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 F1 I1 R1
|
66 |
46.7 |
5280542 |
98.1% |
5180211 |
47.6 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_017635 |
3,110,662 |
A→G |
E31E (GAA→GAG) |
vgrG → |
type VI secretion system tip protein VgrG |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_017635 | 3,110,662 | 0 | A | G | 100.0%
| 27.8
/ NA
| 11 | E31E (GAA→GAG) | vgrG | type VI secretion system tip protein VgrG |
| Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (2/9); total (2/9) |
GCCAGCAAAGTCCGGTGGATGTGCTGACCTTCGAAGGCCGCGAACAACTGAGTACCCCGTTCCGCTACGATATCCAGTTTACCAGT > NC_017635/3110619‑3110704
|
gCCAGCAAAGTCCGGTGGATGTGCTGACCTTTGAAGGCCGCGagcaac < 1:1494359/48‑1 (MQ=11)
cAGCAAAGTCCGGTGGATGTGCTGACCTTTGAAGGCCGCGAGCAACt > 2:1779972/1‑47 (MQ=11)
cTGACCTTTGAAGGCCGCGAGCAACTGAGTACCCCGTTCCGCTACGat < 2:663082/48‑1 (MQ=11)
aCCTTTGAAGGCCGCGAGCAACTGAGTACCCCGTTCCGCTACGata < 2:1537835/46‑1 (MQ=11)
cTTTGAAGGCCGCGAGCAACTGAGTACCCCGTTCCGCTACGATATCCa < 2:1568195/48‑1 (MQ=14)
cTTTGAAGGCCGCGAGCAACTGAGTACCCCGTTCCGCTACGATATCCa < 2:932701/48‑1 (MQ=14)
tgAAGGCCGCGAGCAACTGAGTACCCCGTTCCGCTACGATATCCAg < 2:2625265/45‑1 (MQ=255)
aaGGCCGCGAGCAACTGAGTACCCCGTTCCGCTACGATATCCAGttt < 2:2206314/47‑1 (MQ=255)
aGGCCGCGAGCAACTGAGTACCCCGTTCCGCTACGATATCCAGTTTAc < 1:1756599/48‑1 (MQ=255)
ggCCGCGAGCAACTGAGTACCCCGTTCCGCTACGATATCCAGTTTAc > 1:1628421/1‑47 (MQ=255)
gCCGCGAGCAACTGAGTACCCCGTTCCGCTACGATATCCAGTTTACCa < 2:892980/48‑1 (MQ=255)
cgcgAGCAACTGAGTACCCCGTTCCGCTACGATATCCAGTTTACCAGt < 1:485037/48‑1 (MQ=255)
|
GCCAGCAAAGTCCGGTGGATGTGCTGACCTTCGAAGGCCGCGAACAACTGAGTACCCCGTTCCGCTACGATATCCAGTTTACCAGT > NC_017635/3110619‑3110704
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
GGCCAGCAAAGTCCGGTGGATGTGCTGACCTTCGAAGGCCGCGAACAACTGAGTACCCCGTTCCGCTACGATATCCAGTTTACCAGTAC > NC_017635/3110618‑3110706
|
GGCCAGCAAAGTCCGGTGGATGTGCTGACCTTTGAAGGCCGCGAGCAACTG < M01420:84:000000000‑ABVEH:1:1113:15339:20237/51‑1 (MQ=12)
AAGTCCGGTGGATGTGCTGACCTTCGAAGGCCGCGAACAACTGAGTACCCC > M01420:84:000000000‑ABVEH:1:2105:6093:17066/1‑51 (MQ=0)
GGTGGATGTGCTGACCTTCGAAGGCCGCGAACAACTGAGTACCCCGTTCCG > M01420:84:000000000‑ABVEH:1:2105:14774:18910/1‑51 (MQ=0)
GATGTGCTGACCTTCGAAGGCCGCGAACAACTGAGTACCCCGTTCCGCTAC < M01420:84:000000000‑ABVEH:1:2110:22449:16418/51‑1 (MQ=0)
ATGTGCTGACCTTCGAAGGCCGCGAACAACTGAGTACCCCGTTCCGCTACG > M01420:84:000000000‑ABVEH:1:2101:21744:4131/1‑51 (MQ=0)
GAAGGCCGCGAGCAACTGAGTACCCCGTTCCGCTACGATATCCAGTTTACC < M01420:84:000000000‑ABVEH:1:2111:7670:14852/51‑1 (MQ=39)
AAGGCCGCGAGCAACTGAGTACCCCGTTCCGCTACGATATCCAGTTTACCA < M01420:84:000000000‑ABVEH:1:2101:13577:25983/51‑1 (MQ=39)
AAGGCCGCGAGCAACTGAGTACCCCGTTCCGCTACGATATCCAGTTTACC > M01420:84:000000000‑ABVEH:1:1114:14326:23078/1‑50 (MQ=39)
CCGCGAGCAACTGAGTACCCCGTTCCGCTACGATATCCAGTTTACCAGTAC < M01420:84:000000000‑ABVEH:1:1105:3950:7756/51‑1 (MQ=39)
|
GGCCAGCAAAGTCCGGTGGATGTGCTGACCTTCGAAGGCCGCGAACAACTGAGTACCCCGTTCCGCTACGATATCCAGTTTACCAGTAC > NC_017635/3110618‑3110706
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
