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 R1
|
330 |
0.0 |
2544031 |
91.9% |
2337964 |
62.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
W3110S.gb |
4,315,771 |
(ATC)3→4 |
intergenic (‑111/+16) |
alsA ← / ← alsB |
fused D‑allose transporter subunits and ATP‑binding components of ABC superfamily/D‑allose transporter subunit |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 4,315,761 | 1 | . | C | 93.9%
| 115.5
/ ‑0.1
| 33 | intergenic (‑101/+26) | alsA/alsB | fused D‑allose transporter subunits and ATP‑binding components of ABC superfamily/D‑allose transporter subunit |
| Reads supporting (aligned to +/- strand): ref base . (2/0); new base C (31/0); total (33/0) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.96e-01 |
| * | W3110S.gb | 4,315,761 | 2 | . | A | 93.8%
| 96.4
/ 0.9
| 33 | intergenic (‑101/+26) | alsA/alsB | fused D‑allose transporter subunits and ATP‑binding components of ABC superfamily/D‑allose transporter subunit |
| Reads supporting (aligned to +/- strand): ref base . (2/0); new base A (30/0); total (33/0) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
| * | W3110S.gb | 4,315,761 | 3 | . | T | 93.9%
| 108.3
/ ‑0.0
| 33 | intergenic (‑101/+26) | alsA/alsB | fused D‑allose transporter subunits and ATP‑binding components of ABC superfamily/D‑allose transporter subunit |
| Reads supporting (aligned to +/- strand): ref base . (2/0); new base T (31/0); total (33/0) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
GGCTACATTTATCAGGTCTACGTTCAGGTTATTTTGTTGGCCGGATAAGACACTTCATTAG‑‑‑CATCATCATCCGGCATCATTC > W3110S.gb/4315701‑4315782
|||
ggCTACATTTATCAGGTCTACGTTCAGGTTATTTTGTTGGCCGGATAAGACACTTCATTAG‑‑‑ca < 1:917461/63‑1 (MQ=255)
ggCTACATTTATCAGGTCTACGTTCAGGTTATTTTGTTGGCCGGATAAGACACTTCATTAG‑‑‑ca < 1:356299/63‑1 (MQ=255)
ggCTACATTTATCAGGTCTACGTTCAGGTTATTTTGTTGGCCGGATAAGACACTTCATTAG‑‑‑ca < 1:1739890/63‑1 (MQ=255)
tACGTTCAGGTTAATTTGTTGGCCGGATAAGACACTTCATTAG‑‑‑ca < 1:1663301/45‑1 (MQ=255)
cGTTCAGGTTATTTTGTTGGCCGGATAAGACACTTCATTAGCTTCATCATCATCCGGCATCATTc > 1:542073/1‑65 (MQ=255)
cGTTCAGGTTATTTTGTTGGCCGGATAAGACACTTCATTAGCATCATCATCATCCGGCATCATTc > 1:612427/1‑65 (MQ=255)
cGTTCAGGTTATTTTGTTGGCCGGATAAGACACTTCATTAGCATCATCATCATCCGGCATCATTc > 1:2452841/1‑65 (MQ=255)
cGTTCAGGTTATTTTGTTGGCCGGATAAGACACTTCATTAGCATCATCATCATCCGGCATCATTc > 1:2502439/1‑65 (MQ=255)
cGTTCAGGTTATTTTGTTGGCCGGATAAGACACTTCATTAGCATCATCATCATCCGGCATCATTc > 1:303492/1‑65 (MQ=255)
cGTTCAGGTTATTTTGTTGGCCGGATAAGACACTTCATTAGCATCATCATCATCCGGCATCATTc > 1:310340/1‑65 (MQ=255)
cGTTCAGGTTATTTTGTTGGCCGGATAAGACACTTCATTAGCATCATCATCATCCGGCATCATTc > 1:383026/1‑65 (MQ=255)
