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 |
|
A5 F21 I0 R2
|
316 |
65.6 |
5147759 |
97.4% |
5013917 |
60.3 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
2,680,577 |
C→A |
43.0% |
L275L (CTG→CTT) |
yphG ← |
conserved hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 2,680,577 | 0 | C | A | 43.0%
| 86.5
/ 69.8
| 72 | L275L (CTG→CTT) | yphG | conserved hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base C (29/12); new base A (16/15); total (45/27) |
| Fisher's exact test for biased strand distribution p-value = 1.40e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.97e-01 |
GGCCAAATTCACTGTGTCCCCAACTCCACTG‑TTTTTTACCTGGCGCAATATGGTGGTTGGCAACGTGCAGCAAACCGCCATCTTCATCGTGACACCACGCGCCGACAAAATCGTACTGCGATTTTTCGGCCATATA > W3110S.gb/2680510‑2680645
|
ggCCAAATTCACTGTGTCCCCAACTCCACTG‑TTTTTTACCTGGCGCAATATGGTGGTTGGCAACGTgaag > 1:582696/1‑70 (MQ=255)
aaaTTCACTGTGTCCCCAACTCCACTG‑TTTTTTACCTGGCGCAATATGGTGGTTGGCAACGTGAAGCAAAc > 1:792448/1‑71 (MQ=255)
aaaTTCACTGTGTCCCCAACTCCACTG‑TTTTTTACCTGGCGCAATATGGTGGTTGGCAACGTGAAGCAAAc > 1:3443014/1‑71 (MQ=255)
aaaTTCACTGTGTCCCCAACTCCACTG‑TTTTTTACCTGGCGCAATATGGTGGTTGGCAACGTGAAGCAAAc > 1:3248508/1‑71 (MQ=255)
aTTCACTGTGTCCCCAACTCCACTG‑TTTTTTACCTGGCGCAATATGGTGGTTGGCAACGTGCAGCAAACCg > 1:3980541/1‑71 (MQ=255)
aTTCACTGTGTCCCCAACTCCACTG‑TTTTTTACCTGGCGCAATATGGTGGTTGGCAACGTGCAGCAAACCg > 1:1941361/1‑71 (MQ=255)
aTTCACTGTGTCCCCAACTCCACTG‑TTTTTTACCTGGCGCAATATGGTGGTTGGCAACGTGAAGCAACCCg > 1:3780329/1‑71 (MQ=255)
ttCACTGTGTCCCCAACTCCACTG‑TTTTTTACCTGGCGCAATATGGTGGTTGGCAACGTGCAGCAAACCGc > 1:953088/1‑71 (MQ=255)
ttCACTGTGTCCCCAACTCCACTG‑TTTTTTACCTGGCGCAATATGGTGGTTGGCAACGTGCAGCAAACCGc > 1:2175805/1‑71 (MQ=255)
ttCACTGTGTCCCCAACTCCACTG‑TTTTTTACCTGGCGCAATATGGTGGTTGGCAACGTGAAGCAAACCGc > 1:1052206/1‑71 (MQ=255)
cACTGTGTCCCCAACTCCACTG‑TTTTTTACCTGGCGCAATATGGTGGTTGGCAACGTGCAGCAAACCGCCa > 1:1029956/1‑71 (MQ=255)
tgtgTCCCCAACTCCACTG‑TTTTTTACCTGGCGCAATATGGTGGTTGGCAACGTGCAGCAAACCGcc < 1:3434441/67‑1 (MQ=255)
tgtCCCCAACTCCACTG‑TTTTTTACCTGGCGCAATATGGTGGTTGGCAACGTGCAGCAAACCGCCATCtt < 1:3472118/70‑1 (MQ=255)
tgtCCCCAACTCCACTG‑TTTTTTACCTGGCGCAATATGGTGGTTGGCAACGTGAAGCaaa > 1:1697967/1‑60 (MQ=255)
tCCCCAACTCCACTG‑TTTTTTACCTGGCGCAATATGGTGGTTGGCAACGTGAAGCAAACCGCCATCTTCAt > 1:1999354/1‑71 (MQ=255)
ccAACTCCACTG‑TTTTTTACCTGGCGCAATATGGTGGTTGGCAACGTGCAGCAAACCGCCATCTTCATCGt < 1:4166051/71‑1 (MQ=255)
ccAACTCCACTG‑TTTTTTACCTGGCGCAATATGGTGGTTGGCAACGTGCAGCAAACCGCCATCTTCATCGt < 1:344284/71‑1 (MQ=255)
ccAACTCCACTG‑TTTTTTACCTGGCGCAATATGGTGGTTGGCAACGTGAAGCAAACCGCCATCTTCATCGt < 1:533159/71‑1 (MQ=255)
