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 F169 I0 R1
|
75 |
34.0 |
794130 |
95.7% |
759982 |
140.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
USA300TCH1516_ALE |
749,249 |
C→T |
100% |
S59S (AGC→AGT) |
setC → |
Sugar efflux transporter C |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | USA300TCH1516_ALE | 749,249 | 0 | C | T | 100.0%
| 81.7
/ NA
| 31 | S59S (AGC→AGT) | setC | Sugar efflux transporter C |
| Reads supporting (aligned to +/- strand): ref base C (0/0); new base T (18/13); total (18/13) |
| Rejected as polymorphism: Frequency below/above cutoff threshold. |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
ACTCTTTGTTGCTAATATGTTTCTACTAGGTATGGGTATTGCGGTTACGGTCCCATATCTTGTTCTTTTTGCAACTAAAGATTTAGGTATGACAACAAATCAGTATGGATTACTTCTAGCATCTGCAGCGATTAGCCAGTTTACAGTAAATTCAATTATTGCTAGATTTTCGGATACGCATCACTTTAATAGAAAAATTATTATTATTCTCGCATTATTAATGGGTGCGCTTGGTTTTTCAATATACTTTTTTGTAGATACAATCTGG > USA300TCH1516_ALE/749114‑749381
|
aCTCTTTGTTGCTAATATGTTTCTACTAGGTATGGGTATTGCGGTTACGGTCCCATATCTTGTTCTTTTTGCAACTAAAGATTTAGGTATGACAACAAATCAGTATGGATTACTTCTAGCATCTGCAGCGATTAGTCAGtt < 1:102159/141‑1 (MQ=255)
cctggttgCTAATACGTTTCTACTAGGTATGGGTATTGCGGTTACGGTCCCATATCTTGTTCTTTTTGCAACTAAAGATTTAGGTATGACAACAAAACAGTATGGATTACTTCTAGCATCTGCAGCGATTAGTCAGTTTAc < 2:141827/137‑1 (MQ=255)
gttgCTAATATGTTTCTACTAGGTATGGGTATTGCGGTTACGGTCCCATATCTTGTTCTTTTTGAAACTAAAGATTTAGGTATGCCAACAAATCGGTATGGATTACTTCTAGCATCTGCAGGGATTAGTCAGTTTACAGTa > 2:58778/1‑141 (MQ=255)
tGTTTCTACTAGGTATGGGTATTGCGGTTACGGTCCCATATCTTGTTCTTTTTGCAACTAAAGATTTAGGTATGACAACAAATCAGTATGGATTACTTCTAGCATCTGCAGCGATTAGTCAGTTTACAGTAAATTCAatta > 1:160202/1‑141 (MQ=255)
ctactaGGTATGGGTATTGCGGTTACGGTCCCATTTCTGGTTCTTTTTGCAACTAAAGATTTAGGTATGACAACAAATCAGTATGGATTACTTCTAGCATCTGCAGCGATTAGTCAGTTTACAGTAAATTCAATTATTGCt < 2:216340/141‑1 (MQ=255)
ctactaGGTATGGGTATTGCGGTTACGGTCCCATATCTTGTTCTTTTTGCAACTAAAGATTTAGGTATGACAACAAATCAGTATGGATTACTTCTAGCATCTGCAGCGATTAGTCAGTTTACAGTAAATTAACTTATTGCt > 2:346065/1‑141 (MQ=255)
taGGTATGGGTGTTCAGGTTACGGTCACACATCTTGTTCTTTTTGCTACTAACGCTGTAGATATGACTACAAATCAGTATGGATTACTTCTTGCATCTGTAGCGCGTAGTCAGTTTAGAGTAAATTCACTTATTGCTCGAt > 2:123125/1‑141 (MQ=255)
