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 F8 I0 R2
|
422 |
46.8 |
3726540 |
94.7% |
3529033 |
61.7 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
1,761,776 |
C→T |
100% |
L154L (CTG→CTA) |
sufS ← |
selenocysteine lyase, PLP‑dependent |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 1,761,776 | 0 | C | T | 87.0%
| 119.3
/ 10.2
| 46 | L154L (CTG→CTA) | sufS | selenocysteine lyase, PLP‑dependent |
| Reads supporting (aligned to +/- strand): ref base C (1/5); new base T (30/10); total (31/15) |
| Fisher's exact test for biased strand distribution p-value = 1.05e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.43e-01 |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
AGCACGTTGGAGACATGAGTAATTGCCAGCAGGCGAGTTTTCTCATCAAACAGCGTAGGCAGCGTCTCCAGTTGCAACGTACCATCGGGATTGAGCGGGATCACACGCAGCTCTGCGCCAACGCGTGCGCAAAGCATC > W3110S.gb/1761708‑1761845
|
aGCACGTTGGAGACATGAGTAATTGCCAGCAGGCGAGTTTTCTCATCAAACAGCGTAGGCAGCGTCTCTAg < 1:899447/71‑1 (MQ=255)
cGTTGGAGACATGAGTAATTGCCAGCAGGCGAGTTTTCTCATCAAACAGCGTAGGCAGCGTCTCTAGTTGc < 1:2292353/71‑1 (MQ=255)
aGTAATTGCCAGCAGGCGAGTTTTCTCATCAAACAGCGTAGGCAGCGTCTCTAGTTGCAACGTACCATCgg > 1:517990/1‑71 (MQ=255)
ttGCCAGCAGGCGAGTTTTCTCATCAAACAGCGTAGGCAGCGTCTCTAGTTGCAACGTACCTTCGGGATTg < 1:2185094/71‑1 (MQ=255)
ttGCCAGCAGGCGAGTTTTCTCATCAAACAGCGTAGGCAGCGTCTCTAGTTGCAACGTACAATCGGGATTg < 1:2399499/71‑1 (MQ=255)
gCCAGCAGGCGAGTTTTCTCATCAAACAGCGTAGGCAGCGTCTCTAGTTGCAACGTACCATCGGGATTGa > 1:1260018/1‑70 (MQ=255)
gCCAGCAGGCGAGTTTTCTCATCAAACAGCGTAGGCAGCGTCTCTAGTTGCAACGTACCATCGGGATTGa > 1:2192032/1‑70 (MQ=255)
gCCAGCAGGCGAGTTTTCTCATCAAACAGCGTAGGCAGCGTCTCTAGTTGCAACGTACCATCGGGATTGa > 1:423555/1‑70 (MQ=255)
gCCAGCAGGCGAGTTTTCTCATCAAACAGCGTAGGCAGCGTCTCTAGTTGCAACGTACCATCGGGATTGAg > 1:1689097/1‑71 (MQ=255)
gCCAGCAGGCGAGTTTTCTCATCAAACAGCGTAGGCAGCGTCTCTAGTTGCAACGTACCATCGGGATTGAg > 1:303571/1‑71 (MQ=255)
gCCAGCAGGCGAGTTTTCTCATCAAACAGCGTAGGCAGCGTCTCTAGTTGCAACGTACCATCGGGATTGAg > 1:2135671/1‑71 (MQ=255)
aGTTTTCTCATCAAACAGCGTAGGCAGCGTCTCCAGTTGCAACGTACCATCGGGATTGAGCGGGATcaca > 1:2972882/1‑70 (MQ=255)
gTTTTCTCATCAAACAGCGTAGGCAGCGTCTCTAGTTGCAACGTACCATCGGGATTGAGCGGGATCACACg > 1:1291042/1‑71 (MQ=255)
gTTTTCTCATCAAACAGCGTAGGCAGCGTCTCTAGTTGCAACGTACCATCGGGATTGAGCGGGATCACACg > 1:646546/1‑71 (MQ=255)
ttCTCATCAAACAGCGTAGGCAGCGTCTCTAGTTGCAACGTAc > 1:3040917/1‑43 (MQ=255)
ttCTCATCAAACAGCGTAGGCAGCGTCTCTAGTTGCAACGTAc > 1:799913/1‑43 (MQ=255)
ttCTCATCAAACAGCGTAGGCAGCGTCTCTAGTTGCAACGTACCATCGGGATTGAGCGGGATCACACGCAg > 1:2806427/1‑71 (MQ=255)
ttCTCATCAAACAGCGTAGGCAGCGTCTCTAGTTGCAACGTACCATCGGGATTGAGCGGGATCACACGCAg > 1:390433/1‑71 (MQ=255)
ttCTCATCAAACAGCGTAGGCAGCGTCTCTAGTTGCAACGTACCATCGGGATTGAGCGGGATCACACGCAg > 1:910195/1‑71 (MQ=255)
ttCTCATCAAACAGCGTAGGCAGCGTCTCTAGTTGCAACGTACCATCGGGATTGAGCGGGATCACACGCAg > 1:3045200/1‑71 (MQ=255)
