > NZ_CP009273/1230165‑1230351
|
gacagCCATGATGGTTTCCCTTACCTTACAAATAATCAATGATGTTTTTATGTTTAAACGCAAAGCTTAACGGTCAGGCAGGAGTGAGGCAAGTTTTGAT < SRR3722111.63521/95‑1 (MQ=60)
CCATGATGGTTTCCCTTACCTTACAAATAATCAATGATGTTTTTATGTTTAAACGCAAAGCTTAACGGTCAGGCAGGAGTGAGGCAAGTTTTGATAGTCA > SRR3722111.531893/1‑100 (MQ=60)
ATGGTTTCCCTTACCTTACAAATAATCAATGATGTTTTTATGTTTAAACGCAAAGCTTAACGGTCAGGCAGGAGTGAGGCAAGTTTTGATAGTCAAGGGG < SRR3722111.36434/100‑1 (MQ=60)
GTTTCCCTTACCTTACAAATAATCAATGATGTTTTTATGTTTAAACGCAAAGCTTAACGGTCAGGCAGGAGTGAGGCAAGTTTTGATAGTCAAGGGGAAA > SRR3722111.522843/1‑100 (MQ=60)
ACAAATAATCAATGATGTTTTTATGTTTAAACGCAAAGCTTAACGGTCAGGCAGGAGTGAGGCAAGTTTTGATAGTCAAGGGGAAAGAGATGCGGAAAAT > SRR3722111.574370/1‑100 (MQ=60)
ATGTTTAAACGCAAAGCTTAACGGTCAGGCAGGAGTGAGGCAAGTTTTGATAGTCAAGGGGAAAGAGATGCGGAAAATGAAGCCTTGATCCCTTTTTCTT > SRR3722111.197124/1‑100 (MQ=60)
AGGCAAGTTTTGATAGTCAAGGGGAAAGAGATGCGGAAAATGAAGCCTTGATCCCTTTTTCTTCTTTTTGTCTGCTATCACCGTAGTTAGCCCTCTGGTA < SRR3722111.407303/100‑1 (MQ=60)
GGCAAGTTTTGATAGTCAAGGGGAAAGAGATGCGGAAAATGAAGCCTTGATCCCTTTTTCTTCTTTTTGTCTGCTATCAGCGTAGTTAGCCCTCTGGTAT > SRR3722111.134629/1‑100 (MQ=60)
|
GATCTCCATGATGGTTTCCCTTACCTTACAAATAATCAATGATGTTTTTATGTTTAAACGCAAAGCTTAACGGTCAGGCAGGAGTGAGGCAAGTCTTGATAGTCAAGGGGAAAGAGATGCGGAAAATGAAGCCTTGATCCCTTTTTCTTCTTTTTGTCTGCTATCAGCGTAGTTAGCCCTCTGGTAT > NZ_CP009273/1230165‑1230351
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
