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 I0 R2
|
532 |
47.8 |
3863072 |
94.9% |
3666055 |
61.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
575,770 |
G→A |
100% |
pseudogene (339/1128 nt) |
nmpC ← |
DLP12 prophage region; ECK0544:JW5078:b0553; truncated outer membrane porin |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 575,770 | 0 | G | A | 100.0%
| 13.3
/ NA
| 7 | pseudogene (339/1128 nt) | nmpC | DLP12 prophage region; ECK0544:JW5078:b0553; truncated outer membrane porin |
| Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (3/4); total (3/4) |
| Rejected as polymorphism: Frequency below/above cutoff threshold. |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
GTTTTATCTTTGGAGGAACCTTGAGATTCAGCGCGGTTGCCTTTGAATTCA > W3110S.gb/575756‑575806
|
tttttATCTTTGGAATAACCTTGAGATTCAGcacg < 1:3627245/34‑1 (MQ=25)
gTTTTATCTTTGGAAGAACCTTGAGATTCAGcacg < 1:1365039/35‑1 (MQ=38)
gTTTTATCTTTGGAAGAACCTTGAGATTCAGcacg < 1:1398046/35‑1 (MQ=38)
gTTTTATCTTTGGAAGAACCTTGAGATTCAGcacg < 1:364866/35‑1 (MQ=38)
gtCTTTGGAAGAACCTTGAGATTCAGCACGGTTGCCTTTGAATTCa > 1:2020308/2‑46 (MQ=255)
gtCTTTGGAAGAACCTTGAGATTCAGCACGGTTGCCTTTGAATTCa > 1:2267107/2‑46 (MQ=255)
gtCTTTGGAAGAACCTTGAGATTCAGCACGGTTGCCTTTGAATTCa > 1:463178/2‑46 (MQ=255)
|
GTTTTATCTTTGGAGGAACCTTGAGATTCAGCGCGGTTGCCTTTGAATTCA > W3110S.gb/575756‑575806
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
