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 F28 I2 R2
|
356 |
55.1 |
4139924 |
95.4% |
3949487 |
63.8 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
W3110S.gb |
4,501,608 |
A→G |
K59K (AAA→AAG) |
intB → |
predicted integrase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 4,501,608 | 0 | A | G | 85.3%
| 87.2
/ 7.4
| 34 | K59K (AAA→AAG) | intB | predicted integrase |
| Reads supporting (aligned to +/- strand): ref base A (0/5); new base G (8/21); total (8/26) |
| Fisher's exact test for biased strand distribution p-value = 3.09e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.13e-01 |
TGCCAGAGTACGTCGTGACGAGGCGCGTAAGCTGCTTGCGAATGGCGTCGATCCGGGAGACAAAAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAAAGAAGTCGCGA > W3110S.gb/4501545‑4501663
|
tGCCAGAGTACGTCGTGACGAGGCGCGTAAGCTGCTTGCGAATGGCGTCGATCCGGGAGACAAGAAGaaaa < 1:3010650/71‑1 (MQ=255)
cAGAGTACGTCGTGACGAGGCGCGTAAGCTGCTTGCGAATGGCGTCGATCCGGGAGACAAGAAGAAAAATg < 1:3721038/71‑1 (MQ=255)
aCGAGGCGCGTAAGCTGCTTGCGAATGGCGTCGATCCGGGAGACAAAAAGAAAAATGATAAGGTTGAACa < 1:2257073/70‑1 (MQ=255)
aCGAGGCGCGTAAGCTGCTTGCGAATGGCGTCGATCCGGGAGACAAAAAGAAAAATGATAAGGTTGAACa < 1:2842395/70‑1 (MQ=255)
aCGAGGCGCGTAAGCTGCTTGCGAATGGCGTCGATCCGGGAGACAAAAAGAAAAATGATAAGGTTGAACa < 1:2589795/70‑1 (MQ=255)
aCGAGGCGCGTAAGCTGCTTGCGAATGGCGTCGATCCGGGAGACAAAAAGAAAAATGATAAGGTTGAACa < 1:3987907/70‑1 (MQ=255)
aCGAGGCGCGTAAGCTGCTTGCGAATGGCGTCGATCCGGGAGACAAAAAGAAAAATGATAAGGTTGAACa < 1:812129/70‑1 (MQ=255)
aGGCGCGTAAGCTGCTTGCGAATGGCGTCGATCCGGGAGACAAGAAGAAAAATGATAAGGTTGAACagag > 1:4048462/1‑70 (MQ=255)
aGGCGCGTAAGCTGCTTGCGAATGGCGTCGATCCGGGAGACAAGAAGAAAAATGATAAGGTTGAACagag > 1:2581621/1‑70 (MQ=255)
aGGCGCGTAAGCTGCTTGCGAATGGCGTCGATCCGGGAGACAAGAAGAAAAATGATAAGGTTGAACagag > 1:2142193/1‑70 (MQ=255)
aGCTGCTTGCGAATGGCGTCGATCCGGGAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGa < 1:726961/71‑1 (MQ=255)
aGCTGCTTGCGAATGGCGTCGATCCGGGAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGa < 1:3854754/71‑1 (MQ=255)
aGCTGCTTGCGAATGGCGTCGATCCGGGAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGa < 1:3537415/71‑1 (MQ=255)
aGCTGCTTGCGAATGGCGTCGATCCGGGAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGa < 1:1513914/71‑1 (MQ=255)
aGCTGCTTGCGAATGGCGTCGATCCGGGAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGa < 1:3463630/71‑1 (MQ=255)
aGCTGCTTGCGAATGGCGTCGATCCGGGAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGa < 1:997590/71‑1 (MQ=255)
gctgctTGCGAATGGCGTCGATCCGGGAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGa < 1:3050075/70‑1 (MQ=255)
ctgctTGCGAATGGCGTCGATCCGGGAGACAAGATGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAAc < 1:4081996/71‑1 (MQ=255)
ctgctTGCGAATGGCGTCGATCCGGGAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAAc < 1:2956729/71‑1 (MQ=255)
ctgctTGCGAATGGCGTCGATCCGGGAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAAc < 1:2112693/71‑1 (MQ=255)
ctgctTGCGAATGGCGTCGATCCGGGAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAAc < 1:3568314/71‑1 (MQ=255)
ctgctTGCGAATGGCGTCGATCCGGGAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAAc < 1:2143522/71‑1 (MQ=255)
ctgctTGCGAATGGCGTCGATCCGGGAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAAc < 1:2329414/71‑1 (MQ=255)
gCGTCGATCCGGGAGAGAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGc < 1:3099350/52‑1 (MQ=39)
gCGTCGATCCGGGAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGc < 1:1337889/52‑1 (MQ=255)
gCGTCGATCCGGGAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGc < 1:1305282/52‑1 (MQ=255)
gCGTCGATCCGGGAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGc < 1:997286/52‑1 (MQ=255)
gCGTCGATCCGGGAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGc < 1:2157083/52‑1 (MQ=255)
ccGGGAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAAAGAAGTCGCGa > 1:2143756/1‑67 (MQ=255)
ccGGGAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAAAGAAGTCGCGa > 1:620183/1‑67 (MQ=255)
ccGGGAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAAAGAAGTCGCGa > 1:2708290/1‑67 (MQ=255)
ccGGGAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAAAGAAGTCGCGa > 1:2809720/1‑67 (MQ=255)
ccGGGAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAAAGAAGTCGCGa > 1:3335380/1‑67 (MQ=255)
ggAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGa < 1:3075333/45‑1 (MQ=255)
|
TGCCAGAGTACGTCGTGACGAGGCGCGTAAGCTGCTTGCGAATGGCGTCGATCCGGGAGACAAAAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAAAGAAGTCGCGA > W3110S.gb/4501545‑4501663
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
