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 F8 I0 R2
|
422 |
46.8 |
3726540 |
94.7% |
3529033 |
61.7 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
1,595,724 |
G→A |
72.7% |
pseudogene (56/1401 nt) |
ydeU ← |
ECK1502:JW1502:b1509; conserved hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 1,595,724 | 0 | G | A | 72.7%
| 85.5
/ 39.3
| 55 | pseudogene (56/1401 nt) | ydeU | ECK1502:JW1502:b1509; conserved hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base G (11/4); new base A (29/11); total (40/15) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.86e-01 |
CATCTTATCGGTGGGCGAATTATCGCCGCCCAGCGTCGCGTTGAACGTCATCAGGCCATTGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGT > W3110S.gb/1595657‑1595788
|
cATCTTATCGGTGGGCGAATTATCGCCGCCCAGCGTCGCGTTGATCGTCATCAGGCCATTGTTTCCGGta > 1:199165/1‑70 (MQ=255)
cATCTTATCGGTGGGCGAATTATCGCCGCCCAGCGTCGCGTTGAACGTCATCAGGCCATTGTTTCCGAta > 1:214287/1‑70 (MQ=255)
cATCTTATCGGTGGGCGAATTATCGCCGCCCAGCGTCGCGTTGAACGTCATCAGGCCATTGTTTCCGAta > 1:3196365/1‑70 (MQ=255)
cATCTTATCGGTGGGCGAATTATCGCCGCCCAGCGTCGCGTTGAACGTCATCAGGCCATTGTTTCCGAta > 1:2998657/1‑70 (MQ=255)
cATCTTATCGGTGGGCGAATTATCGCCGCCCAGCGTCGCGTTGAACGTCATCAGGCCATTGTTTCCGAta < 1:3370209/70‑1 (MQ=255)
aTCTTATCGGTGGGCGAATTATCGCCGCCCAGCGTCGCGTTGAACGTCATCAGGCCATTGTTTCCGGtat < 1:1324646/70‑1 (MQ=255)
aTCTTATCGGTGGGCGAATTATCGCCGCCCAGCGTCGCGTTGAACGTCATCAGGCCATTGTTTCCGGtat < 1:3115459/70‑1 (MQ=255)
aTCTTATCGGTGGGCGAATTATCGCCGCCCAGCGTCGCGTTGAACGTCATCAGGCCATTGTTTCCGGtat < 1:1619632/70‑1 (MQ=255)
aTCTTATCGGTGGGCGAATTATCGCCGCCCAGCGTCGCGTTGAACGTCATCAGGCCATTGTTTCCGGtat < 1:2588005/70‑1 (MQ=255)
aTCTTATCGGTGGGCGAATTATCGCCGCCCAGCGTCGCGTTGAACGTCATCAGGCCATTGTTTCCGAtata < 1:3377545/71‑1 (MQ=255)
aTCTTATCGGTGGGCGAATTATCGCCGCCCAGCGTCGCGTTGAACGTCATCAGGCCATTGTTTCCGAtata < 1:373866/71‑1 (MQ=255)
tCGGTGGGCGAATTATCGCCGCCCAGCGTCGCGTTGAACGTCATCAGGCCATTGTTTCCGATATAg < 1:1754927/66‑1 (MQ=255)
ggTGGGCGAATTATCGCCGCCCAGCGTCGCGTTGAACGTCATCAGGCCATTGTTTCCGAta > 1:854416/1‑61 (MQ=255)
tGGGCGAATTATCGCCGCCCAGCGTCGCGTTGAACGTCATCAGGCCATTGTTTCCGATATAGTTGCCGTTa < 1:542860/71‑1 (MQ=255)
ttATCGCCGCCCAGCGTCGCGTTGAACGTCATCAGGCCATTGTTTCCGATATAGTTGCCGTTAACGGt > 1:2380953/1‑68 (MQ=255)
ttATCGCCGCCCAGCGTCGCGTTGAACGTCATCAGGCCATTGTTTCCGATATAGTTGCCGTTAACGGt > 1:868828/1‑68 (MQ=255)
aTCGCCGCCCAGCGTCGCGTTGAACGTCATCAGGCCATTGTTTCCGAtata > 1:3541957/1‑51 (MQ=255)
aTCGCCGCCCAGCGTCGCGTTGAACGTCATCAGGCCATTGTTTCCGAtata > 1:3164196/1‑51 (MQ=255)
aTCGCCGCCCAGCGTCGCGTTGAACGTCATCAGGCCATTGTTTCCGAtata > 1:2115321/1‑51 (MQ=255)
aTCGCCGCCCAGCGTCGCGTTGAACGTCATCAGGCCATTGTTTCCGAtata > 1:572785/1‑51 (MQ=255)
aTCGCCGCCCAGCGTCGCGTTGAACGTCATCAGGCCATTGTTTCCGATATAGTTGCCGTTAACGGTCAGTa > 1:1740074/1‑71 (MQ=255)
tCGCCGCCCAGCGTCGCGTTGAACGTCATCAGGCCATTGTTTCCGATATAGTTGCCGTTAACGGTCAGTa < 1:335919/70‑1 (MQ=255)