ttCTCATCAAACAGCGTAGGCAGCGTCTCTAGTTGCAACGTACCATCGGGATTGAGCGGGATCACACGCAg > 1:3059165/1‑71 (MQ=255)
ttCTCATCAAACAGCGTAGGCAGCGTCTCTAGTTGCAACGTACCATCGGGATTGAGCGGGATCACACGCAg > 1:3060315/1‑71 (MQ=255)
ttCTCATCAAACAGCGTAGGCAGCGTCTCTAGTTGCAACGTACCATCGGGATTGAGCGGGATCACACGCAg > 1:2183279/1‑71 (MQ=255)
ttCTCATCAAACAGCGTAGGCAGCGTCTCTAGTTGCAACGTACCATCGGGATTGAGCGGGATCACACGCAg > 1:1165914/1‑71 (MQ=255)
ttCTCATCAAACAGCGTAGGCAGCGTCTCTAGTTGCAACGTACCATCGGGATTGAGCGGGATCACACGCAg > 1:1706436/1‑71 (MQ=255)
ttCTCATCAAACAGCGTAGGCAGCGTCTCTAGTTGCAACGTACCATCGGGATTGAGCGGGATCACACGCAg > 1:1899452/1‑71 (MQ=255)
atcaAACAGCGTAGGCAGCGTCTCTAGTTGCAACGTACCATAGGGATTGAGCGGGATCACACGCAGctc < 1:2312383/69‑1 (MQ=255)
aGCGTAGGCAGCGTCTCTAGTTGCAACGTACCATCGGGATTGAGCGGGATCACACGCAGCTCTGCGCCaa > 1:1913599/1‑70 (MQ=255)
aGCGTAGGCAGCGTCTCTAGTTGCAACGTACCATCGGGATTGAGCGGGATCACACGCAGCTCTGCGCCAAc > 1:1864037/1‑71 (MQ=255)
ggcggcGTCTCTAGTTGCAACGTACCATCGGGATTGAGCGGGATCACACGCAGCTCTGCGCCAACGCGTg > 1:3373779/1‑70 (MQ=255)
ggCAGCGTCTCTAGTTGCAACGTAGCATCGGGATTGAGCGGGATCACACGCAGCTCTGCGCCAACGCGTgc > 1:3267053/1‑71 (MQ=255)
ggCAGCGTCTCTAGTTGCAACGTACCATCGGGATTGAGCGGGATCACACGCAGCTCTGCGCCAACGCGTgc > 1:2800298/1‑71 (MQ=255)
ggCAGCGTCTCTAGTTGCAACGTACCATCGGGATTGAGCGGGATCACACGCAGCTCTGCGCCAACGCGTgc > 1:1922538/1‑71 (MQ=255)
ggCAGCGTCTCTAGTTGCAACGTACCATCGGGATTGAGCGGGATCACACGCAGCTCTGCGCCAACGCGTgc > 1:2599840/1‑71 (MQ=255)
ggCAGCGTCTCTAGTTGCAACGTACCATCGGGATTGAGCGGGATCACACGCAGCTCTGCGCCAACGCGTg > 1:2823891/1‑70 (MQ=255)
ggCAGCGTCTCTAGTTGCAACGTACCATCGGGATTGAGCGGGATCACACGCAGCTCTGCGCCAACGCGTg > 1:277389/1‑70 (MQ=255)
cAGCGTCTCCAGTTGCAACGTACCATCGGGATTGAGCGGGATCACACGCAGCTCTGCGCCAACGCGTgcgc < 1:2829086/71‑1 (MQ=255)
cAGCGTCTCCAGTTGCAACGTACCATCGGGATTGAGCGGGATCACACGCAGCTCTGCGCCAACGCGTgcgc < 1:122874/71‑1 (MQ=255)
tctcTAGTTGCAACGTACCATCGGGATTGAGCGGGATCACACGCAGCTCTGCGCCAACGCGTGCGCa < 1:1123141/67‑1 (MQ=255)
tctcTAGTTGCAACGTACCATCGGGATTGAGCGGGATCACACGCAGCTCTGCGCCAACGCGTGCGCa < 1:2619132/67‑1 (MQ=255)
tctcTAGTTGCAACGTACCATCGGGATTGAGCGGGATCACACGCAGCTCTGCGCCAACGCGTGCGCa < 1:2103142/67‑1 (MQ=255)
tctcTAGTTGCAACGTACCATCGGGATTGAGCGGGATCACACGCAGCTCTGCGCCAACGCGTGCGCAAAGc < 1:2281515/71‑1 (MQ=255)
tctcTAGTTGCAACGTACCATCGGGATTGAGCGGGATCACACGCAGCTCTGCGCCAACGCGTGCGCAAAGc < 1:916294/71‑1 (MQ=255)
tctcCAGTTGCAACGTACCATCGGGATTGAGCGGGATCACACGCAGCTCTGCGCCAACGCGTGCGCAAAGc < 1:2641687/71‑1 (MQ=255)
tctcCAGTTGCAACGTACCATCGGGATTGAGCGGGATCACACGCAGCTCTGCGCCAACGCGTGCGCAAAGc < 1:2637267/71‑1 (MQ=255)
tctcCAGTTCCAACGTACCATCGGGATTGAGCGGGATCACACGCAGCTCTGCGCCAACGCGTGCGCAAAGc < 1:1781565/71‑1 (MQ=255)
cAGTTGCAACGTACCATCGGGATTGAGCGGGATCACACGCAGCTCTGCGCCAACGCGTGCGCAAAGCATc < 1:1023567/70‑1 (MQ=255)
|
AGCACGTTGGAGACATGAGTAATTGCCAGCAGGCGAGTTTTCTCATCAAACAGCGTAGGCAGCGTCTCCAGTTGCAACGTACCATCGGGATTGAGCGGGATCACACGCAGCTCTGCGCCAACGCGTGCGCAAAGCATC > W3110S.gb/1761708‑1761845
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
