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 |
3,576,634 |
A→G |
R79R (CGA→CGG) |
BW25113_RS17825 → |
YrhA family protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 3,576,634 | 0 | A | G | 100.0%
| 35.0
/ NA
| 12 | R79R (CGA→CGG) | BW25113_RS17825 | YrhA family protein |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (6/6); total (6/6) |
GAAGTTAGTATTCTTTTTAAGAATCAACCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGATTATTTAGCCTCTCGATTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGA > NZ_CP009273/3576551‑3576711
|
gAAGTTAGTATTCTTTTTAAGAATCAACCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGGTTAttt > 2:431656/1‑90 (MQ=255)
ttAGTATTCTTTTTAAGAATCAACCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGGTTATTTAGcc < 1:16284/90‑1 (MQ=255)
ttAGTATTCTTTTTAAGAATCAACCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGGTTATTTAGcc < 2:308896/90‑1 (MQ=255)
tAGTATTCTTTTTAAGAATCAACCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGGTTATTTAGCct > 1:303823/1‑90 (MQ=255)
tAGTATTCTTTTTAAGAATCAACCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGGTTATTTAGCct > 2:452506/1‑90 (MQ=255)
tCTTTTTAAGAATCAACCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGGTTATTTAGCCTCTCGAt < 1:70237/90‑1 (MQ=255)
tttttAAGAATCAACCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGGTTATTTAGCCTCTCGATTc > 1:55433/1‑90 (MQ=255)
tCAACCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGGTTATTTAGCCTCTCGATTCCAGAACCTTc < 1:474085/90‑1 (MQ=255)
gagCAATGGATGGATTCGAAGTTAATGGATTACGGTTATTTAGCCTCTCGATTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATg < 2:303823/90‑1 (MQ=255)
gAAGTTAATGGATTACGGTTATTTAGCCTCTCGATTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAaataat > 1:133294/1‑90 (MQ=255)
gAAGTTAATGGATTACGGTTATTTAGCCTCTCGATTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAaataat > 2:508850/1‑90 (MQ=255)
tAATGGATTACGGTTATTTAGCCTCTCGATTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAAtgatga < 2:147262/90‑1 (MQ=255)
|
GAAGTTAGTATTCTTTTTAAGAATCAACCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGATTATTTAGCCTCTCGATTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGA > NZ_CP009273/3576551‑3576711
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
GTAATGAAGTTAGTATTCTTTTTAAGAATCAACCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGATTATTTAGCCTCTCGATTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATAAACCCTGATCTAC > NZ_CP009273/3576546‑3576731
|
GTAATGAAGTTAGTATTCTTTTTAAGAATCAACCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGGTTATTTAGCCT > SRR3722092.309171/1‑100 (MQ=60)
GTTAGTATTCTTTTTAAGAATCAACCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGGTTATTTAGCCTCTCGATTC > SRR3722092.56346/1‑100 (MQ=60)
TTAGTATTCTTTTTAAGAATCAACCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGGTTATTTAGCCTCTCGATTCC < SRR3722092.16571/100‑1 (MQ=60)
TCTTTTTAAGAATCAACCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGGTTATTTAGCCTCTCGATTCCAGAACCT < SRR3722092.71409/100‑1 (MQ=60)
TCAACCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGGTTATTTAGCCTCTCGATTCCAGAACCTTCAGTTAAAAAC < SRR3722092.483489/100‑1 (MQ=60)
GGATGGATTCGAAGTTAATGGATTACGGTTATTTAGCCTCTCGATTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAAT > SRR3722092.135544/1‑100 (MQ=60)
GGATTACGGTTATTTAGCCTCTCGATTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATAAACCCTG > SRR3722092.5880/1‑100 (MQ=60)
CGGTTATTTAGCCTCTCGATTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATAAACCCTGATCTAC > SRR3722092.268788/1‑100 (MQ=60)
|
GTAATGAAGTTAGTATTCTTTTTAAGAATCAACCTGATTATCTTACTTTTTTAAGAGCAATGGATGGATTCGAAGTTAATGGATTACGATTATTTAGCCTCTCGATTCCAGAACCTTCAGTTAAAAACCTTTTTGCCGTAAATGAATTTTATAGAAATAATGATGATTTCATAAACCCTGATCTAC > NZ_CP009273/3576546‑3576731
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