ccAACTCCACTG‑TTTTTTACCTGGCGCAATATGGTGGTTGGCAACGTGAAGCAAACCGCCATCTTCATCGt < 1:3832247/71‑1 (MQ=255)
aaCTCCACTG‑TTTTTTACCTGGCGCAATATGGTGGTGGGCAACGTGAAGCAAACCGCCATCTTCATCGTGa < 1:2385756/71‑1 (MQ=255)
aCTCCACTG‑TTTTTTACCTGGCGCAATATGGTGGTTGGCAACGTGCAGCaa < 1:2700917/51‑1 (MQ=255)
aCTCCACTG‑TTTTTTACCTGGCGCAATATGGTGGTTGGCAACGTGCAGCAAACCGCCATCTTCATCGTGac < 1:4144821/71‑1 (MQ=255)
aCTCCACTG‑TTTTTTACCTGGCGCAATATGGTGGTTGGCAACGTGAAGCAAACCGCCATc < 1:4487924/60‑1 (MQ=255)
aCTCCACTG‑TTTTTTACCTGGCGCAATATGGTGGTTGGCAACGTGAAGCAAACCGCCATc < 1:1047614/60‑1 (MQ=255)
aCTCCACTG‑TTTTTTACCTGGCGCAATATGGTGGTTGGCAACGTGAAGCAAACCGCCATc < 1:620314/60‑1 (MQ=255)
cTCCACTG‑TTTTTTACCTGGCGCAATATGGTGGTTGGCAACGTGCAGCAAAc > 1:3940475/1‑52 (MQ=255)
cTCCACTG‑TTTTTTACCTGGCGCAATATGGTGGTTGGCAACGTGCAGCAAAc > 1:3632806/1‑52 (MQ=255)
tCCACTGTTTTTTTACCTGGCGCAATATGGTGGTTGGCAACGTGAAGCaa < 1:2408577/50‑1 (MQ=255)
tCCACTG‑TTTTTTACCTGGCGCAATATGGTGGTTGGCAACGTGCAGCAAACCGCCATCTTCATCGTGacac > 1:1057167/1‑71 (MQ=255)
cACTG‑TTTTTTACCTGGCGCAATATGGTGGTTGGCAACGTGCAGCAAACCGCCATCTTCATCGTGAcacca > 1:3159737/1‑71 (MQ=255)
cACTG‑TTTTTTACCTGGCGCAATATGGTGGTTGGCAACGTGAAGCaaa > 1:4047812/1‑48 (MQ=255)
cACTG‑TTTTTTACCTGGCGCAATATGGTGGTTGGCAACGTGAAGCaa > 1:79518/1‑47 (MQ=255)
cACTG‑TTTTTTACCTGGCGCAATATGGTGGTTGGCAACGTGAAGCAAACCGCCATCTTCATCGTGacac < 1:3642775/69‑1 (MQ=255)
cACTG‑TTTTTTACCTGGCGCAATATGGTGGTTGGCAACGTGAAGCAAACCGCCATCTTCATCGTGaaac < 1:2126103/69‑1 (MQ=255)
cTG‑TTTTTTACCTGGCGCAATATGGTGGTTGGCAACGTGCAGCAAACCGCCATCTTCATCGTGACACCAcg < 1:2782/71‑1 (MQ=255)
cTG‑TTTTTTACCTGGCGCAATATGGTGGTTGGCAACGTGAAGCAAACCGCCATCTTCATCGTGACACCAcg > 1:3599423/1‑71 (MQ=255)
tG‑TTTTTTACCTGGCGCAATATGGTGGTTGGCAACGTGAAGCAAACCGCCATc < 1:5023988/53‑1 (MQ=255)
tG‑TTTTTTACCTGGCGCAATATGGTGGTTGGCAACGTGAAGCAAACCGCCATc < 1:2854511/53‑1 (MQ=255)
tG‑TTTTTTACCTGGCGCAATATGGTGGTTGGCAACGTGAAGCAAACCGCCATCtt < 1:2145171/55‑1 (MQ=255)
ttttttACCTGGCGCAATATGGTGGTTGGCAACGTGAAGCAAACCGCCATCtt > 1:711096/1‑53 (MQ=255)
ttttACCTGGCGCAATATGGTGGTTGGCAACGTGCAGCAAACCGCCATCTTCATCGTGACACCACGCGcc > 1:2540051/1‑70 (MQ=255)
ttttACCTGGCGCAATATGGTGGTTGGCAACGTGCAGCAAACCGCCATCTTCATCGTGACACCACGCGcc > 1:3735424/1‑70 (MQ=255)
ttttACCTGGCGCAATATGGTGGTTGGCAACGTGAAGCAAACCGCCATCTTCATCGTGac > 1:2374563/1‑60 (MQ=255)
ccTGGCGCTATATGGTGGGTGGCAACGTGAAGCAAACCGCCATc < 1:1934349/44‑1 (MQ=38)
ggCGCAATATGGTGGTTGGCAACGTGCAGCAAACCGCCATCTTCATCGTGACACCACGCGCCGACAAAATc > 1:3149657/1‑71 (MQ=255)
gcgcAATATGGTGGTTGGCAACGTGCAGCAAACCGCCATCTTCATCGTGACACCACGCGCCGACaaa < 1:4950432/67‑1 (MQ=255)