aGGTATGGGTATTGCGGTTACGGTCCCATATCTTGTTCTTTTTGCAACTAAAGATTTAGGTATGACAACAAATCAGTATGGATTACTTCTAGCATCTGCAGCGATTAGTCAGTTTACAGTAAATTCAATTATTGCTAGAtt > 2:127195/1‑141 (MQ=255)
gTATGGCGGTGACGGTCCCATAGCTTGTTCTTTTTGCCACTAAAGATTCAGCTATGACAATCAATCAGTATGGATTACCTCTAGCATCTGCAGCGATTAGTCAGTTTACAGTAAATTCAATTATTGCTAGATTTTCGGATa < 2:208019/141‑1 (MQ=255)
ttACGGTCCCATATCTTGTTCTTTTTTCAACTAAAGATTTAGGTATGACAACAAATCAGTATGGATTACTTCTAGCATCTGCAGCGATTAGTCAGTTTACAGTAAATTCAATTATTGCTAGATTTTCGGATACGCATCACt > 2:165737/1‑141 (MQ=255)
ctACGGTCCCACATCTTGTTCTTTTCGCAACCAAAGATGCAGGTATGACAACAAATCACTATGGATCACTTCTAGCATCCGCAGCGATTAGTCAGTTTACAGTAAATTCAATTATTGCTAGATTTTCGGATACGCATCACt > 2:124567/2‑141 (MQ=255)
tCTTGTTCATTTTGAAACTAAAGCTTTAAGTATGACAACAAATAAGTCTGGATTACTTCTCGCATCCGCAGCGATTAGTCAGCTTACAGTAAATTCAATTATAGCTAGATTTTCGGATACGCATCACTTTAATAGAAAAat > 2:99629/1‑141 (MQ=255)
tttAGGTATGACAACAAATCAGTATGGATTACTTCTAGCATCTGCAGCGATTAGTCAGTTTACAGTAAATTCAATTATTGCTAGATTTTCGGATACGCATCACTTTAATAGAAAAATTATTATTATTCTCGCATTATTAAt > 1:165740/1‑141 (MQ=255)
gTATGACAACAAATCAGTATGGATTACTTCTAGCATCTGCAGCGATTAGTCAGTTTACAGTAAATTCAATTATTGCTAGATTTTCGGATACGCATCACTTTAATAGAAAAATTATTATTATTCTCGCATTATTAATGGGTg > 2:207773/1‑141 (MQ=255)
tGACAACAACTCAGTATGGATTACTTCTAGCATCTGCAGCGATTAGTCAGTTTACAGTAAATTCAATTATTGCTAGATTTTCGGATACGCATCACTTTAATAGAAAAATTATTATTATTCTCGCATTATTAATGGGTgcgc < 2:316858/141‑1 (MQ=255)
tGACAACAAATCCTTATGGATTACTTCTAGCATCTGCAGCGATTAGTCAGTTTACAGTAAATTCAATTATTGCTAGATTTTCGGATACGCATCACTTTAATAGAAAAATTATTATTATTCTCGCATTATTAATGGGTgcgc < 1:309341/141‑1 (MQ=255)
ggACAACAAATCAGTATGGATTACTTCGAGCATCTGCAGCGATTAGTCAGTTTACAGTAAATTCAATTATTGCTAGATTTTCGGATACGCATCACTTTAATAGAAAAATTATTATTATTCTCGCATTATTAATGGGTgcgc < 1:361642/140‑1 (MQ=255)
ataacaaATCAGTATGGAGTACTTTTAGCATCTGCAGCGATTAGTCAGTTTACAGTAGATTCAATTATTGCTAGATTTTCGGATACGCATCACTTTAATAGAAAAATTATTATTATTCTCGCATTATTAATGGGTGCGCtt < 2:52493/139‑1 (MQ=255)
acaacaAGTCCGTATGGATGACTTCTAGCATCTGCAGNGATTAGTCAGTTTACAGTAAATTCAATTATTGCTAGATTTTCGGATACGCATCACTTTAATAGAAAAATTATTATTATTCTCGCATTATTAATGGGTGCGCtt < 2:269117/141‑1 (MQ=255)
acaacaAATCAGTATGGATTACTTCTAGCATCTGCAGCGATTAGTCAGTTTACAGTAAATTCAATTATTGCTAGATTTTCGGATACGCATCACTTTAATAGAAAAATTATTATTATTCTCGCATTATTAATGGGTGCGCtt < 2:315375/141‑1 (MQ=255)
