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 |
2,009,919 |
C→T |
50.0% |
pseudogene (108/411 nt) |
yghX ← |
ECK2993:JW5926:b2999; predicted hydrolase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,009,919 | 0 | C | T | 50.0%
| ‑4.7
/ 47.5
| 54 | pseudogene (108/411 nt) | yghX | ECK2993:JW5926:b2999; predicted hydrolase |
| Reads supporting (aligned to +/- strand): ref base C (8/19); new base T (19/8); total (27/27) |
| Fisher's exact test for biased strand distribution p-value = 5.97e-03 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.62e-01 |
TCGGCAGTGGGTGCCTGACGACCATAAAACGGCACCGCGCAGGCCAGTTCCGGATACGCGACAGCCGCCGCGTTCGATACGCCACCGCCATAGCAAAATCCGGTAATACCCACTTTGCCTGTCGCTTGCGGATA > minE/2009854‑2009987
|
tCGGCAGTGGGTGCCTGACGACCATAAAACGGCACCGCGCAGGCCAGTTCCGGATACGCGACAgccgcc > 1:895654/1‑69 (MQ=255)
tCGGCAGTGGGTGCCTGACGACCATAAAACGGCACCGCGCAGGCCAGTTCCGGATACGCGACAgccgcc > 1:1364156/1‑69 (MQ=255)
tCGGCAGTGGGTGCCTGACGACCATAAAACGGCACCGCGCAGGCCAGTTCCGGATACGCGACAgccgcc > 1:2114490/1‑69 (MQ=255)
tCGGCAGTGGGTGCCTGACGACCATAAAACGGCACCGCGCAGGCCAGTTCCGGATACGCGACAgccgcc > 1:378099/1‑69 (MQ=255)
gggTGCCTGACGACCATAAAACGGCACCGCGCAGGCCAGTTCCGGATACGCGACAGCCGCCGCGTTc < 1:953306/67‑1 (MQ=255)
gggTGCCTGACGACCATAAAACGGCACCGCGCAGGCCAGTTCCGGATACGCGACAGCCGCCGCGTTc < 1:2702948/67‑1 (MQ=255)
gggTGCCTGACGACCATAAAACGGCACCGCGCAGGCCAGTTCCGGATACGCGACAGCCGCCGCGTTc < 1:1227533/67‑1 (MQ=255)
gggTGCCTGACGACCATAAAACGGCACCGCGCAGGCCAGTTCCGGATACGCGACAGCCGCCGCGTTc < 1:476323/67‑1 (MQ=255)
gggTGCCTGACGACCATAAAACGGCACCGCGCAGGCCAGTTCCGGATACGCGACAGCCGCCGCGTTCGa < 1:2252645/69‑1 (MQ=255)
gggTGCCTGACGACCATAAAACGGCACCGCGCAGGCCAGTTCCGGATACGCGACAGCCGCCGCGTTCGa < 1:3315177/69‑1 (MQ=255)
gggTGCCTGACGACCATAAAACGGCACCGCGCAGGCCAGTTCCGGATACGCGACAGCCGCCGCGTTCGa < 1:2669978/69‑1 (MQ=255)
gggTGCCTGACGACCATAAAACGGCACCGCGCAGGCCAGTTCCGGATACGCGACAGCCGCCGCGTTCGa < 1:1947348/69‑1 (MQ=255)
gggTGCCTGACGACCATAAAACGGCACCGCGCAGGCCAGTTCCGGATACGCGACAGCCGCCGCGTTCGa < 1:1497989/69‑1 (MQ=255)
ggTGCCTGACGACCATAAAACGGCACCGCGCAGGCCAGTTCCGGATACGCGACAGCCGCCGCGTTCGAt > 1:3380699/1‑69 (MQ=255)
