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 |
|
A3 F1 I1 R1
|
502 |
34.8 |
1912488 |
98.2% |
1878063 |
80.6 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
3,112,442 |
T→G |
pseudogene (479/867 nt) |
yghF ← |
putative type II secretion system C‑type protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 3,112,442 | 0 | T | G | 100.0%
| 157.9
/ NA
| 44 | pseudogene (479/867 nt) | yghF | putative type II secretion system C‑type protein |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base G (25/19); total (25/19) |
GCCAGTGCCTGACGCACGGCAGCCGGGATCTCAACTGGCACACTGACAGCAGGCTCAGCAACAGCTTGCTTTGCTTCGTCACTGACGGCTTTTTTGTTGGTCACAGCAACAGTGGAACGTTCCTCTTCTGCCAGACTCAGACGCTCTATTTTTCC > NC_000913/3112364‑3112518
|
gCCAGTGCCTGACGCACGGCAGCCGGGATCTCAACTGGCACACTGACAGCAGGCTCAGCAACAGCTTGCTTTGCTTCGGCa > 2:570729/1‑81 (MQ=255)
gCCAGTGCCTGACGCACGGCAGCCGGGATCTCAACTGGCACACTGACAGCAGGCTCAGCAACAGCTTGCTTTGCTTCGGCa > 2:570728/1‑81 (MQ=255)
gCCAGTGCCTGACGCACGGCAGCCGGGATCTCAACTGGCACACTGACAGCAGGCTCAGCAACAGCTTGCTTTGCTTCGGCa > 1:570731/1‑81 (MQ=255)
gCCTGACGCACGGCAGCCGGGATCTCAACTGGCACACTGACAGCAGGCTCAGCAACAGCTTGCTTTGCTTCGGCACTGACg > 1:570720/1‑81 (MQ=255)
ccTGACGCACGGCAGCCGGGATCTCAACTGGCACACTGACAGCAGGCTCAGCAACAGCTTGCTTTGCTTCGGCACTGACgg < 2:570670/81‑1 (MQ=255)
tGACGCACGGCAGCCGGGATCTCAACTGGCACACTGACAGCAGGCTCAGCAACAGCTTGCTTTGCTTCGGCACTGACGGCt > 2:570742/1‑81 (MQ=255)
gACGCACGGCAGCCGGGATCTCAACTGGCACACTGACAGCAGGCTCAGCAACAGCTTGCTTTGCTTCGGCACTGACGGCtt > 2:570727/1‑81 (MQ=255)
aCGCACGGCAGCCGGGATCTCAACTGGCACACTGACAGCAGGCTCAGCAACAGCTTGCTTTGCTTCGGCACTGACGGCtt < 2:570671/80‑1 (MQ=255)
gCACGGCAGCCGGGATCTCAACTGGCACACTGACAGCAGGCTCAGCAACAGCTTGCTTTGCTTCGGCACTGACGGCttttt > 1:570721/1‑81 (MQ=255)
gCAGCCGGGATCTCAACTGGCACACTGACAGCAGGCTCAGCAACAGCTTGCTTTGCTTCGGCACTGACGGCTTTTttgttg < 1:570672/81‑1 (MQ=255)
gCAGCCGGGATCTCAACTGGCACACTGACAGCAGGCTCAGCAACAGCTTGCTTTGCTTCGGCACTGACGGCTTTTttgttg > 1:570733/1‑81 (MQ=255)
cAGCCGGGATCTCAACTGGCACACTGACAGCAGGCTCAGCAACAGCTTGCTTTGCTTCGGCACTGACGGCTTTTTTGTTgg < 1:570673/81‑1 (MQ=255)
cAGCCGGGATCTCAACTGGCACACTGACAGCAGGCTCAGCAACAGCTTGCTTTGCTTCGGCACTGACGGCTTTTTTGTTgg > 1:570695/1‑81 (MQ=255)
aGCCGGGATCTCAACTGGCACACTGACAGCAGGCTCAGCAACAGCTTGCTTTGCTTCGGCACTGACGGCTTTTTTGTTGGt > 2:570739/1‑81 (MQ=255)
gCCGGGATCTCAACTGGCACACTGACAGCAGGCTCAGCAACAGCTTGCTTTGCTTCGGCACTGACGGCTTTTTTGTTGGTc < 2:570674/81‑1 (MQ=255)
cGGGATCTCAACTGGCACACTGACAGCAGGCTCAGCAACAGCTTGCTTTGCTTCGGCACTGACGGCTTTTTTGTTGGTca > 1:570723/1‑80 (MQ=255)
gATCTCAACTGGCACACTGACAGCAGGCTCAGCAACAGCTTGCTTTGCTTCGGCACTGACGGCTTTTTTGTTGGTCACAg > 2:570722/1‑80 (MQ=255)
aTCTCAACTGGCACACTGACAGCAGGCTCAGCAACAGCTTGCTTTGCTTCGGCACTGACGGCTTTTTTGTTGGTCACAGc > 1:570738/1‑80 (MQ=255)
aaCTGGCACACTGACAGCAGGCTCAGCAACAGCTTGCTTTGCTTCGGCACTGACGGCTTTTTTGTTGGTCACAGCAACAGt > 1:570732/1‑81 (MQ=255)
aaCTGGCACACTGACAGCAGGCTCAGCAACAGCTTGCTTTGCTTCGGCACTGACGGCTTTTTTGTTGGTCACAGCAACAGt > 1:570734/1‑81 (MQ=255)
