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 |
|
A5 F71 I1 R1
|
31 |
24.1 |
564604 |
94.3% |
532421 |
140.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
USA300TCH1516_ALE |
2,825,493 |
T→C |
intergenic (‑308/+540) |
cap8A_2 ← / ← icaR |
Capsular polysaccharide type 8 biosynthesis protein cap8A/Biofilm operon icaADBC HTH‑type negative transcriptional regulator IcaR |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | USA300TCH1516_ALE | 2,825,493 | 0 | T | C | 100.0%
| 70.5
/ NA
| 22 | intergenic (‑308/+540) | cap8A_2/icaR | Capsular polysaccharide type 8 biosynthesis protein cap8A/Biofilm operon icaADBC HTH‑type negative transcriptional regulator IcaR |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (9/13); total (9/13) |
CTTATTTATATTTTTGCACAAGATATAATATTGTCCAACTTTAAATATCCAAACCTATTAATAATAAAACTAGATACCATCGTACTCTATCATGGCTTTCTTATAATCGAGTAGAAGCATCATCATTACTTGATTATTTGCTCTTTACAACACCGAGCGTGCCCGTACTCGGTAATTCAATACCTTGCGTAACCCGTCACTGTGAGTTGGGTTAATGATAATAAAGCCCACACCTTTTAAAAAGATGTGGGTAATTTATATAATTTTTA > USA300TCH1516_ALE/2825355‑2825623
|
cTTATTTATATTTTTGCACAAGATATAATATTGTCCAACTTTAAATATCCAAACCTATTAATAATAAAACTAGATACCATCGTACTCTATCATGGCTTTCTTATAATCGAGTAGAAGCATCATCATTACTTGATTATTCGc > 2:179442/1‑141 (MQ=255)
tttGCACAAGATATAATATTGTCCAACTTTAAATATCCAAACCTATTAATAATAATACTAAATACCGTCGTACTCTATCATGGCTTTCTTATAATCGAGTAGAAGCATCATCATTACTTGATTATTCGCTCTTTACAacac < 2:200962/141‑1 (MQ=255)
tGCACAAGAGATAATATTGTCCAACTTTAAATATCCAAACCTATTAATAATAAAACTAGATACCATCGTACTCTATCATGGCTTTCTTATAATCGAGTAGAAGCATCATCATTACTTGATTATTCGCTCTTTACAACACCg < 1:23076/141‑1 (MQ=255)
gCACAAGATATAATATTGTCCAACTTTAAATATCCAAACCTATTAATAATAAAACTAGATACCATCGTACTCTATCATGGCTTTCTTATAATCGAGTAGAAGCATCATCATTACTTGATTATTCGCTCTTTACAACACCGa > 1:28315/1‑141 (MQ=255)
taataTTGTCCAACTTTAAATATCCAAACCTATTAATAATAAAACTAGATACCATCGTACTCTATCATGGCTTTCTTATAATCGAGTAGAAGCATCATCATTACTTGATTATTCGCTCTTTACAACACCGAGCGTGCCCGt < 1:146077/141‑1 (MQ=255)
taataTTGTCCAACTTTAAATATCCAAACCTATTAATAATAAAACTAGATACCATCGTACTCTATCATCGCTTTCTTATAATCGAGTAGAAGCATCATCATTACTTGATTATTCGCTCTTTACAACACCGAGCGTGCCCGt < 2:278474/141‑1 (MQ=255)
taataTTGTCCAACTGTAAATATCCAAACCTATTAATAATAAAACTAGATACCATCGTACTCTATCATGGCTTTCTTATAATCGAGTAGAAGCATCATCATTACTTGATTATTCGCTCTTTACAACACCGAGCGTGCCCGt < 1:87582/141‑1 (MQ=255)
tatTGTCCAACTTTAAATATCCAAACCTATTAATAATAAAACTAGATACAATAGTACTCTAGCATGGCTTTCTTATAATCGAGTAGAAGCATCATCATTACTTGATTATTCGCTCTTTACAACACCGAGCGTGCCCGTACt < 1:266631/141‑1 (MQ=255)
aaCTTTAAATATCCAAACCTATTAATAATAAAACTAGATACCATCGTACTCTATCATGGCTTTCTTATAATCGAGTAGAAGCATCATCATTACTTGATTATTCGCTCTTTACAACACCGAGCGTGCCCGTACTCGGTAAtt > 1:113420/1‑141 (MQ=255)