ggTGCCTGACGACCATAAAACGGCACCGCGCAGGCCAGTTCCGGATACGCGACAGCCGCCGCGTTCGAt > 1:1585629/1‑69 (MQ=255)
acgacCTTAAAACGGCACCGCGCAGGCCAGTTCCGGATACGCGACAGCCGCCGCGTTc < 1:2340077/58‑1 (MQ=255)
ccATAAAACGGCACCGCGCAGGCCAGTTCCGGATACGCGACTGCTGCCGCGTTCGATACGCCCCCGCCa < 1:2579099/69‑1 (MQ=255)
ccATAAAACGGCACCGCGCAGGCCAGTTCCGGATACGCGACTGCTGCCGCGTTCGATACGCCCCCGCCa < 1:401526/69‑1 (MQ=255)
ccATAAAACGGCACCGCGCAGGCCAGTTCCGGATACGCGACTGCTGCCGCGTTCGATACGCCCCCGCCa < 1:2949205/69‑1 (MQ=255)
ccATAAAACGGCACCGCGCAGGCCAGTTCCGGATACGCGACTGCTGCCGCGTTCGATACGCCCCCGCCa < 1:2912647/69‑1 (MQ=255)
ccATAAAACGGCACCGCGCAGGCCAGTTCCGGATACGCGACTGCTGCCGCGTTCGATACGCCCCCGCCa < 1:1780203/69‑1 (MQ=255)
ccATAAAACGGCACCGCGCAGGCCAGTTCCGGATACGCGACTGCTGCCGCGTTCGATACGCCCCCGCCa < 1:1381936/69‑1 (MQ=255)
cATAAAACGGCACCGCGCAGGCCAGTTCCGGATACGCGACTGCTGCCGCGTTCGATACGCCCCCGCCa < 1:683938/68‑1 (MQ=255)
aaaCGGCACCGCGCAGGCCAGTTCCGGATACGCGACAGCCGCCGCGTTCGATACGCCACCGCCATAGc > 1:1023712/1‑68 (MQ=255)
aaaCGGCACCGCGCAGGCCAGTTCCGGATACGCGACAGCCGCCGCGTTCGATACGCCACCGCCATAGc > 1:942607/1‑68 (MQ=255)
aaaCGGCACCGCGCAGGCCAGTTCCGGATACGCGACAGCCGCCGCGTTCGATACGCCACCGCCATAGc > 1:3383086/1‑68 (MQ=255)
aCGGCACCGCGCAGGCCAGTTCCGGATACGCGACAGCCGCCGCGTTCGATACGCCACCGCCATAGCaa < 1:1437565/68‑1 (MQ=255)
cgcgCAGGCCAGTTCCGGATACGCGACTGCTGCCGCGTTCGATACGCCCCCGCCATAGGAAAATcc > 1:2250304/1‑66 (MQ=255)
cgcgCAGGCCAGTTCCGGATACGCGACTGCTGCCGCGTTCGATACGCCCCCGCCATAGCAAAATcc > 1:2156744/1‑66 (MQ=255)
cgcgCAGGCCAGTTCCGGATACGCGACTGCTGCCGCGTTCGATACGCCCCCGCCATAGCAAAATcc > 1:3010789/1‑66 (MQ=255)
cgcgCAGGCCAGTTCCGGATACGCGACTGCTGCCGCGTTCGATACGCCCCCGCCATAGCAAAATcc > 1:911269/1‑66 (MQ=255)
cgcgCAGGCCAGTTCCGGATACGCGACTGCTGCCGCGTTCGATACGCCCCCGCCATAGCAAAATcc > 1:2589361/1‑66 (MQ=255)
cgcgCAGGCCAGTTCCGGATACGCGACTGCTGCCGCGTTCGATACGCCCCCGCCATAGCAAAATcc > 1:206417/1‑66 (MQ=255)
cgcgCAGGCCAGTTCCGGATACGCGACTGCTGCCGCGTTCGATACGCCCCCGCCATAGCAAAATcc > 1:2272008/1‑66 (MQ=255)
cgcgCAGGCCAGTTCCGGATACGCGACTGCTGCCGCGTTCGATACGCCCCCGCCATAGCAAAATcc > 1:405478/1‑66 (MQ=255)
cgcgCAGGCCAGTTCCGGATACGCGACAGCCGCCGCGTTCGATACGCCACCGCCATAGCAAAATCCGGt < 1:3335104/69‑1 (MQ=255)
cgcgCAGGCCAGTTCCGGATACGCGACAGCCGCCGCGTTCGATACGCCACCGCCATAGCAAAATCCGGt < 1:1049247/69‑1 (MQ=255)
