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 |
|
A2 F3 I0 R1
|
328 |
90.1 |
2317887 |
85.2% |
1974839 |
62.5 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
446,205:1 |
+C |
100% |
coding (1511/2685 nt) |
kdpD ← |
fused sensory histidine kinase in two‑component regulatory system with KdpE |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 446,205 | 1 | . | C | 100.0%
| 14.6
/ NA
| 6 | V504G (GTA→GGA) | kdpD | fused sensory histidine kinase in two‑component regulatory system with KdpE |
| Reads supporting (aligned to +/- strand): ref base . (0/0); new base C (6/0); total (6/0) |
| Rejected as polymorphism: Frequency below/above cutoff threshold. |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
GTGTGCGTTGCTCGCGGTAACGGGCTA‑CCCGCGCCTGATAACGCACGCCAGCAGTAAGGTTCCCG > minE/446179‑446243
|
gtgtGCGTTGCTCGCGGTAACGGGCTACCCCGCGCCTGATACCGCCCGCCAGCAGTAAGGTTCCCg > 1:1542300/1‑66 (MQ=255)
gtgtGCGTTGCTCGCGGTAACGGGCTACCCCGCGCCTGATAACGCCCGCCAGCAGTAAGGTTCCCg > 1:838890/1‑66 (MQ=255)
gtgtGCGTTGCTCGCGGTAACGGGCTACCCCGCGCCTGATAACGCACGCCAGCAGTAAGGTTCCCg > 1:1534355/1‑66 (MQ=255)
gtgtGCGTTGCTCGCGGTAACGGGCTACCCCGCGCCTGATAACGCACGCCAGCAGTAAGGTTCCCg > 1:1712635/1‑66 (MQ=255)
gtgtGCGTTGCTCGCGGTAACGGGCTACCCCGCGCCTGATAACGCACGCCAGCAGTAAGGTTCCCg > 1:1759989/1‑66 (MQ=255)
gtgtGCGTTGCTCGCGGTAACGGGCTACCCCGCGCCTGATAACGCACGCCAGCAGTAAGGTTCCCg > 1:652111/1‑66 (MQ=255)
|
GTGTGCGTTGCTCGCGGTAACGGGCTA‑CCCGCGCCTGATAACGCACGCCAGCAGTAAGGTTCCCG > minE/446179‑446243
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