cTGGCACACTGACAGCAGGCTCAGCAACAGCTTGCTTTGCTTCGGCACTGACGGCTTTTTTGTTGGTCACAGCAACAGTg > 1:570749/1‑80 (MQ=255)
acTGACAGCAGGCTCAGCAACAGCTTGCTTTGCTTCGGCACTGACGGCTTTTTTGTTGGTCACAGCAACAGTGGAACGTTc > 2:570747/1‑81 (MQ=255)
acTGACAGCAGGCTCAGCAACAGCTTGCTTTGCTTCGGCACTGACGGCTTTTTTGTTGGTCACAGCAACAGTGGAACGTTc < 1:570675/81‑1 (MQ=255)
cTGACAGCAGGCTCAGCAACAGCTTGCTTTGCTTCGGCACTGACGGCTTTTTTGTTGGTCACAGCAACAGTGGAACGTTcc < 2:570676/81‑1 (MQ=255)
tGACAGCAGGCTCAGCAACAGCTTGCTTTGCTTCGGCACTGACGGCTTTTTTGTTGGTCACAGCAACAGTGGAACGTTCct > 1:570754/1‑81 (MQ=255)
aCAGCAGGCTCAGCAACAGCTTGCTTTGCTTCGGCACTGACGGCTTTTTTGTTGGTCACAGCAACAGTGGAACGTTCctct > 2:570677/1‑81 (MQ=255)
gcagGCTCAGCAACAGCTTGCTTTGCTTCGGCACTGACGGCTTTTTTGTTGGTCACAGCAACAGTGGAACGTTCCtcttct < 2:570678/81‑1 (MQ=255)
cagGCTCAGCAACAGCTTGCTTTGCTTCGGCACTGACGGCTTTTTTGTTGGTCACAGCAACAGTGGAACGTTCCTCTTCTg > 1:570753/1‑81 (MQ=255)
cagGCTCAGCAACAGCTTGCTTAGCTTCGGCACTGACGGCTTTTTTGTTGGTCACAGCAACAGTGGAACGTTCCTCTTCTg < 1:570679/81‑1 (MQ=255)
agGCTCAGCAACAGCTTGCTTTGCTTCGGCACTGACGGCTTTTTTGTTGGTCACAGCAACAGTGGAACGTTCCTCTTCTGc > 1:570748/1‑81 (MQ=255)
agGCTCAGCAACAGCTTGCTTTGCTTCGGCACTGACGGCTTTTTTGTTGGTCACAGCAACAGTGGAACGTTCCTCTTCTGc < 1:570680/81‑1 (MQ=255)
gCTCAGCAACAGCTTGCTTTGCTTCGGCACTGACGGCTTTTTTGTTGGTCACAGCAACAGTGGAACGTTCCTCTTCTGCCa < 1:570681/81‑1 (MQ=255)
cTCAGCAACAGCTTGCTTTGCTTCGGCACTGACGGCTTTTTTGTTGGTCACAGCAACAGTGGAACGTTCCTCTTCTGCCAg < 2:570683/81‑1 (MQ=255)
cTCAGCAACAGCTTGCTTTGCTTCGGCACTGACGGCTTTTTTGTTGGTCACAGCAACAGTGGAACGTTCCTCTTCTGCCAg < 1:570682/81‑1 (MQ=255)
aGCAACAGCTTGCTTTGCTTCGGCACTGACGGCTTTTTTGTTGGTCACAGCAACAGTGGAACGTTCCTCTTCTGCCAGAc < 1:570684/80‑1 (MQ=255)
gCAACAGCTTGCTTTGCTTCGGCACTGACGGCTTTTTTGTTGGTCACAGCAACAGTGGAACGTTCCTCTTCTGCCAGACTc < 2:570685/81‑1 (MQ=255)
gCAACAGCTTGCTTTGCTTCGGCACTGACGGCTTTTTTGTTGGTCACAGCAACAGTGGAACGTTCCTCTTCTGCCAGACTc < 1:570686/81‑1 (MQ=255)
aGCTTGCTTTGCTTCGGCACTGACGGCTTTTTTGTTGGTCACAGCAACAGTGGAACGTTCCTCTTCTGCCAGACTCAGACg < 2:570687/81‑1 (MQ=255)
gcttgcttTGCTTCGGCACTGACGGCTTTTTTGTTGGTCACAGCAACAGTGGAACGTTCCTCTTCTGCCAGACTCAGACGc > 1:570745/1‑81 (MQ=255)
ttgctttgctTCGGCACTGACGGCTTTTTTGTTGGTCACAGCAACAGTGGAACGTTCCTCTTCTGCCAGACTCAGACGctc > 2:570741/1‑81 (MQ=255)
gctttgcttCGGCACTGACGGCTTTTTTGTTGGTCACAGCAACAGTGGAACGTTCCTCTTCTGCCAGACTCAGACGctct < 2:570688/80‑1 (MQ=255)
cttCGGCACTGACGGCTTTTTTGTTGGTCACAGCAACAGTGGAACGTTCCTCTTCTGCCAGACTCAGACGCTCTATTTTTc < 2:570689/81‑1 (MQ=255)
cttCGGCACTGACGGCTTTTTTGTTGGTCACAGCAACAGTGGAACGTTCCTCTTCTGCCAGACTCAGACGCTCTATTTTTc > 2:570760/1‑81 (MQ=255)
ttCGGCACTGACGGCTTTTTTGTTGGTCACAGCAACAGTGGAACGTTCCTCTTCTGCCAGACTCAGACGCTCTATTTTTcc > 1:570750/1‑81 (MQ=255)
|
GCCAGTGCCTGACGCACGGCAGCCGGGATCTCAACTGGCACACTGACAGCAGGCTCAGCAACAGCTTGCTTTGCTTCGTCACTGACGGCTTTTTTGTTGGTCACAGCAACAGTGGAACGTTCCTCTTCTGCCAGACTCAGACGCTCTATTTTTCC > NC_000913/3112364‑3112518
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
