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 |
|
A0 F0 I1 R1
|
61 |
39.0 |
4165548 |
97.4% |
4057243 |
49.6 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_017635 |
3,127,431 |
C→T |
pseudogene (747/1425 nt) |
tssA → |
type VI secretion system protein TssA |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_017635 | 3,127,431 | 0 | C | T | 100.0%
| 10.6
/ NA
| 8 | pseudogene (747/1425 nt) | tssA | type VI secretion system protein TssA |
| Reads supporting (aligned to +/- strand): ref base C (0/0); new base T (4/4); total (4/4) |
AGCAGGCCGACCTGATGTTCAGCACCGGCGTCAGCCATTTCTGGCTGGACATCCAGTGGTATCTGCATCAGG > NC_017635/3127406‑3127477
|
aGCAGGCCGACCTGATGTTCAGCACTGGCGTCAGCCATTTCTGGCTGGAc < 1:57796/50‑1 (MQ=12)
cAGGCCGACCTGATGTTCAGCACTGGCGTCAGCCATTTCTGCCTGGACAt > 1:2043104/1‑50 (MQ=11)
aGGCCGACCTGATGTTCAGCACTGGCGTCAGCCATTTCTGGCTGGACAtt > 1:1401216/1‑49 (MQ=255)
ggCCGACCTGATGTTCAGCACTGGCGTCAGCCATTTCTGGCTGGACAttc < 2:658572/50‑3 (MQ=11)
gCCGACCTGATGTTCAGCACTGGCGTCAGCCATTTCTGGCTGGACAtt > 2:1773650/1‑47 (MQ=255)
aTGTTCAGCACTGGCGTCAGCCATTTCTGGCTGGACATTCAGTGGTATc < 1:199993/49‑1 (MQ=11)
aTGTTCAGCACTGGCGTCAGCCATTTCTGGCTGGACATTCAGTGGTATCt < 2:1148457/50‑1 (MQ=11)
cACTGGCGTCAGCCATTTCTGGCTGGACATTCAGTGGTATCTGCATCAgg > 2:1773599/1‑50 (MQ=11)
|
AGCAGGCCGACCTGATGTTCAGCACCGGCGTCAGCCATTTCTGGCTGGACATCCAGTGGTATCTGCATCAGG > NC_017635/3127406‑3127477
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
