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 |
|
A2 F1 I0 R1
|
4577 |
57.4 |
3436498 |
77.7% |
2670158 |
63.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
2,044,257 |
A→G |
100% |
V227V (GTA→GTG) |
yqiK → |
conserved hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,044,257 | 0 | A | G | 85.2%
| 91.3
/ 5.1
| 53 | V227V (GTA→GTG) | yqiK | conserved hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base A (7/1); new base G (34/11); total (41/12) |
| Fisher's exact test for biased strand distribution p-value = 6.65e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.74e-01 |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
CAGAGCGCCGTCGCCGCGAACGTAACGAAGTTGAACAGGATGTAGAAGTTGCGGTGCGTGAAAAAAATCGCGATGCGCTATCGCGCAAGCTGGAGATTG > minE/2044214‑2044312
|
cAGAGCGCCGTCGCCGCGAACGTAACGAAGTTGAACAGGATGTAGAAGTTGCGGTGCGTGAAAAAAATc > 1:540795/1‑69 (MQ=255)
gcgAACGTAACGAAGTTGAACAGGATGTGGAAGTCGCAGTGCGTGAGAAAAACCGTGATGCACTTTcgc < 1:2469348/69‑1 (MQ=255)
gcgAACGTAACGAAGTTGAACAGGATGTGGAAGTCGCAGTGCGTGAGAAAAACCGTGATGCACTTTcgc < 1:873387/69‑1 (MQ=255)
gcgAACGTAACGAAGTTGAACAGGATGTGGAAGTCGCAGTGCGTGAGAAAAACCGTGATGCACTTTcgc < 1:1478995/69‑1 (MQ=255)
gcgAACGTAACGAAGTTGAACAGGATGTGGAAGTCGCAGTGCGTGAGAAAAACCGTGATGCACTTTcgc < 1:3221523/69‑1 (MQ=255)
gcgAACGTAACGAAGTTGAACAGGATGTGGAAGTCGCAGTGCGTGAGAAAAACCGTGATGCACTTTcgc < 1:1755652/69‑1 (MQ=255)
gcgAACGTAACGAAGTTGAACAGGATGTGGAAGTCGCAGTGCGTGAGAAAAACCGTGATGCACTTTcgc < 1:3023459/69‑1 (MQ=255)
gcgAACGTAACGAAGTTGAACAGGATGTGGAAGTCGCAGTGCGTGAGAAAAACCGTGATGCACTTTcgc < 1:3002907/69‑1 (MQ=255)
gcgAACGTAACGAAGTTGAACAGGATGTGGAAGTCGCAGTGCGTGAGAAAAACCGTGATGCACTTTcgc < 1:2374282/69‑1 (MQ=255)
gcgAACGTAACGAAGTTGAACAGGATGTGGAAGTCGCAGTGCGTGAGAAAAACCGTGATGCACTTTcgc < 1:225590/69‑1 (MQ=255)
gcgAACGTAACGAAGTTGAACAGGATGTGGAAGTCGCAGTGCGTGAGAAAAACCGTGATGCACTTTcgc < 1:1022997/69‑1 (MQ=255)
gcgAACGTAACGAAGTTGAACAGGATGTGGAAGCCGCAGTGCGTGAGAAAAACCGTGATGCACTTTcgc < 1:186851/69‑1 (MQ=255)
cGAAGTTGAACAGGATGTGGAAGTCGCAGTGCGTGAGAAAAACcgt > 1:3319535/1‑45 (MQ=255)
cGAAGTTGAACAGGATGTGGAAGTCGCAGTGCGTGAGAAAAACcgt > 1:534172/1‑45 (MQ=255)
cGAAGTTGAACAGGATGTGGAAGTCGCAGTGCGTGAGAAAAACcgt > 1:420559/1‑45 (MQ=255)
cGAAGTTGAACAGGATGTGGAAGTCGCAGTGCGTGAGAAAAACcgt > 1:379699/1‑45 (MQ=255)
cGAAGTTGAACAGGATGTGGAAGTCGCAGTGCGTGAGAAAAACcgt > 1:2873206/1‑45 (MQ=255)
cGAAGTTGAACAGGATGTGGAAGTCGCAGTGCGTGAGAAAAACcgt > 1:2934590/1‑45 (MQ=255)
cGAAGTTGAACAGGATGTGGAAGTCGCAGTGCGTGAGAAAAACcgt > 1:3159343/1‑45 (MQ=255)
cGAAGTTGAACAGGATGTGGAAGTCGCAGTGCGTGAGAAAAACcgt > 1:3056765/1‑45 (MQ=255)
cGAAGTTGAACAGGATGTGGAAGTCGCAGTGCGTGAGAAAAACcgt > 1:3092223/1‑45 (MQ=255)
cGAAGTTGAACAGGATGTGGAAGTCGCAGTGCGTGAGAAAAACcgt > 1:3113674/1‑45 (MQ=255)
cGAAGTTGAACAGGATGTGGAAGTCGCAGTGCGTGAGAAAAACcgt > 1:587205/1‑45 (MQ=255)
