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 |
|
A6 F21 I0 R1
|
2169 |
63.0 |
3952800 |
76.2% |
3012033 |
62.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
2,823,628 |
G→A |
57.4% |
intergenic (+373/+585) |
nrfG → / ← pheU |
heme lyase (NrfEFG) for insertion of heme into c552, subunit NrfG/tRNA‑Phe |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,823,628 | 0 | G | A | 57.4%
| 20.8
/ 62.2
| 54 | intergenic (+373/+585) | nrfG/pheU | heme lyase (NrfEFG) for insertion of heme into c552, subunit NrfG/tRNA‑Phe |
| Reads supporting (aligned to +/- strand): ref base G (17/6); new base A (16/15); total (33/21) |
| Fisher's exact test for biased strand distribution p-value = 1.58e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
CGGGGAACGGCGCTCCATTGAGGAAGTCATTCATAATAGAAACTCATTCGAAAAGGGAATGATGCGATGATAATTGCCACAACCTATTTTTACCATCTATAGATGGGTTTATTTACATATTATTGGTGAATGC > minE/2823563‑2823695
|
cGGGGAACGGCGCTCCATTGAGGAAGTCATTCATAATAGAAACTCATTCGAAAAGGGAATGATGCgatga > 1:3131097/1‑70 (MQ=255)
ggggAACGGCGCTCCATTGAGGAAGTCATTCATAATAGAAACTCATTCGAAAAGGGAATGATGCgatgat > 1:2534500/1‑70 (MQ=255)
gggAACGGCGCTCCATTGAGGAAGTCATTCATAATAGAAACTCATTCGAAAAGGGAATGATGCGATGATaa < 1:3557644/71‑1 (MQ=255)
gggAACGGCGCTCCATTGAGGAAGTCATTCATAATAGAAACTCATTCGAAAAGGGAATGATGCGATGATaa < 1:1858426/71‑1 (MQ=255)
tCCATTGAGGAAGTCATTCATAATAGAAACTCATTCGAAAAGGGAATGATGCGATGATAATTGCCACAAcc > 1:2366561/1‑71 (MQ=255)
cATTGAGGAAGTCATTCATAATAGAAACTCATTCGAAAAGGGAATGATGCGATGATAATTg > 1:1974583/1‑61 (MQ=255)
cATTGAGGAAGTCATTCATAATAGAAACTCATTCGAAAAGGGAATGATGCGATGATAATTGCCACAACCTa > 1:3130884/1‑71 (MQ=255)
aTTGAGGAAGTCATTCATAATAGAAACTCATTCGAAAAGGGAATGATGCGATGATAATTGCCACAACCTa > 1:481594/1‑70 (MQ=255)
ggAAGTCATTCATAATAGAAACTCATTCGAAAAGGGAATGATGCGATGATAATTGCCACAACCTATTTTTa < 1:2870863/71‑1 (MQ=255)
tgcatAATAGAAACTCATTCGAAAAGGGAATGATGCAATGATAATTg < 1:3923497/45‑1 (MQ=39)
gcatAATAGAAACTCATTCGAAAAGGGAATGATGCAATGATAATTGCCACAACCTATTTTTACCATCta > 1:709694/2‑69 (MQ=255)
catAATAGAAACTCATTCGAAAAGGGAATGATGCAATGATAATTGCCACAACCTATTTTTACCATCtata < 1:1450243/70‑1 (MQ=255)
ataataGAAACTCATTCGAAAAGGGAATGATGCAATGATAATTGCCACAACCTATTTTTACCATCTATAg < 1:2889668/70‑1 (MQ=255)
taataGAAACTCATTCGAAAAGGGAATGATGCGATGATAATTGCCACAACCTATTTTTACCATCTATAGAt < 1:712636/71‑1 (MQ=255)
taataGAAACTCATTCGAAAAGGGAATGATGCAATGATaa > 1:2641708/1‑40 (MQ=255)
ataGAAACTCATTCGAAAAGGGAATGATGCAATGATAATTGCCACAAc > 1:2675189/1‑48 (MQ=255)
ataGAAACTCATTCGAAAAGGGAATGATGCAATGATAATTGCCACAACCTATTTTTACCATCTATAGATgg > 1:3491852/1‑71 (MQ=255)
taGAAACTCATTCGAAAAGGGAATGATGCGATGATAATTGCCACAACCTATTTTTACCATCTATAGATggg > 1:3848025/1‑71 (MQ=255)
gAAACTCATTCGAAAAGGGAATGATGCGATGATAATTGCCACAACCTATTTTTAc > 1:3076674/1‑55 (MQ=255)
aaaCTCATTCGAAAAGGGAATGATGCGATGATAATTGCCACAACCTATTTTTACCATCTATAGATGGGtt > 1:3530730/1‑70 (MQ=255)
aaaCTCATTCGAAAAGGGAATGATGCGATGATAATTGCCACAACCTATTTTTACCATCTATAGATGGGtt > 1:2856020/1‑70 (MQ=255)
aaaCTCATTCGAAAAGGGAATGATGCGATGATAATTGCCACAACCTATTTTTACCATCTATAGATGGGtt > 1:458278/1‑70 (MQ=255)
aaaCTCATTCGAAAAGGGAATGATGCAATGATAATTGCCACAACCTATTTTTACCATCTATAGATGGGttt < 1:1629726/71‑1 (MQ=255)
