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 |
|
A7 F123 I0 R1
|
30 |
27.0 |
575273 |
98.7% |
567794 |
141.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
USA300TCH1516_ALE |
2,027,672 |
C→A |
100% |
G92V (GGC→GTC) |
vraS ← |
Sensor protein VraS |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | USA300TCH1516_ALE | 2,027,672 | 0 | C | A | 95.0%
| 57.3
/ ‑4.8
| 19 | G92V (GGC→GTC) | vraS | Sensor protein VraS |
| Reads supporting (aligned to +/- strand): ref base C (1/0); new base A (9/9); total (10/9) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.94e-01 |
| Rejected as polymorphism: E-value score below prediction cutoff. |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
TTTCATTGGTTAAGTTTTGAGTTTTAAGTCGCAACTTATGCAATTCTTGATTTAAAGGTACAAGTGTATGGTATAAATCTAACGTTTCACTATATATTTCTATATTTTGATCATTAATGCCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGG > USA300TCH1516_ALE/2027553‑2027808
|
tttCATTGGTTAAGTTTTGAGTTTTAAGTCGCAACTTATGCAATTCTTGATTTAAAGGTACAAGTGTATGGTATAAATCTAACGTTTCACTATATATTTCTATATTTTGATCATTAATGACAACTGTTTCGCCTTCCATTg < 1:572377/141‑1 (MQ=255)
tCATTGGTTAAGTTTTGAGTTTTAAGTCGCAACTTATGCAATTCTTGATTTAAAGGTACAAGTGTATGGTATAAATCTAACGTTTCACTATATATTTCTATATTTTGATCATTAATGACAACTGTTTCGCCTTCCATTGaa < 1:187762/141‑1 (MQ=255)
tGAGTTTTAAGTCGCAACTTATGCAATTCTTGATTTAAAGGTACAAGTGTATGGTATAAATCTAACGTTTCACTATATATTTCTATATTTTGATCATTAATGCCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTc > 1:429559/1‑141 (MQ=255)
aGTCGCAACTTATGCAATTCTTGATTTAAAGGTACAAGTGTATGGTATAAATCTAACGTTTCACTATATATTTCTATATTTTGATCATTAATGACAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCaa < 1:47337/141‑1 (MQ=255)
gCAACTTATGCAATTCTTGATTTAAAGGTACAAGTGTATGGTATAAATCTAACGTTTCACTATATATTTCTATATTTTGATCATTAATGACAACTGTTTCGCGTTCCATTAAACGCTCAATTTGCGTCTTACTCCAATCAt > 1:535940/1‑141 (MQ=255)
aTGCAATTCTTGATTTAAAGGTACAAGTGTATGGTATAACTCTAACGTTTCACTATATATTTCTATATTTTGATCATTAATGACAACTGTTTCGCCTTCCATTGACCGCTCAATTTGCGTCTTAATCCAATCATTTTGCtg < 1:173366/141‑1 (MQ=255)
ttAAAGGTACAAGTGTATGGTATAAATCTAACGTCTCACTATATATTTCTATATTTTGATCATTAATGACAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAg < 1:157283/141‑1 (MQ=255)
aGGTACAAGTGTATGGTATAAATCTAACGTTTCACTATATATTTCTATATTTTGATCATTAATGACAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAg > 1:171034/1‑141 (MQ=255)
gtgtATGGTATAAATCTAACGTTTCACTATATATTTCTATATTTTGATCATTAATGACAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAAc < 1:451517/141‑1 (MQ=255)
aTGGTATAAATCTAACGTTTCACTATATATTTCTATATTTTGATCATTAATGACAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACcaac < 1:256326/141‑1 (MQ=255)
aaCGTTTCACTATATATTTCTATATTTTGATCATTAATGACAACTGTTTCGCATTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATGTTGCTGATTGATTTTGTAAGCGAGTGCCGAACCAACAATAATACAAaat > 1:505025/1‑141 (MQ=255)
aCTATATATTTCTATATTTTGATCATTAATGACAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATatgat > 1:360636/1‑141 (MQ=255)
aCTATATATTTCTATATTTTGATCATTAATGACAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATatgat < 1:50218/141‑1 (MQ=255)
tttCTATATTTTGATCATTAATGACAACAGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATGTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATATGATGATGAGAt < 1:399183/141‑1 (MQ=255)
cTATATTTTGATCATTAATGACAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACAAAATAATATGATGATGAGATTta > 1:525167/1‑141 (MQ=255)
tatTTTGATCATTAATGACAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATAAGATGATCAGATTtaaaa > 1:406505/1‑141 (MQ=255)
tttGATCATTAATGACAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATATAATGATGAGATTtaaaaata > 1:181730/1‑141 (MQ=255)
tCATTAATGACAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATaaaaaa > 1:236550/1‑141 (MQ=255)
aaTGACAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAACCGAGTACCAAACCAACAATAATACACAATATTATGATGCTGAGATTTAAAAATAAAAAAACTgg > 1:260480/1‑141 (MQ=255)
|
TTTCATTGGTTAAGTTTTGAGTTTTAAGTCGCAACTTATGCAATTCTTGATTTAAAGGTACAAGTGTATGGTATAAATCTAACGTTTCACTATATATTTCTATATTTTGATCATTAATGCCAACTGTTTCGCCTTCCATTGAACGCTCAATTTGCGTCTTAATCCAATCATTTTGCTGATTGATTTTGTAAGCGAGTACCGAACCAACAATAATACACAATAATATGATGATGAGATTTAAAAATAAAAAAACTGG > USA300TCH1516_ALE/2027553‑2027808
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