tCGCCGCCCAGCGTCGCGTTGAACGTCATCAGGCCATTGTTTCCGATATAGTTGCCGTTAACGGTCAGTa < 1:739576/70‑1 (MQ=255)
ttGAACGTCATCAGGCCATTGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTcccccc > 1:2364966/1‑71 (MQ=255)
ttGAACGTCATCAGGCCATTGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTcccccc > 1:2934021/1‑71 (MQ=255)
ttGAACGTCATCAGGCCATTGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTcccccc > 1:1711710/1‑71 (MQ=255)
tcatcaGGCCATTGTTTCCGATATAGTTGCCGTTaa > 1:3651252/1‑36 (MQ=255)
tcatcaGGCCATTGTTTCCGATATAGTTGCCGTTaa > 1:343723/1‑36 (MQ=255)
tcatcaGGCCATTGTTTCCGATATAGTTGCCGTTaa > 1:385255/1‑36 (MQ=255)
tcatcaGGCCATTGTTTCCGATATAGTTGCCGTTaa > 1:106504/1‑36 (MQ=255)
tcatcaGGCCATTGTTTCCGATATAGTTGCCGTTaa > 1:2898696/1‑36 (MQ=255)
tcatcaGGCCATTGTTTCCGATATAGTTGCCGTTaa > 1:1010944/1‑36 (MQ=255)
tcatcaGGCCATTGTTTCCGATATAGTTGCCGTTaa > 1:1582206/1‑36 (MQ=255)
caGGCCATTGTTTCCGATATAGTTGCCGTTAACGGTCAGTACATTCCCCgg > 1:1518382/1‑51 (MQ=255)
caGCCCATTGTTTCCGATATAGTTGCCGTTAACGGTCAGTACATTCCCCggg > 1:3319493/1‑51 (MQ=255)
aGGCCATTGTTTCCGATATAGTTGCCGTTAACGGt > 1:3149855/1‑35 (MQ=255)
aGGCCATTGTTTCCGATATAGTTGCCGTTAACGGt > 1:3154102/1‑35 (MQ=255)
aTTGTTTCCGATATAGTTGCCGTTAACGGTCAGTACa > 1:3134503/1‑37 (MQ=255)
aTTGTTTCCGATATAGTTGCCGTTAACGGTCAGTACa > 1:750684/1‑37 (MQ=255)
ttGTTTCCGATATAGTTTCCGTTAACGGTCAGTACATTCCCCGGttt < 1:1934497/47‑1 (MQ=255)
ttGTTTCCGATATAGTTGCCGTTAACGGTCAGTACATTCCCCGGttt < 1:3325743/47‑1 (MQ=255)
ttGTTTCCGATATAGTTGCCGTTAACGGTCAGTACATTCCCCGGttt < 1:3001638/47‑1 (MQ=255)
tGTTTCCGATATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTccccca > 1:430757/1‑51 (MQ=255)
tGTTTCCGATATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAAc > 1:2825548/1‑70 (MQ=255)
agTTTCCGATATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCAATTGAAc > 1:3621332/2‑70 (MQ=255)
gTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCCg > 1:1290325/1‑41 (MQ=255)
gTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTccccc > 1:3478921/1‑50 (MQ=255)
gTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTccccc > 1:898931/1‑50 (MQ=255)
gTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTcccc > 1:193857/1‑49 (MQ=255)
gTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTcccc > 1:1513528/1‑49 (MQ=255)
gTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTcccc > 1:3468545/1‑49 (MQ=255)
gTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTcccc > 1:2758203/1‑49 (MQ=255)
gTTTCCGATATAGTTGCCGTTAACGGTCAGTACATTCCCCg > 1:562217/1‑41 (MQ=255)
gTTTCCGATATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTAt > 1:269768/1‑59 (MQ=255)
tttCCGATATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGt < 1:1736706/71‑1 (MQ=255)
|
CATCTTATCGGTGGGCGAATTATCGCCGCCCAGCGTCGCGTTGAACGTCATCAGGCCATTGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGT > W3110S.gb/1595657‑1595788
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