cGTTCAGGTTATTTTGTTGGCCGGATAAGACACTTCATTAGCATCATCATCATCCGGCATCATTc > 1:490937/1‑65 (MQ=255)
cGTTCAGGTTATTTTGTTGGCCGGATAAGACACTTCATTAGCATCATCATCATCCGGCATCATTc > 1:609530/1‑65 (MQ=255)
cGTTCAGGTTATTTTGTTGGCCGGATAAGACACTTCATTAGCATCATCATCATCCGGCATCATTc > 1:1138826/1‑65 (MQ=255)
cGTTCAGGTTATTTTGTTGGCCGGATAAGACACTTCATTAGCATCATCATCATCCGGCATCATTc > 1:721830/1‑65 (MQ=255)
cGTTCAGGTTATTTTGTTGGCCGGATAAGACACTTCATTAGCATCATCATCATCCGGCATCATTc > 1:806127/1‑65 (MQ=255)
cGTTCAGGTTATTTTGTTGGCCGGATAAGACACTTCATTAGCATCATCATCATCCGGCATCATTc > 1:829656/1‑65 (MQ=255)
cGTTCAGGTTATTTTGTTGGCCGGATAAGACACTTCATTAGCATCATCATCATCCGGCATCATTc > 1:853254/1‑65 (MQ=255)
cGTTCAGGTTATTTTGTTGGCCGGATAAGACACTTCATTAGCATCATCATCATCCGGCATCATTc > 1:968562/1‑65 (MQ=255)
cGTTCAGGTTATTTTGTTGGCCGGATAAGACACTTCATTAGCATCATCATCATCCGGCATCATTc > 1:993562/1‑65 (MQ=255)
cGTTCAGGTTATTTTGTTGGCCGGATAAGACACTTCATTAGCATCATCATCATCCGGCATCATTc > 1:1849801/1‑65 (MQ=255)
cGTTCAGGTTATTTTGTTGGCCGGATAAGACACTTCATTAGCATCATCATCATCCGGCATCATTc > 1:1074359/1‑65 (MQ=255)
cGTTCAGGTTATTTTGTTGGCCGGATAAGACACTTCATTAGCATCATCATCATCCGGCATCATTc > 1:1183877/1‑65 (MQ=255)
cGTTCAGGTTATTTTGTTGGCCGGATAAGACACTTCATTAGCATCATCATCATCCGGCATCATTc > 1:1330287/1‑65 (MQ=255)
cGTTCAGGTTATTTTGTTGGCCGGATAAGACACTTCATTAGCATCATCATCATCCGGCATCATTc > 1:1401561/1‑65 (MQ=255)
cGTTCAGGTTATTTTGTTGGCCGGATAAGACACTTCATTAGCATCATCATCATCCGGCATCATTc > 1:1642711/1‑65 (MQ=255)
cGTTCAGGTTATTTTGTTGGCCGGATAAGACACTTCATTAGCATCATCATCATCCGGCATCATTc > 1:1661510/1‑65 (MQ=255)
cGTTCAGGTTATTTTGTTGGCCGGATAAGACACTTCATTAGCATCATCATCATCCGGCATCATTc > 1:1765405/1‑65 (MQ=255)
cGTTCAGGTTATTTTGTTGGCCGGATAAGACACTTCATTAGCATCATCATCATCCGGCATCATTc > 1:1824037/1‑65 (MQ=255)
cGTTCAGGTTATTTTGTTGGCCGGATAAGACACTTCATTAGCATCATCATCATCCGGCATCATTc > 1:187508/1‑65 (MQ=255)
cGTTCAGGTTATTTTGTTGGCCGGATAAGACACTTCATTAGCATCATCATCATCCGGCATCATTc > 1:1911001/1‑65 (MQ=255)
cGTTCAGGTTATTTTGTTGGCCGGATAAGACACTTCATTAGCATCATCATCATCCGGCATCATTc > 1:1940595/1‑65 (MQ=255)
cGTTCAGGTTATTTTGTTGGCCGGATAAGACACTTCATTAGCATCATCATCATCCGGCATCATTc > 1:208255/1‑65 (MQ=255)
cGTTCAGGTTATTTTGTTGGCCGGATAAGACACTTCATTAGCATCATCATCATCCGGCATCATTc > 1:2309175/1‑65 (MQ=255)
cGTTCAGGTTATTTTGTTGGCCGGATAAGACACTTCATTAGCATCATCATCATCCGGCATCATTc > 1:2312193/1‑65 (MQ=255)
cGTTCAGGTTATTTTGTTGGCCGGATAAGACACTTCATTAG‑‑‑ca > 1:253193/1‑43 (MQ=255)
cGTTCAGGTTATTTTGTTGGCCGGATAAGACACTTCATTAG‑‑‑Catcatcatca > 1:2311305/1‑51 (MQ=255)
cGTTCAGGTTATTTTGTTGGCCGGATAAGACACTTCATTAG‑‑‑Catcatcatc > 1:2337952/1‑51 (MQ=255)
|||
GGCTACATTTATCAGGTCTACGTTCAGGTTATTTTGTTGGCCGGATAAGACACTTCATTAG‑‑‑CATCATCATCCGGCATCATTC > W3110S.gb/4315701‑4315782
|
| 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