aTTAATAATAAAACTAGATACCATCGTACTCTATCATGGCTTTCTTATAATCGAGTAGAAGCATCATCATTACTTGATTATTCGCTCTTTACAACACCGAGCGTGCCCGTACTCGGTAATTCAATACCTTGCGTAACCCGt < 1:123830/141‑1 (MQ=255)
aataataaAACTAGATACCATCGTACTCTATCATGGCTTTCTTATAATCGAGTAGAAGCATCATCATTACTTGATTATTCGCTCTTTACAACACCGAGCGTGCCCGTACTCGGTAATTCAATACCTTGCGTAACCCGTCAc > 2:141769/1‑141 (MQ=255)
aGATACCATCGTACTCTATCATGGCTTTCTTATAATCGAGTAGAAGCATCATCATTACTTGATTATTCGCTCTTTACAACACCGAGCGTGCCCGTACTCGGTAATTCAATACCTTGCGTAACCCGTCACTGTGAGTTGGGt < 1:29521/141‑1 (MQ=255)
cttACTCTATCATGGTTTTTTTATAATCTAGTAGAAGCATCATCATTACTTGATTATTCGCTCTTTACAACACCGAGCGTGCCCGTACTCGGTAATTCAATACCTTGCGTAACCCGTCACTGTGAGTTGGGTTAATGataa < 2:256468/139‑1 (MQ=255)
tACTCTATCATGGCTTTCTTATAATCGAGTAGAAGCATCATCATTACTTGATTATTCGCTCTTTACAACACCGAGCGTGCCCGTACTCGGTAATTCAATACCTTGCGTAACCCGTCCCTGTGAGTTGGGTTAATGatacta > 2:45899/1‑141 (MQ=255)
ataATCGAGTAGAAGCATCATCATTACTTGATTATTCGCTCTTTACAACACCGAGCGTGCCCGTACTCGGTAATTCAATACCTTGCGTAACCCGTCACTGTGAGTTGGGTTAATGATAATAAAGCCCACACCTTTTaaaaa > 2:78766/1‑141 (MQ=255)
tAGAAGCATCATCATTACTTGATTATTCGCTCTTTACAACACCGAGCGTGCCCGTACTCGGTAATTCAATACCTTGCGTAACCCGTCACTGTGAGTTGGGTTAATGATAATAAAGCCCACACCTTTTAAAAAGATGTGGGt > 2:225659/1‑141 (MQ=255)
aaGCATCATCATTACTTGATTATTCGCTCTTTACAACACCGAGCGTGCCCGTACTCGGTAATTCAATACCTTGCGTAACCCGTCACTGTGAGTTGGGTTAATGATAATAAAGCCCAGACCTTTTAAAAAGATGTGGGTact > 1:259580/1‑139 (MQ=255)
aGCATCATCATTACTTGATTATTCGCTCTTTACAACGCCGCGCGTCCCCGGACTCGGTAATTCAATACCTTGCGTAACCCGTCACTGTGAGTTGGGTTAATGATAATAAAGCCCACACCTTTTAAAAAGATGTGGGTAAtt < 1:106610/141‑1 (MQ=255)
tcatcatTACTTGATTATTCGCTCTTTACAACACCGAGCGTGCCCGTACTCGGTAATTCAATACCTTGCGTAACCCGTCACTGTGAGTTGGGTTAATGATAATAAAGCCCACACCTTTTAAAAAGATGTGGGTAATTtata < 1:141769/141‑1 (MQ=255)
atcatTACTTGATTATTCGCTCTTTACAACACCGAGCGTGCCCGTACTCGGTAATTCAATACCTTGCGTAACCCGTCACTGTGAGTTGGGTTAATGATAATACAGCCCACACCTCTCCAACAGATGTGGGTAATTtatata < 1:282116/141‑1 (MQ=255)
tACTTGATTATTCGCTCTTTACAACACCGAGCGTCCCAACACTGGTGAAGGCAATACCTTGCGTAACCCGTCACTGTGAGTTGGGTTAATGATAATAAAGCCCACACCTTTTAAAAAGATGTGGGTAATTTATATAAtttt < 1:52590/141‑1 (MQ=255)
cTTGATTATTCGCTCTTTACAACACCGAGCGTGCCCGTACTCGGTAATTCAATACCTTGCGTAACCCGTCACTGTGAGTTGGGTTAATGATAATAAAGCCCACACCTTTTAAAAAGATGTGGGTAATTTATATACTTttta > 2:107789/1‑141 (MQ=255)
|
CTTATTTATATTTTTGCACAAGATATAATATTGTCCAACTTTAAATATCCAAACCTATTAATAATAAAACTAGATACCATCGTACTCTATCATGGCTTTCTTATAATCGAGTAGAAGCATCATCATTACTTGATTATTTGCTCTTTACAACACCGAGCGTGCCCGTACTCGGTAATTCAATACCTTGCGTAACCCGTCACTGTGAGTTGGGTTAATGATAATAAAGCCCACACCTTTTAAAAAGATGTGGGTAATTTATATAATTTTTA > USA300TCH1516_ALE/2825355‑2825623
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
