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 |
|
A13 F68 I0 R1
|
25 |
50.4 |
1217238 |
93.3% |
1135683 |
133.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
USA300TCH1516_ALE |
2,279,705 |
G→A |
100% |
A943V (GCA→GTA) |
ebh_3 ← |
Extracellular matrix‑binding protein ebh |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | USA300TCH1516_ALE | 2,279,705 | 0 | G | A | 92.9%
| 134.0
/ ‑4.4
| 53 | A943V (GCA→GTA) | ebh_3 | Extracellular matrix‑binding protein ebh |
| Reads supporting (aligned to +/- strand): ref base G (2/2); new base A (19/26); total (21/32) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
| Rejected as polymorphism: E-value score below prediction cutoff. |
GTTGATTCTACTTCTGGTTTACTAGTTACATCGTTATCCATTGTCGGACTGTTTGTTGATGCATCT‑ACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTGCTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTATTTTCTGGTGTTGCATTAGCATTTGAATT > USA300TCH1516_ALE/2279582‑2279835
|
gTTGACTCTATTTCTGGTTTACTAGTTACATCGTTATCCATTGTCGGACTGTTTGTTGATGCATCT‑ACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTc < 1:305480/134‑1 (MQ=255)
ttGATTCTACTTCTGGTTTACTAGTTACATCGTTATCCATTGTCGGACTGTTTGTTGATGCATCT‑ACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCa < 1:220565/134‑1 (MQ=255)
ggttCTACTTCTGGTTTACTAGTTACATCGTTATCCATTGTCGGTCTGTTTGTTGATGCATCT‑ACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCAcc < 1:478360/132‑1 (MQ=255)
gATTCTACTTCTGGTTTACTAGTTACATCGTTATCCATTGTCGGACTGTTTGTTGATGCATCT‑ACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCAcc < 2:51992/134‑1 (MQ=255)
gATTCTACTTCTGGTTTACTAGTTACATCGTTATCCAGTGTCGGACTGTTTGTTGATGCATCT‑ACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCAcc < 1:316196/134‑1 (MQ=255)
aCTTCTGGTTTACTAGTTACATCGTTATCCATTGTCGGACTGTTTGTTGATGCATCT‑ACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTGCTGTTGTTTCACCTGTTGc > 2:131407/1‑134 (MQ=255)
aCTTCTGGTTTACTAGTTACATCGTTATCCATTGTCGGACTGTTTGTTGATGCATCT‑ACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGATGTTTCAACTGTTGc > 1:375508/1‑134 (MQ=255)
gtCTGGTTTACTAGTTACTTCGTTATCCAGTGTCGGATTGTTTGTTGATGCATCT‑ACACTAGCATTGTTATTAGCGTGCGCTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCg < 2:9989/133‑1 (MQ=255)
tgtACTAGTTACATCGTTATACTCTGTAGGACTGTTTGATCAAGTATATAATATTATACTT‑TTCATAGTTCACGGTTTATCATTTGCATCATCAGTAGCTCAGGATTCTTTTCTTTCACTTGTTGCCGCATCAc < 2:460524/132‑1 (MQ=255)
tACTAGTTACATCGTTATTCATTGTTGGACTGTTTGTTGATGCATCT‑ACACTAGAATTGTTAGTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACta < 1:410636/134‑1 (MQ=255)
tACTAGTTACATCGTTATCCATTGTCGGACTGTTTGTTGATGCATCT‑ACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACta < 1:96736/134‑1 (MQ=255)
aGTTACATCGTTATCCATTGTCGGACTGTTTGTTGATGCATCT‑ACACTAGAATTGTTATTAGATTGCGGTTTATCATATGCATCATCAGTTGCTGATGTTAGTGTTAGTTTAGCTGCTGCCGCATCCAtattct > 2:381490/1‑132 (MQ=255)
ttACATCGTTATCCATTGTCGGACTGTTTGTTGATGCATCT‑ACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTAttt > 1:385417/1‑134 (MQ=255)
cGTTATCCATTGTCGGACTGTTTGTTGATGCATCT‑ACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGtgtt > 1:27908/1‑134 (MQ=255)
tATCCATTGTCGGACTGTTTGTTGATGCATCT‑ACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTATc > 1:248105/1‑134 (MQ=255)
tCCATTGTCGGACTCTTTGTTGATGCATCT‑TCATTCTTATTTTTATTTGCTTCCGGTTTATCATGTGCAACATCAGGTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCgg < 1:4060/134‑1 (MQ=255)
ttGTCGGACTGTTTGTTGATGCATCT‑ACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTGGCTGATGGTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGaa < 1:147404/134‑1 (MQ=255)
cGGACTGTTTGTTTATGCATCT‑ACACTAGAATTGTTATTAGCTTGCTGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTCTTCCTTGTAGTGGTCGGAGAAGCGt < 2:75033/134‑1 (MQ=255)
acttcttgttgATGCATCT‑CCACTATAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTg < 2:369618/129‑1 (MQ=255)
ttgttgATGCATCT‑ACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTg < 1:407391/134‑1 (MQ=255)
ttgATGCATCT‑ACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTCTTTGGTGTTGTCGGAGCAGCGTCTTCTTTGCCa > 1:409734/1‑134 (MQ=255)
tGCATCT‑ACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTGCTGTTGTTTCCCCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAg > 1:494887/1‑134 (MQ=255)
gCATTT‑ACGCTAGAGTTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCCCCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGc < 2:608000/134‑1 (MQ=255)
