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 |
2,139,611 |
C→T |
39.6% |
K499K (AAG→AAA) |
infB ← |
fused protein chain initiation factor 2, IF2 |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,139,611 | 0 | C | T | 39.6%
| 29.5
/ 40.2
| 63 | K499K (AAG→AAA) | infB | fused protein chain initiation factor 2, IF2 |
| Reads supporting (aligned to +/- strand): ref base C (20/18); new base T (23/2); total (43/20) |
| Fisher's exact test for biased strand distribution p-value = 9.48e-04 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.79e-01 |
CAGGATGCCGTACTGGGAGAGTTCGTTCTTAACGCGATCCGGATCAGCTTCTGGTTTATCGATCTTGTTCACTGCAACCACCACCGGTACCTGCGCCGCTTTCGCGTGCTGGATTGCTTCGATGGTCTG > minE/2139548‑2139676
|
cAGGATGCCGTACTGGGAGAGTTCGTTCTTAACGCGATCCGGATCAGCTTCTGGTTTATCGATCTTGtt < 1:2860309/69‑1 (MQ=255)
cAGGATGCCGTACTGGGAGAGTTCGTTCTTAACGCGATCCGGATCAGCTTCTGGTTTATCGATCTTGtt < 1:2476966/69‑1 (MQ=255)
cAGGATGCCGTACTGGGAGAGTTCGTTCTTAACGCGATCCGGATCAGCTTCTGGTTTATCGATCTTGtt < 1:2429523/69‑1 (MQ=255)
cAGGATGCCGTACTGGGAGAGTTCGTTCTTAACGCGATCCGGATCAGCTTCTGGTTTATCGATCTTGtt < 1:2199806/69‑1 (MQ=255)
cAGGATGCCGTACTGGGAGAGTTCGTTCTTAACGCGATCCGGATCAGCTTCTGGTTTATCGATCTTGtt < 1:610696/69‑1 (MQ=255)
cAGGATGCCGTACTGGGAGAGTTCGTTCATAACGCGATCCGGATCAGCTTCTGGTTTATCGATCTTGtt < 1:3348275/69‑1 (MQ=255)
aGGATGCCGTACTGGGAGAGTTCGTTCTTAACGCGATCCGGATCAGCTTCTGGTTTATCGATCTTGtt < 1:384372/68‑1 (MQ=255)
gCCGTACTGGGAGAGTTCGTTCTTAACGCGATCCGGATCAGCTTCTGGTTTTTCGATCTTGTTCACTGc > 1:2112661/1‑69 (MQ=255)
gCCGTACTGGGAGAGTTCGTTCTTAACGCGATCCGGATCAGCTTCTGGTTTATCGATCTTGTTCACTg > 1:399036/1‑68 (MQ=255)
gCCGTACTGGGAGAGTTCGTTCTTAACGCGATCCGGATCAGCTTCTGGTTTATCGATCTTGTTCACTGc > 1:1064760/1‑69 (MQ=255)
gCCGTACTGGGAGAGTTCGTTCTTAACGCGATCCGGATCAGCTTCTGGTTTATCGATCTTGTTCACTGc > 1:2882583/1‑69 (MQ=255)
gCCGTACTGGGAGAGTTCGTTCTTAACGCGATCCGGATCAGCTTCTGGTTTATCGATCTTGTTCACTGc > 1:2928264/1‑69 (MQ=255)
cTGGGAGAGTTCGTTCTTAACGCGATCCGGATCGGCTTCTGGTTTATCGATTTTGTTCACAGCAaccac < 1:1674802/69‑1 (MQ=255)
cTGGGAGAGTTCGTTCTTAACGCGATCCGGATCGGCTTCTGGTTTATCGATTTTGTTCACAGCAaccac < 1:2781949/69‑1 (MQ=255)