cGAAGTTGAACAGGATGTGGAAGTCGCAGTGCGTGAGAAAAACcgt > 1:2563649/1‑45 (MQ=255)
cGAAGTTGAACAGGATGTGGAAGTCGCAGTGCGTGAGAAAAACcgt > 1:2210772/1‑45 (MQ=255)
cGAAGTTGAACAGGATGTGGAAGTCGCAGTGCGTGAGAAAAACcgt > 1:2195939/1‑45 (MQ=255)
cGAAGTTGAACAGGATGTGGAAGTCGCAGTGCGTGAGAAAAACcgt > 1:2165656/1‑45 (MQ=255)
cGAAGTTGAACAGGATGTGGAAGTCGCAGTGCGTGAGAAAAACcgt > 1:2121326/1‑45 (MQ=255)
cGAAGTTGAACAGGATGTGGAAGTCGCAGTGCGTGAGAAAAACcgt > 1:614931/1‑45 (MQ=255)
cGAAGTTGAACAGGATGTGGAAGTCGCAGTGCGTGAGAAAAACcgt > 1:800275/1‑45 (MQ=255)
cGAAGTTGAACAGGATGTGGAAGTCGCAGTGCGTGAGAAAAACcgt > 1:1171446/1‑45 (MQ=255)
cGAAGTTGAACAGGATGTGGAAGTCGCAGTGCGTGAGAAAAACcg > 1:1501528/1‑45 (MQ=255)
agAAGTTGAACAGGATGTGGAAGTCGCAGTGCGTGAGAAAAACcgt > 1:2227568/2‑45 (MQ=255)
ttGAACAGGATGTGGAAGTCGCAGTGCGTGAGAAAAACCGTGATGCACTTTCGCTCAAGTTGGAGATTg > 1:235295/1‑69 (MQ=255)
ttGAACAGGATGTGGAAGTCGCAGTGCGTGAGAAAAACCGTGATGCACTTTCGCGCAAGTTGGAGATTg > 1:345994/1‑69 (MQ=255)
ttGAACAGGATGTGGAAGTCGCAGTGCGTGAGAAAAACCGTGATGCACTTTCGCGCAAGTTGGAGATTg > 1:959056/1‑69 (MQ=255)
ttGAACAGGATGTGGAAGTCGCAGTGCGTGAGAAAAACCGTGATGCACTTTCGCGCAAGTTGGAGATTg > 1:961334/1‑69 (MQ=255)
ttGAACAGGATGTGGAAGTCGCAGTGCGTGAGAAAAACCGTGATGCACTTTCGCGCAAGTTGGAGATTg > 1:2753194/1‑69 (MQ=255)
ttGAACAGGATGTGGAAGTCGCAGTGCGTGAGAAAAACCGTGATGCACTTTCGCGCAAGTTGGAGATTg > 1:303857/1‑69 (MQ=255)
ttGAACAGGATGTGGAAGTCGCAGTGCGTGAGAAAAACCGTGATGCACTTTCGCGCAAGTTGGAGATTg > 1:2956381/1‑69 (MQ=255)
ttGAACAGGATGTGGAAGTCGCAGTGCGTGAGAAAAACCGTGATGCACTTTCGCGCAAGTTGGAGATTg > 1:2872005/1‑69 (MQ=255)
ttGAACAGGATGTGGAAGTCGCAGTGCGTGAGAAAAACCGTGATGCACTTTCGCGCAAGTTGGAGATTg > 1:2676581/1‑69 (MQ=255)
ttGAACAGGATGTGGAAGTCGCAGTGCGTGAGAAAAACCGTGATGCACTTTCGCGCAAGTTGGAGATTg > 1:2656473/1‑69 (MQ=255)
ttGAACAGGATGTGGAAGTCGCAGTGCGTGAGAAAAACCGTGATGCACTTTCGCGCAAGTTGGAGATTg > 1:2654327/1‑69 (MQ=255)
ttGAACAGGATGTGGAAGTCGCAGTGCGTGAGAAAAACCGTGATGCACTTTCGCGCAAGTTGGAGATTg > 1:2635116/1‑69 (MQ=255)
ttGAACAGGATGTGGAAGTCGCAGTGCGTGAGAAAAACCGTGATGCACTTTCGCGCAAGTTGGAGATTg > 1:103551/1‑69 (MQ=255)
gAACAGGATGTAGAAGTTGCGGTGCGTGAAAAAAATCGCGATGCGCTATCGCGCAAGCTGGAGATTg > 1:533079/1‑67 (MQ=255)
gAACAGGATGTAGAAGTTGCGGTGCGTGAAAAAAATCGCGATGCGCTATCGCGCAAGCTGGAGATTg > 1:2585797/1‑67 (MQ=255)
gAACAGGATGTAGAAGTTGCGGTGCGTGAAAAAAATCGCGATGCGCTATCGCGCAAGCTGGAGATTg > 1:2105802/1‑67 (MQ=255)
gAACAGGATGTAGAAGTTGCGGTGCGTGAAAAAAATCGCGATGCGCTATCGCGCAAGCTGGAGATTg > 1:1939834/1‑67 (MQ=255)
gAACAGGATGTAGAAGTTGCGGTGCGTGAAAAAAATCGCGATGCGCTATCGCGCAAGCTGGAGATTg > 1:928756/1‑67 (MQ=255)
gAACAGGATGTAGAAGTTGCGGTGCGTGAAAAAAATCGCGATGCGCTATCGCGCAAGCTGGAGATTg > 1:1247106/1‑67 (MQ=255)
aGGATGTAGAAGTTGCGGTGCGTGAAAAAAATcgc < 1:1452943/35‑1 (MQ=255)
|
CAGAGCGCCGTCGCCGCGAACGTAACGAAGTTGAACAGGATGTAGAAGTTGCGGTGCGTGAAAAAAATCGCGATGCGCTATCGCGCAAGCTGGAGATTG > minE/2044214‑2044312
|
| 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