gCACCT‑ACGCTAGAATTGTGAGTCGCTTGCGGTTTAGCATTTGCATCATCAGTGGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGc < 1:556757/134‑1 (MQ=255)
tAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCa < 1:114464/134‑1 (MQ=255)
gtgattaGCTGGCGGTTTATCATTGGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTCGCTGTCGTCTCAGATACGt < 1:374635/131‑1 (MQ=255)
gTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTAATGTTGTTTCACCTGTTGCCGCATAACTATTATTTGGTGTTGTCGGAGAAGCATCTGCTTGGCCATTAGCTGGCGTGTGAGATACGt > 2:85494/1‑134 (MQ=255)
ttattaGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGtt < 1:92842/134‑1 (MQ=255)
ttattaGCTTGCGGTTTATCATTTGCATCATCACTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGtt < 2:605668/134‑1 (MQ=255)
ttaTCTTGCGGTTTATCATTTGCATCATCAGTTGGTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGTCATTAGCTGTCGTCTCAGATACGTTAgg < 1:258614/134‑1 (MQ=255)
taGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGt > 1:228424/1‑134 (MQ=255)
gCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTg < 2:540872/134‑1 (MQ=255)
gCTTGCGGTTTATCAGTTGCATCATCAGTTGCTTATGTTACTATTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTTAGATACGTTAGGTTg < 2:98194/134‑1 (MQ=255)
tGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGCTGTcc > 2:404113/1‑134 (MQ=255)
cgttttATCATTTGCATCTTTAGTTGTTTATGTTCCTGTTGTTTCTCCTTTTGCCGCATTACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAg < 2:203342/131‑1 (MQ=255)
cgttttATCATTTACATCACCAGTTTCTGATGTTACTGTTGTTCGACGTGTTACCTCTTCTCTATTCGCAGGTGTGGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAg < 2:590169/131‑1 (MQ=255)
tATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTCTTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCTTTAGCTGTCGTCCCAGCTACGTTAGGTCGTTCAGTAttt > 1:36611/1‑134 (MQ=255)
tATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTGGTCTCAGATACGTTAGGTTGTCCAGTAttt > 2:48622/1‑134 (MQ=255)
tATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTAAGATACGTTAGGTTGTCCAGTAttt > 2:467491/1‑134 (MQ=255)
tATCATTTGCATCATCAATTGCAGATGTTACTGTTGTTTCACCTGTTGCCGAATCACTATTAATTGGTGGTGTCGGAGAAGCGTCCGATTTGCAATTAGCTATCGACTCAGAGAAAATCGGTAGTCCAGtgagt > 2:412888/1‑130 (MQ=255)
cgttGCTTCATTAGTTGCTGTTGTTGCTGTTGTTTCTCCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGTCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTATTTTCTg < 2:154421/132‑1 (MQ=255)
aTTTGCATCATCAGTTGCTGATGTTATTGTTTTTTCACCTGTTGCCGCATCACTATTCTTTTGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGTTACGTTAGGTTGTCCAGTATTTTCTg < 2:181528/134‑1 (MQ=255)
aTTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCCTTAGCTGTCGTCTCAGATACGTTAGGCTGTCCAGTATTTTCTg > 1:70737/1‑134 (MQ=255)
atcatcAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATAATTTGTTGGTGGCGGAGAAGCGTCTGCTTTGCCCTTAGCTGTCGTCTCAGATACGCTAGGTTGTCCAGTATTCTCTGGTGTTg > 2:9043/1‑134 (MQ=255)
tcatcaGTTGCTAATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTCTTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTATTTTCTGGTATTGc > 2:285280/1‑134 (MQ=255)
catcaGTTGCTGATGTTACTGTTGTTTCTCCTGTTGCCGCATCACTATTATTTGGTGTTGTCGTATAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTATTTTCTGGTGTTGCa < 1:443425/134‑1 (MQ=255)
tcaGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCCTCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTATATTCTGGTGTTGCAtt > 1:592806/1‑134 (MQ=255)
tGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTATTTTCTGGTGTTGCATTAGCAt < 2:253172/134‑1 (MQ=255)
tGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATATGGTGTTGTCGGAGAAGAGTCTGCTTTGCCATTAGATGTCGTCTCAGATAAGTTACGTTGTCAAGTAGTGTCTGGTGTTGCATTAGCaa > 2:57688/1‑133 (MQ=255)
cTGATGTTTCTGTTTTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTATTTTCTGGTGTTGCATTAGCAttt < 2:332913/134‑1 (MQ=255)
gATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTATTTTCTGGTGTTGCATTAGCATTTGa > 2:151886/1‑134 (MQ=255)
gTTTCTGTTGTTGCACCTAGTGCCGCATCACTATTATTTTGTGTTGTAGAAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTATTTTCTGGTGTTGCATTAGCATTTGAAtt < 1:223575/134‑1 (MQ=255)
gTTGCTGTTGTTTGACGTGTTGCTGCATCCCTATTTTTTGGTGTTGTCGGAGTAGCGTGTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTATTTTCTGTTGTTGCATTAGCATTTGAAtt < 2:506286/134‑1 (MQ=255)
|
GTTGATTCTACTTCTGGTTTACTAGTTACATCGTTATCCATTGTCGGACTGTTTGTTGATGCATCT‑ACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTGCTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTATTTTCTGGTGTTGCATTAGCATTTGAATT > USA300TCH1516_ALE/2279582‑2279835
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