cTTAACGCGATCCGGATCAGCTTCTGGTTTATCGATCTTGTTCACTGCAACCACCACCGGTACCTgcgc > 1:1223523/1‑69 (MQ=255)
cTTAACGCGATCCGGATCAGCTTCTGGTTTATCGATCTTGTTCACTGCAACCACCACCGGTACCTgcg > 1:761335/1‑68 (MQ=255)
cTTAACACGATCCGGATCAGCTTCTGGTTTATCGATCTTGTTCACTGCAACCACCACCGGTACCTgcgc > 1:1829153/1‑69 (MQ=255)
gcgATCCGGATCGGCTTCTGGTTTATCGATTTTGTTCACAGCacc > 1:1645108/1‑43 (MQ=37)
gcgATCCGGATCGGCTTCTGGTTTATCGATTTTGTTCACAGCAac > 1:2858213/1‑45 (MQ=38)
gcgATCCGGATCGGCTTCTGGTTTATCGATTTTGTTCACAGCAac > 1:3289092/1‑45 (MQ=38)
gcgATCCGGATCGGCTTCTGGTTTATCGATTTTGTTCACAGCAac > 1:3088553/1‑45 (MQ=38)
gcgATCCGGATCGGCTTCTGGTTTATCGATTTTGTTCACAGCAac > 1:569458/1‑45 (MQ=38)
gcgATCCGGATCGGCTTCTGGTTTATCGATTTTGTTCACAGCAac > 1:619088/1‑45 (MQ=38)
gcgATCCGGATCGGCTTCTGGTTTATCGATTTTGTTCACAGCAac > 1:629618/1‑45 (MQ=38)
gcgATCCGGATCGGCTTCTGGTTTATCGATTTTGTTCACAGCAac > 1:2899556/1‑45 (MQ=38)
gcgATCCGGATCGGCTTCTGGTTTATCGATTTTGTTCACAGCAac > 1:853464/1‑45 (MQ=38)
gcgATCCGGATCGGCTTCTGGTTTATCGATTTTGTTCACAGCAac > 1:883173/1‑45 (MQ=38)
gcgATCCGGATCGGCTTCTGGTTTATCGATTTTGTTCACAGCAac > 1:895180/1‑45 (MQ=38)
gcgATCCGGATCGGCTTCTGGTTTATCGATTTTGTTCACAGCAac > 1:978494/1‑45 (MQ=38)
gcgATCCGGATCGGCTTCTGGTTTATCGATTTTGTTCACAGCAac > 1:1198228/1‑45 (MQ=38)
gcgATCCGGATCGGCTTCTGGTTTATCGATTTTGTTCACAGCAac > 1:2498405/1‑45 (MQ=38)
gcgATCCGGATCGGCTTCTGGTTTATCGATTTTGTTCACAGCAac > 1:1262587/1‑45 (MQ=38)
gcgATCCGGATCGGCTTCTGGTTTATCGATTTTGTTCACAGCAac > 1:1290037/1‑45 (MQ=38)
gcgATCCGGATCGGCTTCTGGTTTATCGATTTTGTTCACAGCAac > 1:1290749/1‑45 (MQ=38)
gcgATCCGGATCGGCTTCTGGTTTATCGATTTTGTTCACAGCAac > 1:1312317/1‑45 (MQ=38)
gcgATCCGGATCGGCTTCTGGTTTATCGATTTTGTTCACAGCAac > 1:1371726/1‑45 (MQ=38)
gcgATCCGGATCGGCTTCTGGTTTATCGATTTTGTTCACAGCAac > 1:1447760/1‑45 (MQ=38)
gcgATCCGGATCGGCTTCTGGTTTATCGATTTTGTTCACAGCAac > 1:1727225/1‑45 (MQ=38)
gcgATCCGGATCGGCTTCTGGTTTATCGATTTTGTTCACAGCAac > 1:1862369/1‑45 (MQ=38)
gcgATCCGGAT‑GGCTTCTGGTTTATCGATTTTGTTCACAGCAac > 1:1421889/1‑44 (MQ=25)
cgATCCGGATCAGCTTCTGGTTTATCGATCTTGTTCACTGCAaccacca > 1:2911087/1‑49 (MQ=255)
cgATCCGGATCAGCTTCTGGTTTATCGATCTTGTTCACTGCAACCACCACCGGTACCTGCGCCGCTTTc > 1:2818086/1‑69 (MQ=255)
cgATCCGGATCAGCTTCTGGTTTATCGATCTTGTTCACTGCAACCACCACCGGTACCTGCGCCGCTTTc > 1:3336187/1‑69 (MQ=255)