acaaATCAGTATGGATTACTTCTAGCATCTGCAGCGATTAGTCACTTTACAGTAAGTTCAATTAGTGCTAGATTTTCGGATACGCTTCACTTTAATAGAAAAATTATTATTATTCTCGCATTATTAATGAGTGCACTTGGt > 2:217820/1‑141 (MQ=255)
acaaATCAGTATGGATTACTTCTAGCATCTACAGCGATTAGTCAGTTTACAGTACATTTAATTATTGCTAGATATTAGGATATGCATCACTGTAATAGAAAAATTATTCTTATTCTCGCATTATTAATGGGTGCGTTTGGt > 2:196143/1‑141 (MQ=255)
aaaTCAGTATGGATTACTTCTAGCATCTGCAGCGATTAGTCAGTTTACAGTAACTTCAATTATTGCTAGATTTTCGGACACGCATCACTTTAATAGAAAAATTATTATTATTCTCGCATTATTAATGGGTGCGCTTGGttt < 2:338379/141‑1 (MQ=255)
tGGATTACTTCTAGCATCTGCAGCGATTAGTCAGTTTACAGTAAATTCAATTATTGCTAGATTTTCGGATACGCATCACTTTAATAGAAAAATTATTATTATTCTCGCATTATTAATGGGTGCGCTTGGTTTTTCAAtata > 2:342437/1‑141 (MQ=255)
aCTTCCAGCATCTGAAAGAATTAGTCAGCTTATAGTAAATTCAATTATTGCTAGATTTTCGGATACGAATCACTTTAATAGAAAAATTATTATTATTCTCGCATTATTAATGGGTGCGCTTGGTTTTTCAATATACttttt < 2:126284/141‑1 (MQ=255)
tCTGCAGCGATTAGTCAGTTTACAGTAAATTCAATTATTGCTAGATTTTCGGATACGCATCACTTTAATAGAAAAATTATTATTATTCTCGCATTATTAATGGGTGCGCTTGGTTTTTCAATATACTTTTTTGTAGATAcc > 2:306906/1‑140 (MQ=255)
cTGCAGCGATTAGTCAGTTTACAGTAAATTCAATTATTGCTAGATTTTCGGATACGCAACGCTTTAATAGAAAGATTGTTATTATTCTCGCATTATTAATGGGTGCGCTTGGTTTTTCAATATACTTTTTTGTAGATACaa > 2:338900/1‑141 (MQ=255)
cAGCGATTAGTCAGTTTACAGTAAATTCAATTATTGCTAGATTTTCGGATACGCATCACTTTAATAGAAAAATTATTATTATTCTCGCATTATTAATGGGTGCGCTTGGTTTTTCAATATACTTTTTTGTAGATACAATCt > 2:362783/1‑141 (MQ=255)
cAGCGATTAGTCAGTTTACAGTAAATTCAATTATTGCTAGATTTTCGGATACGCATCACTTTAATAGAAAAATTATTATTATTCTCGCATTATTAATGGGTGCGCTTGGTTTTTCAATATACTTTTTTGTAGATACAATCt < 2:160202/141‑1 (MQ=255)
cAGCGATTAGTCAGTTTACAGTAAATTCAATTATTGCTAGATTTTCGGATACGCATCACTTTAATAAAAAAATTATTCTTGTTCTCGCATTATTAATGGGTGCGCTTGGTTTTTCAATATGCTTTTTTGTAGATACAATCt > 2:25496/1‑141 (MQ=255)
gCGATTAGTCAATTTACCGTAAATTCAATTATTGCTAGATTTTCGGATACGCATCACTTTAATAGAAAAATTATGATTATTCTCGCATTATTAATGGGGGCGCTTGGTTTTGCAATATACTTTTTGGTAGCTACAATCTgg > 2:113757/1‑141 (MQ=255)
|
ACTCTTTGTTGCTAATATGTTTCTACTAGGTATGGGTATTGCGGTTACGGTCCCATATCTTGTTCTTTTTGCAACTAAAGATTTAGGTATGACAACAAATCAGTATGGATTACTTCTAGCATCTGCAGCGATTAGCCAGTTTACAGTAAATTCAATTATTGCTAGATTTTCGGATACGCATCACTTTAATAGAAAAATTATTATTATTCTCGCATTATTAATGGGTGCGCTTGGTTTTTCAATATACTTTTTTGTAGATACAATCTGG > USA300TCH1516_ALE/749114‑749381
|
| 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