aCTCATTCGAAAAGGGAATGATGCAATGATAATTGCCACAACCTAtttt < 1:3667546/49‑1 (MQ=255)
aCTCATTCGAAAAGGGAATGATGCAATGATAATTGCCACAACCTATTTTTa > 1:2707739/1‑51 (MQ=255)
cTCATTCGAAAAGGGAATGATGCAATGATAATTGCCACAACCTATTTTTACCATCTATAGATGGGtttatt < 1:233826/71‑1 (MQ=255)
tCATTCGAAAAGGGAATGATGCGATGATAATTGCCACAACCTATTTTTACCATCTATAGATGGGtttatt > 1:3516907/1‑70 (MQ=255)
tCATTCGAAAAGGGAATGATGCAATGATAATTGCcac > 1:3306008/1‑37 (MQ=255)
cATTCGAAAAGGGAATGATGCGATGATAATTGCCACAACCTAtttt > 1:801855/1‑46 (MQ=255)
cATTCGAAAAGGGAATGATGCGATGATAATTGCCACAACCTAtttt > 1:1657890/1‑46 (MQ=255)
cATTCGAAAAGGGAATGATGCGATGATAATTGCCACAACCTATTTTTACCATCTATAGATGGGtttattta > 1:691986/1‑71 (MQ=255)
cATTCGAAAAGGGAATGATGCAATGATAATTGCCACAACCTATTTTTACCATCt < 1:2947553/54‑1 (MQ=255)
cATTCGAAAAGGGAATGATGCAATGATAATTGCCACAACCTATTTTTACCATCt < 1:2675215/54‑1 (MQ=255)
aTTCGAAAAGGGAATGATGCAATGATAATTGCCACAAc > 1:2370294/1‑38 (MQ=255)
aTTCGAAAAGGGAATGATGCAATGATAATTGCCACAACCTATTTTTACCATCTATAGATGGGtttattta < 1:587040/70‑1 (MQ=255)
aTTCGAAAAGGGAATGATGCAATGATAATTGCCACAACCTATTTTTACCATCTATAGATGGGtttattta < 1:2724532/70‑1 (MQ=255)
tCGAAAAGGGAATGATGCAATGATAATTGCCACAACCTATTTTTACCATCTATAGATGGGTTTATTTACa > 1:2756361/1‑70 (MQ=255)
cGAAAAGGGAATGATGCAATGATAATTGCCACAACCTATTTTTa > 1:30851/1‑44 (MQ=255)
cGAAAAGGGAATGATGCAATGATAATTGCCACAACCTATTTTTa > 1:2096698/1‑44 (MQ=255)
gAAAAGGGAATGATGCAATGATAATTGCCACAACCTAtt < 1:2091873/39‑1 (MQ=255)
aaaGGGAATGATGCAATGATAATTGCCACAACCTATTTTTACCATCTATAGATGGGTTTATTTACAtatta > 1:2036331/1‑71 (MQ=255)
aaGGGAATGATGCGATGATAATTGCCACAACCTATTTTTACCATCTATAGATGGGTTTATTTACAtattat < 1:1411081/71‑1 (MQ=255)
aaGGGAATGATGCAATGATAATTGCCACAACCTAt > 1:2722872/1‑35 (MQ=255)
gggAATGATGCAATGATAATTGCCACAACCTATTTTTACCATCTATAGATGGGTTTATTTACATATTATTg < 1:2317849/71‑1 (MQ=255)
gAATGATGCAATGATAATTGCCACAACCTATTTTTACCATCTATAGATGGGTTTATTTACATATTATTGGt < 1:139914/71‑1 (MQ=255)
gAATGATGCAATGATAATTGCCACAACCTATTTTTACCATCTATAGATGGGTTTATTTACATATTATTGGt < 1:3580111/71‑1 (MQ=255)
gAATGATGCAATGATAATTGCCACAACCTATTTTTACCATCTATAGATGGGTTTATTTACATATTATTGGt > 1:3425810/1‑71 (MQ=255)
aaTGATGCGATGATAATTGCCACAACCTATTTTTACCATCTATAGATGGGTTTATTTACATATTATTGGt > 1:885227/1‑70 (MQ=255)
aaTGATGCAATGATAATTGCCACAACCTATTTTTACCATCTATAGATGGGTTTATTTACATATTATTGGt > 1:2893798/1‑70 (MQ=255)
atgatgCAATGATAATTGCCACAACCTATTTTTACCATCTATAGATgg > 1:537962/1‑48 (MQ=255)
tgatgCAATGATAATTGCCACAACCTATTTTTACCATCTATAGATGGGTTTATTTACATATTATTGGTGaa > 1:1435725/1‑71 (MQ=255)
atgCGATGATAATTGCCACAACCTATTTTTACCATCTATAGATGGGTTTATTTACATATTATTGGTGAAt < 1:2162312/70‑1 (MQ=255)
atgCAATGATAATTGCCACAACCTATTTTTACCATCtat < 1:1234501/39‑1 (MQ=255)
tgCGATGATAATTGCCACAACCTATTTTTACCATCtata > 1:3249752/1‑39 (MQ=255)
tgCGATGATAATTGCCACAACCTATTTTTACCATCtata > 1:2820293/1‑39 (MQ=255)
gCGATGATAATTGCCACAACCTATTTTTACCATCTATAGATGGGTTTATTTACATATTATTGGTGAATGc > 1:3216771/1‑70 (MQ=255)
|
CGGGGAACGGCGCTCCATTGAGGAAGTCATTCATAATAGAAACTCATTCGAAAAGGGAATGATGCGATGATAATTGCCACAACCTATTTTTACCATCTATAGATGGGTTTATTTACATATTATTGGTGAATGC > minE/2823563‑2823695
|
| 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