cgcgCAGGCCAGTTCCGGATACGCGACAGCCGCCGCGTTCGATACGCCACCGCCATAGCAAAATCCGGt < 1:2935195/69‑1 (MQ=255)
cgcgCAGGCCAGTTCCGGATACGCGACAGCCGCCGCGTTCGATACGCCACCGCCATAGCAAAATCCGGt < 1:2097641/69‑1 (MQ=255)
gcgcAGGCCAGTTCCGGATACGCGACAGCCGCCGCGTTCGATACGCCACCGCCATAGCAAAATCCGGt > 1:369885/1‑68 (MQ=255)
ggCCAGTTCCGGATACGCGACAGCCGCCGCGTTCGa < 1:485490/36‑1 (MQ=255)
ttCCGGATACGCGACTGCTGCCGCGTTCGATACGCCCCCGCCa < 1:451315/43‑1 (MQ=255)
ccGGATACGCGACAGCCGCCGCGTTCGATACGCCACCGCCATAGCAAAATCCGGTAATACCCACTTTGc > 1:1111753/1‑69 (MQ=255)
ccGGATACGCGACAGCCGCCGCGTTCGATACGCCACCGCCATAGCAAAATCCGGTAATACCCACTTTGc > 1:1257310/1‑69 (MQ=255)
gcgACTGCTGCCGCGTTCGATACGCCCCCGCCATATCAAAATcc > 1:1326441/1‑44 (MQ=25)
gcgACTGCTGCCGCGTTCGATACGCCCCCGCCATAGCAAAAt > 1:9762/1‑42 (MQ=37)
gcgACTGCTGCCGCGTTCGATACGCCCCCGCCATAGCAAAATcc > 1:536393/1‑44 (MQ=38)
gcgACTGCTGCCGCGTTCGATACGCCCCCGCCATAGCAAAATcc > 1:1079669/1‑44 (MQ=38)
gcgACTGCTGCCGCGTTCGATACGCCCCCGCCATAGCAAAATcc > 1:1166805/1‑44 (MQ=38)
gcgACTGCTGCCGCGTTCGATACGCCCCCGCCATAGCAAAATcc > 1:781017/1‑44 (MQ=38)
gcgACTGCTGCCGCGTTCGATACGCCCCCGCCATAGCAAAATcc > 1:298104/1‑44 (MQ=38)
gcgACTGCTGCCGCGTTCGATACGCCCCCGCCATAGCAAAATcc > 1:2839332/1‑44 (MQ=38)
gcgACTGCTGCCGCGTTCGATACGCCCCCGCCATAGCAAAATcc > 1:2257189/1‑44 (MQ=38)
gcgACTGCTGCCGCGTTCGATACGCCCCCGCCATAGCAAAATcc > 1:2386801/1‑44 (MQ=38)
gcgACTGCTGCCGCGTTCGATACGCCCCCGCCATAGCAAAATcc > 1:2620553/1‑44 (MQ=38)
cAGCCGCCGCGTTCGATACGCCACCGCCATAGCAAAATCCGGTAATACCCACTTTGCCTGTCGCTTGCg < 1:2878955/69‑1 (MQ=255)
cAGCCGCCGCGTTCGATACGCCACCGCCATAGCAAAATCCGGTAATACCCACTTTGCCTGTCGCTTGCg < 1:653060/69‑1 (MQ=255)
cAGCCGCCGCGTTCGATACGCCACCGCCATAGCAAAATCCGGTAATACCCACTTTGCCTGTCGCTTGCg < 1:354797/69‑1 (MQ=255)
cgccgcGTTCGATACGCCACCGCCATAGCAAAATCCGGTAATACCCACTTTGCCTGTCGCTTGCGGATa > 1:2464920/1‑69 (MQ=255)
cgccgcGTTCGATACGCCACCGCCATAGCAAAATCCGGTAATACCCACTTTGCCTGTCGCTTGCGGATa > 1:1328978/1‑69 (MQ=255)
|
TCGGCAGTGGGTGCCTGACGACCATAAAACGGCACCGCGCAGGCCAGTTCCGGATACGCGACAGCCGCCGCGTTCGATACGCCACCGCCATAGCAAAATCCGGTAATACCCACTTTGCCTGTCGCTTGCGGATA > minE/2009854‑2009987
|
| 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
