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 |
|
A19 F106 I0 R1
|
88 |
30.3 |
670850 |
93.2% |
625232 |
140.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
CP000730 |
2,679,847 |
G→A |
100% |
G111S (GGT→AGT) |
USA300HOU_2536 → |
possible secretory antigen |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | CP000730 | 2,679,847 | 0 | G | A | 91.7%
| 64.0
/ ‑0.8
| 24 | G111S (GGT→AGT) | USA300HOU_2536 | possible secretory antigen |
| Reads supporting (aligned to +/- strand): ref base G (1/1); new base A (7/15); total (8/16) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.86e-01 |
| Rejected as polymorphism: E-value score below prediction cutoff. |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
ATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAGTTGTTGAACAAGTATATAAAAACGGTAGTATTAAAGTTTCAGAATACAACTTTTATCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTT > CP000730/2679713‑2679980
|
aTGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAGTTGTTGAACAAGTATATAAAAACAgtagta > 1:116622/1‑141 (MQ=255)
aaaaaTTGGGATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAGTTGTTGAACAAGTATATAAAAACAGTAGTATTaaa < 1:131622/141‑1 (MQ=255)
ttGGTATTCAAATGCACGTAAATCAAAATAGGCGACTGGTCGTACACCAACAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAGTTGTTGAACAAGTATATAAAAACAGTAGTATTAAAGTTTc < 1:96040/141‑1 (MQ=255)
ggTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAGTTGTTGAACAAGTATATAAAAACAGTAGTATTAAAGTTTCAg < 1:241970/141‑1 (MQ=255)
tATTACAATGCACGTAAATCAAAATATGCGAATGGTCGTACACCAAGAAAATTTGATGTCATGCAATCAACTGCAGGATATTATGGCCATGTCGCAGTTGTTGAACAAGTATATAAAAACAGTAGTATTAAAGTTTCAGaa < 1:181230/141‑1 (MQ=255)
aaTGCTCGTAAATCAAAATATGCGACTGTTCGTACACCAAAAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAGTTGTTGAACAAGTATATAAAAACAGTAGTATTAAAGTTTCAGAATACAAc < 1:151879/141‑1 (MQ=255)
aTGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAGTTGTTGAACAAGTATATAAAAACAGTAGTATTAAAGTTTCAGAATACAACt < 1:120320/141‑1 (MQ=255)
atatGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAGTTGTTGAACAAGTATATAAAAACAGTAGTATTAAAGTTTCAGAATACAACTTTTATCGCCCATTaaa < 1:277019/141‑1 (MQ=255)
tGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAGTTGTTGAACAAGTATATAAAAACAGTAGTATTAAAGTTTCAGAATACAACTTTTATCGCCCATTAAaatacaatac < 2:164092/141‑1 (MQ=255)
tACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAGTTGTTGAACAAGTATATAAAAACAGTAGTATTAAAGTTTCAGAATACAACTTTTATCGCCCATTAAAATACAATACACgtgt > 1:217984/1‑141 (MQ=255)
aGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACAGGTCGCAGTTGTTGAACAAGTATATAAAAACGGTAGTATTAAAGTTTCAGAATACAACTTTTATCGCCCATTAAAATACAATACACGTGTACTAAGc < 2:266676/141‑1 (MQ=255)
aaaTTTGCGGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAGTTGTTGAACAAGTATATAAAAACAGTAGTATTAAAGTTTCAGAATACAACTTTTATCGCCCATTAAAATACAATACACGTGTACTAAGCaaa < 1:179197/141‑1 (MQ=255)
aTTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAGTTGTTGAACAAGTATATAAAAACGGTAGTATTAAAGTTTCAGAATACAACTTTTATCGCCCATTAAAATACAATACACGTGTACTAAGCaaaaa > 2:75194/1‑141 (MQ=255)
ttGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAGTTGTTGAACAAGTATATAAAAACAGTAGTATTAAAGTTTCAGAATACAACTTTTATCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAgg < 1:262741/141‑1 (MQ=255)
cTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAGTTGTTGAACAAGTATATAAAAACAGTAGTATTAAAGTTTCAGAATACAACTTTTATCGCCCATTAAAAGACAATACACGTGTACTAAGCAAAAAGgcag > 2:210764/1‑141 (MQ=255)
gCAATCAACTGCAGGATATTATGGACATGTCGCAGTTGTTGAACAAGTATATAAAAACAGTAGTATTAAAGTTTCAGAATACAACTTTTATCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTaa > 2:38628/1‑141 (MQ=255)
aCTGCAGGATATTATGGACATGTCGCAGTTGTTGAACAAGTATATAAAAACAGTAGTATTAAAGTTTCAGAATACAACTTTTATCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAAc < 2:123025/141‑1 (MQ=255)
aCTGCAGGATATTATGGACATGTCGCAGTTGTTGAACAAGTATATAAAAACAGTAGTATTAAAGTTTCAGAATACAACTTTTATCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAAc < 2:31212/141‑1 (MQ=255)
tatGGACATGTCGCAGTTGTTGAACAAGTATATAAAAACAGTAGTATTAAAGTTTCAGAATACAACTTTTATCGCCCATTAAATTACTATACTTTTGTAAAAATTCTTAAGGCAGCGCGTAACTTTAACTCGATTTACTaa < 1:244315/141‑1 (MQ=255)
gTCGCAGTTGTTGAACAAGTATATAAAAACAGTCGTATTAAAGTTTAAGAATACAACTTTTCTCGCCCATTAAAATCCAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAAc < 1:69769/141‑1 (MQ=255)
gCAGTTGTTGAACAAGTATATAAAAACAGTAGTATTAAAGTTTCAGAATACAACTTTTATCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTc < 1:6312/141‑1 (MQ=255)
gCAGTTGTTGAACAAGTATATAAAAACAGTAGTATTAAAGTTTCAGAATACAACTTTTATCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACAATATTTACTAATCAAAAAACTTc > 2:137466/1‑141 (MQ=255)
aaCAAGTATATAAAAACAGTAGTATTAAAGTTTCAGAATACAACTTTTATCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAAc > 1:89432/1‑141 (MQ=255)
taAAAACAGTAGTATTAAAGTTTCAGAATACAACTTTTATCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAAttt > 1:163786/1‑141 (MQ=255)
|
ATGCTAAAAATTGGTATTACAATGCACGTAAATCAAAATATGCGACTGGTCGTACACCAAGAAAATTTGCTGTCATGCAATCAACTGCAGGATATTATGGACATGTCGCAGTTGTTGAACAAGTATATAAAAACGGTAGTATTAAAGTTTCAGAATACAACTTTTATCGCCCATTAAAATACAATACACGTGTACTAAGCAAAAAGGCAGCACGTAACTTTAACTATATTTACTAATCAAAAAACTTCTATCACGAACGCTTCAATTT > CP000730/2679713‑2679980
|
| 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
