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 F17 I0 R2
|
276 |
45.3 |
3729697 |
93.0% |
3468618 |
60.6 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
4,501,608 |
A→G |
100% |
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 | 79.6%
| 95.2
/ 18.5
| 44 | K59K (AAA→AAG) | intB | predicted integrase |
| Reads supporting (aligned to +/- strand): ref base A (0/9); new base G (16/19); total (16/28) |
| Fisher's exact test for biased strand distribution p-value = 1.64e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
GCCAGAGTACGTCGTGACGAGGCGCGTAAGCTGCTTGCGAATGGCGTCGATCCGGGAGACAAAAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAAAGAAGTCGCGATTGAGTGG > W3110S.gb/4501546‑4501671
|
gCCAGAGTACGTCGTGACGAGGCGCGTAAGCTGCTTGCGAATGGCGTCGATCCGGGAGACAAGAAGaaa < 1:143828/69‑1 (MQ=255)
gTACGTCGTGACGAGGCGCGTAAGCTGCTTGCGAATGGCGTCGATCCGGGAGACAAGAAGAAAAATGAt < 1:1276783/69‑1 (MQ=255)
gTACGTCGTGACGAGGCGCGTAAGCTGCTTGCGAATGGCGTCGATCCGGGAGACAAAAAGAAAAATGAt < 1:289494/69‑1 (MQ=255)
gTACGTCGTGACGAGGCGCGTAAGCTGCTTGCGAATGGCGTCGATCCGGGAGACAAAAAGAAAAATGAt < 1:269502/69‑1 (MQ=255)
gTACGTCGTGACGAGGCGCGTAAGCTGCTTGCGAATGGCGTCGATCCGGGAGACAAAAAGAAAAATGAt < 1:2575266/69‑1 (MQ=255)
tACGTCGTGACGAGGCGCGTAAGCTGCTTGCGAATGGCGTCGATCCGGGAGACAAGAAGAAAAATGATa > 1:2400249/1‑69 (MQ=255)
cgtcgtGACGAGGCGCGTAAGCTGCTTGCGAATGGCGTCGATCCGGGAGACAAGAAGAAAAATGATAAg > 1:2920462/1‑69 (MQ=255)
cgtcgtGACGAGGCGCGTAAGCTGCTTGCGAATGGCGTCGATCCGGGAGACAAAAAGAAAAATGATaa < 1:1089455/68‑1 (MQ=255)
cgtcgtGACGAGGCGCGTAAGCTGCTTGCGAATGGCGTCGATCCGGGAGACAAAAAGAAAAATGATaa < 1:876015/68‑1 (MQ=255)
gtcgtGACGAGGCGCGTAAGCTGCTTGCGAATGGCGTCGATCCGGGAGACAAGAAGAAAAATGATAAgg > 1:3350312/1‑69 (MQ=255)
tcgtGACGAGGCGCGTAAGCTGCTTGCGAATGGCGTCGATCCGGGAGACAAGAAGAAAAATGATAAgg > 1:3577129/1‑68 (MQ=255)
tcgtGACGAGGCGCGTAAGCTGCTTGCGAATGGCGTCGATCCGGGAGACAAGAAGAAAAATGATAAgg > 1:3159202/1‑68 (MQ=255)
tcgtGACGAGGCGCGTAAGCTGCTTGCGAATGGCGTCGATCCGGGAGACAAGAAGAAAAATGATAAgg > 1:3139161/1‑68 (MQ=255)
aCGAGGCGCGTAAGCTGCTTGCGAATGGCGTCGATCCGGGAGACAAGAAGAAAAATGATAAGGTTg > 1:1390132/1‑66 (MQ=255)
aCGAGGCGCGTAAGCTGCTTGCGAATGGCGTCGATCCGGGAGACAAGAAGAAAAATGATAAGGTTg < 1:3079218/66‑1 (MQ=255)
gcgcGTAAGCTGCTTGCGAATGGCGTCGATCCGGGAGACAAGAAGAAAAATGATAAGGTTGAACagag > 1:2817503/1‑68 (MQ=255)
gcgcGTAAGCTGCTTGCGAATGGCGTCGATCCGGGAGACAAGAAGAAAAATGATAAGGTTGAACagag > 1:548208/1‑68 (MQ=255)
ctgctTGCGAATGGCGTCGATCCGGGAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACg < 1:1572878/68‑1 (MQ=255)
ctgctTGCGAATGGCGTCGATCCGGGAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGa < 1:3192233/69‑1 (MQ=255)
tgctTGCGAATGGCGTCGATCCGGGAGACAAGAAGaaa > 1:2928135/1‑38 (MQ=255)
tgctTGCGAATGGCGTCGATCCGGGAGACAAGAAGaaa < 1:462638/38‑1 (MQ=255)
