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 I210 R1
|
226 |
19.6 |
1130256 |
95.4% |
1078264 |
84.4 |
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%
| 33.3
/ NA
| 10 | 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 (7/3); total (7/3) |
ATGATGGTTTCCCTTACCTTACAAATAATCAATGATGTTTTTATGTTTAAACGCAAAGCTTAACGGTCAGGCAGGAGTGAGGCAAGTCTTGATAGTCAAGGGGAAAGAGATGCGGAAAATGAAGCCTTGATCCCTTTTTCTTCTTTTTGTCTGCTATCAGCGTAGTTAGCCC > NZ_CP009273/1230172‑1230343
|
atgatgGTTTCCCTTACCTTACAAATAATCAATGATGTTTTTATGTTTAAACGCAAAGCTTAACGGTCAGGCAGGAGTGAGGCAAGtttt < 2:511581/90‑1 (MQ=255)
atgatgGTTTCCCTTACCTTACAAATAATCAATGATGTTTTAATGTTTAAACGCAAAGCTTAACGGTCAGGCAGGAGTGAGGCAAGtttt > 2:450518/1‑90 (MQ=255)
atgGTTTCCCTTACCTTACAAATAATCAATGATGTTTTTATGTTTAAACGCAAAGCTTAACGGTCAGGCAGGAGTGAGGCAAGTTTTGAt > 2:162488/1‑90 (MQ=255)
gTTTCCCTTACCTTACAAATAATCAATGATGTTTTTATGTTTAAACGCAAAGCTTAACGGTCAGGCAGGAGTGAGGCAAGTTTTGATAGt > 2:520574/1‑90 (MQ=255)
aatCAATGATGTTTTTATGTTTAAACGCAAAGCTTAACGGTCAGGCAGGAGTGAGGCAAGTTTTGATAGTCAAGGGGAAAGAGATGCGGa > 2:118014/1‑90 (MQ=255)
tgatgTTTTTATGTTTAAACGCAAAGCTTAACGGTCAGGCAGGAGTGAGGCAAGTTTTGATAGTCAAGGGGAAAGAGATGCGGAAAATGa < 1:148552/90‑1 (MQ=255)
ttAAACGCAAAGCTTAACGGTCAGGCAGGAGTGAGGCAAGTTTTGATAGTCAAGGGGAAAGAGATGCGGAAAATGAAGCCTTGATCCCtt > 2:263122/1‑90 (MQ=255)
aaaCGCAAAGCTTAACGGTCAGGCAGGAGTGAGGCAAGTTTTGATAGTCAAGGGGAAAGAGATGCGGAAAATGAAGCCTTGATCCCtttt > 1:200308/1‑90 (MQ=255)
cTTAACGGTCAGGCAGGAGTGAGGCAAGTTTTGATAGTCAAGGGGAAAGAGATGCGGAAAATGAAGCCTTGATCCCTTTTTCTTCttttt < 1:450518/90‑1 (MQ=255)
caggcaggAGTGAGGCAAGTTTTGATAGTCAAGGGGAAAGAGATGCGGAAAATGAAGCCTTGATCCCTTTTTCTTCTTTTTGTCTGCTAt > 1:47248/1‑90 (MQ=255)
aGGCAAGTTTTGATAGTCAAGGGGAAAGAGATGCGGAAAATGAAGCCTTGATCCCTTTTTCTTCTTTTTGTCTGCTATCAGCGTAGTTAg > 2:318057/1‑90 (MQ=255)
cAAGTTTTGATAGTCAAGGGGAAAGAGATGCGGAAAATGAAGCCTTGATCCCTTTTTCTTCTTTTTGTCTGCTATCAGCGTAGTTAGccc < 1:263122/90‑1 (MQ=255)
|
ATGATGGTTTCCCTTACCTTACAAATAATCAATGATGTTTTTATGTTTAAACGCAAAGCTTAACGGTCAGGCAGGAGTGAGGCAAGTCTTGATAGTCAAGGGGAAAGAGATGCGGAAAATGAAGCCTTGATCCCTTTTTCTTCTTTTTGTCTGCTATCAGCGTAGTTAGCCC > NZ_CP009273/1230172‑1230343
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ 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
AGGAGATCTCCATGATGGTTTCCCTTACCTTACAAATAATCAATGATGTTTTTATGTTTAAACGCAAAGCTTAACGGTCAGGCAGGAGTGAGGCAAGTCTTGATAGTCAAGGGGAAAGAGATGCGGAAAATGAAGCCTTGATCCCTTTTTCTTCTTTTTGTCTGCTATCAGCGTAGTTAGCCCTCTGGTATGA > NZ_CP009273/1230161‑1230353
|
AGGAGATCTCCATGATGGTTTCCCTTACCTTACAAATAATCAATGATGTTTTTATGTTTAAACGCAAAGCTTAACGGTCAGGCAGGAGTGAGGCAAGTTT < SRR3722092.266472/100‑1 (MQ=60)
TGATGTTTTTATGTTTAAACGCAAAGCTTAACGGTCAGGCAGGAGTGAGGCAAGTTTTGATAGTCAAGGGGAAAGAGATGCGGAAAATGAAGCCTTGATC < SRR3722092.151052/100‑1 (MQ=60)
TTTTATGTTTAAACGCAAAGCTTAACGGTCAGGCAGGAGTGAGGCAAGTTTTGATAGTCAAGGGGAAAGAGATGCGGAAAATGAAGCCTTGATCCCTTTT > SRR3722092.203618/1‑100 (MQ=60)
GCTTAACGGTCAGGCAGGAGTGAGGCAAGTTTTGATAGTCAAGGGGctgtctcttatacacatctgacgctgccgacgaccatcttagtgtagatctcgg > SRR3722092.194719/1‑46 (MQ=60)
GCTTAACGGTCAGGCAGGAGTGAGGCAAGTTTTGATAGTCAAGGGGAAAGAGATGCGGAAAATGAAGCCTTGATCCCTTTTTCTTCTTTTTGTCTGCTAT > SRR3722092.48049/1‑100 (MQ=60)
CTTAACGGTCAGGCAGGAGTGAGGCAAGTTTTGATAGTCAAGGGGAAAGAGATGCGGAAAATGAAGCCTTGATCCCTTTTTCTTCTTTTTGTCTGCTATC < SRR3722092.459397/100‑1 (MQ=60)
GAGTGAGGCAAGTTTTGATAGTCAAGGGGAAAGAGATGCGGAAAATGAAGCCTTGATCCCTTTTTCTTCTTTTTGTCTGCTATCAGCGTAGTTAGCCCTC > SRR3722092.276733/1‑100 (MQ=60)
CAAGTTTTGATAGTCAAGGGGAAAGAGATGCGGAAAATGAAGCCTTGATCCCTTTTTCTTCTTTTTGTCTGCTATCAGCGTAGTTAGCCCTCTGGTATGA < SRR3722092.267472/100‑1 (MQ=60)
|
AGGAGATCTCCATGATGGTTTCCCTTACCTTACAAATAATCAATGATGTTTTTATGTTTAAACGCAAAGCTTAACGGTCAGGCAGGAGTGAGGCAAGTCTTGATAGTCAAGGGGAAAGAGATGCGGAAAATGAAGCCTTGATCCCTTTTTCTTCTTTTTGTCTGCTATCAGCGTAGTTAGCCCTCTGGTATGA > NZ_CP009273/1230161‑1230353
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