cgATCCGGATCAGCTTCTGGTTTATCGATCTTATTCACTGCAACCACCACCGGTACCTGCGCCGCTTTc > 1:1175369/1‑69 (MQ=255)
ccGGATCAGCTTCTGGTTTATCGATCTTGTTCACTGCAACCACCACCGGt < 1:736594/50‑1 (MQ=255)
tCAGCTTCTGGTTTATCGATCTTGTTCACTGCAACCACCACCGGTACCTGCGCCGCTTTCGCGTGCTgg > 1:2958566/1‑69 (MQ=255)
tCAGCTTCTGGTTTATCGATCTTGTTCACTGCAACCACCACCGGTACCTGCGCCGCTTTCGCGTGCTgg > 1:1662209/1‑69 (MQ=255)
tCAGCTTCTGGTTTATCGATCTTGTTCACTGCAACCACCACCGGTACCTGCGCCGCTTTCGCGTGCTgg > 1:585032/1‑69 (MQ=255)
tCAGCTTCTGGTTTATCGATCTTGTTCACTGCAACCACCACCGGTACCTGCGCCGCTTTCGCGTGCTg > 1:2808046/1‑68 (MQ=255)
tCTGGTTTATCGATCTTGTTCACTGCAACCACCACCGGTACCTGCGCCGCTTTCGCGTGCTGGATTg > 1:1448757/1‑67 (MQ=255)
ggTTTATCGATCTTGTTCACTGCAACCACCACCGGTACCTGCGCCGCTTTCGCGTGCTGGATTGCTTc < 1:2045386/68‑1 (MQ=255)
ggTTTATCGATCTTGTTCACTGCAACCACCACCGGTACCTGCGCCGCTTTCGCGTGCTGGATTGCTTc < 1:3046274/68‑1 (MQ=255)
ggTTTATCGATCTTGTTCACTGCAACCACCACCGGTACCTGCGCCGCTTTCGCGTGCTGGATTGCTTc < 1:3372597/68‑1 (MQ=255)
ggTTTATCGATCTTGTTCACTGCAACCACCACCGGTACCTGCGCCGCTTTCGCGTGCTGGATTGCTTc < 1:2207705/68‑1 (MQ=255)
ggTTTATCGATCTTGTTCACTGCAACCACCACCGGTACCTGCGCCGCTTTCGCGTGCTGGATTGCTTc < 1:675419/68‑1 (MQ=255)
ggTTTATCGATCTTGTTCACTGCAACCACCACCGGTACCTGCGCCGCTTTCGCGTGCTGGATTGCTTc < 1:3151236/68‑1 (MQ=255)
ggTTTATCGATCTTGTTCACTGCAACCACCACCGGTACCTGCGCCGCTTTCGCGTGCTGGATTGCTTc < 1:2911330/68‑1 (MQ=255)
ggTTTATCGATCTTGTTCACTGCAACCACCACCGGTACCTGCGCCGCTTTCGCGTGCTGGATTGCTTc < 1:2266052/68‑1 (MQ=255)
ggTTTATCGATCTTGTTCACTGCAACCACCACCGGTACCTGCGCCGCTTTCGCGTGCTGGATTGCTTc < 1:975317/68‑1 (MQ=255)
ggTTTATCGATCTTGTTCACTGCAACCACCACCGGTACCTGCGCCGCTTTCGCGTGCTGGATTGCTTc < 1:3222302/68‑1 (MQ=255)
gATCTTGTTCACTGCAACCACCACCGGTACCTGCGCCGCt > 1:395187/1‑40 (MQ=255)
gATCTTGTTCACTGCAACCACCACCGGTACCTGCGCCGCTTTCGCGTGCTGGATTGCTTCGATGGTCTg > 1:2414259/1‑69 (MQ=255)
gATCTTGTTCACTGCAACCACCACCGGTACCTGCGCCGCTTTCGCGTGCTGGATTGCTTCGATGGTCTg > 1:2592341/1‑69 (MQ=255)
|
CAGGATGCCGTACTGGGAGAGTTCGTTCTTAACGCGATCCGGATCAGCTTCTGGTTTATCGATCTTGTTCACTGCAACCACCACCGGTACCTGCGCCGCTTTCGCGTGCTGGATTGCTTCGATGGTCTG > minE/2139548‑2139676
|
| 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