tgctTGCGAATGGCGTCGATCCGGGAGACAAGAAGaaa > 1:1421404/1‑38 (MQ=255)
tgctTGCGAATGGCGTCGATCCGGGAGACAAGAAGaaa < 1:2422656/38‑1 (MQ=255)
tgctTGCGAATGGCGTCGATCCGGGAGACAAGAAGaaa < 1:1636871/38‑1 (MQ=255)
tGCGAATGGCGTCGATCCGGGAGACAAGAAGAAAAATGATAAGGtt > 1:3652828/1‑46 (MQ=255)
tGCGAATGGCGTCGATCCGGGAGACAAGAAGAAAAATGATAAGGTTg > 1:766834/1‑47 (MQ=255)
tGCGAATGGCGTCGATCCGGGAGACAAGAAGAAAAATGATAAGGTTg > 1:2025316/1‑47 (MQ=255)
tGCGAATGGCGTCGATCCGGGAGACAAGAAGAAAAATGATAAGGTTg > 1:3330327/1‑47 (MQ=255)
tcGAATGGCGGCGATCCGGGAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCttt < 1:1620203/68‑1 (MQ=255)
aTGGCGTCGATCCGGGAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCttt < 1:3651269/65‑1 (MQ=255)
gCGTCGATCCGGGAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCAGGAACCTTTAaagaag < 1:1982691/69‑1 (MQ=255)
gCGTCGATCCGGGAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAaagaag < 1:1388928/69‑1 (MQ=255)
gCGTCGATCCGGGAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAaagaag < 1:922882/69‑1 (MQ=255)
gCGTCGATCCGGGAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAaagaag > 1:1328673/1‑69 (MQ=255)
cGATCCGGGAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAAAGAAGTcgc < 1:232602/69‑1 (MQ=255)
cGATCCGGGAGACAAAAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAAAGAAGTcgc < 1:66548/69‑1 (MQ=255)
cGGGAGACAAAAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAAAGAAGTCGCGATTg < 1:3206177/69‑1 (MQ=255)
ggAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAAAGAAGTcgc < 1:334758/62‑1 (MQ=255)
ggAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAAAGAAGTcgc < 1:1459764/62‑1 (MQ=255)
ggAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAAAGAAGTCGCGATTGAg < 1:150558/69‑1 (MQ=255)
ggAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAAAGAAGTCGCGATTGAg < 1:773388/69‑1 (MQ=255)
gaCAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAAAGAAGTcgc < 1:3011197/59‑1 (MQ=255)
gaCAAAATGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAAAGAAGTCGCGATTGAGtgg < 1:1410261/69‑1 (MQ=255)
gaCAAAATGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAAAGAAGTCGCGATTGAGtgg < 1:2312072/69‑1 (MQ=255)
aaaaGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTa < 1:3661553/45‑1 (MQ=255)
aaaaGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTa < 1:2363923/45‑1 (MQ=255)
aaaaGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTa < 1:988387/45‑1 (MQ=255)
|
GCCAGAGTACGTCGTGACGAGGCGCGTAAGCTGCTTGCGAATGGCGTCGATCCGGGAGACAAAAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAAAGAAGTCGCGATTGAGTGG > W3110S.gb/4501546‑4501671
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