gcgcAATATGGTGGTTGGCAACGTGAAGCAAACCGCCATCTTCATCGTGACACCACGCGCCGACAAAATCg < 1:3770110/71‑1 (MQ=255)
gcgcAATATGGTGGTTGGCAACGTGAAGCAAACCGCCATCTTCATCGTGACACCACGCGCCGACAAAATCg < 1:3257703/71‑1 (MQ=255)
aaTATGGTGGTTGGCAACGTGCAGCAAACCGCCATCTTCATCGTGACACCACGCGCCGACAAAATCg < 1:4390494/67‑1 (MQ=255)
atatGGTGGTTGGCAACGTGCAGCAAACCGCCATCTTCATCGt < 1:2117094/43‑1 (MQ=255)
atGGTGGTTGGCAACGTGCAGCAAACCGCCATCTTCATCGt > 1:2490872/1‑41 (MQ=255)
atGGTGGTTGGCAACGTGCAGCAAACCGCCATCTTCATCGt > 1:525234/1‑41 (MQ=255)
atGGTGGTTGGCAACGTGCAGCAAACCGCCATCTTCATCGTGa > 1:4652885/1‑43 (MQ=255)
atGGTGGTTGGCAACGTGCAGCAAACCGCCATCTTCATCGTGACACCACGCGCCGACAAAATCGTACTGc > 1:4849550/1‑70 (MQ=255)
atGGTGGTTGGCAACGTGCAGCAAACCGCCATCTTCATCGTGACACCACGCGCCGACAAAATCGTACTGc > 1:4104167/1‑70 (MQ=255)
atGGTGGTTGGCAACGTGCAGCAAACCGCCATCTTCATCGTGACACCACGCGCCGACAAAATCGTACTGc > 1:2031961/1‑70 (MQ=255)
atGGTGGTTGGCAACGTGCAGCAAACCGCCATCTTCATAGTGACACCACGCGCCGACAAAATCGTACTGc > 1:3435352/1‑70 (MQ=255)
atGGTGGTTGGCAACGTGAAGCAAACCGCCATCTTCATCGTGACACCACGCGCCGACAAAATCGTACTGc > 1:3432101/1‑70 (MQ=255)
tggtggTTGGCAACGTGCAGCAAACCGCCATCTTCATCGTGa > 1:1729743/1‑42 (MQ=255)
tggtggTTGGCAACGTGCAGCAAACCGCCATCTTCATCGTGa > 1:792753/1‑42 (MQ=255)
tggtggTTGGCAACGTGCAGCAAACCGCCATCTTCATCGTGa > 1:2931759/1‑42 (MQ=255)
tggtggTTGGCAACGTGCAGCAAACCGCCATCTTCATCGTGACACCACGCGCCGACAAAAt > 1:3517024/1‑61 (MQ=255)
tggtggTTGGCAACGTGCAGCAAACCGCCATCTTCATCGTGACACCACGCGCCGACAAAATCGTACTGCGa > 1:388527/1‑71 (MQ=255)
tggtTGGCAACGTGCAGCAAACCGCCATCTTCATCGTGACACCACGCGCCGACAAAATCGTACTGCGAttt < 1:3826056/71‑1 (MQ=255)
gtTGGCAACGTGCAGCAAACCGCCATCTTCATCGTGACACCACGCGCCGACAAAATCGTa > 1:1406440/1‑60 (MQ=255)
gtTGGCAACGTGCAGCAAACCGCCATCCTCATCGTGACACCACGCGCCGACAAAATCGTa > 1:1006897/1‑60 (MQ=255)
ggCAACGTGCAGCAAACCGCCATCTTCATCGTGACACCACGCGCCGACaaaa > 1:2822225/1‑52 (MQ=255)
gCAACGTGCAGCAAACCGCCATCTTCATCGTGACACCACGCGCCGACAAAATCGTACTGCGATTTTTCGGc < 1:4473730/71‑1 (MQ=255)
gTGAAGCAAACCGCCATCTTCATCGTGACACCACGCGCCGACAAAATCGTa > 1:4615205/1‑51 (MQ=255)
gTGAAGCAAACCGCCATCTTCATCGTGACACCACGCGCCGACAAAATCGTa > 1:408669/1‑51 (MQ=255)
gTGAAGCAAACCGCCATCTTCATCGTGACACCACGCGCCGACAAAATCGTACTGCGATTTTTCGGCCata > 1:3499457/1‑70 (MQ=255)
tGCAGCAAACCGCCATCTTCATCGTGACACCACGCGCCGACAAAATCGTACTGCGATTTTTCGGCCatata > 1:2124814/1‑71 (MQ=255)
tGCAGCAAACCGCCATCTTCATCGTGACACCACGCGCCGACAAAATCGTACTGCGATTTTTCGGCCatata > 1:244556/1‑71 (MQ=255)
|
GGCCAAATTCACTGTGTCCCCAACTCCACTG‑TTTTTTACCTGGCGCAATATGGTGGTTGGCAACGTGCAGCAAACCGCCATCTTCATCGTGACACCACGCGCCGACAAAATCGTACTGCGATTTTTCGGCCATATA > W3110S.gb/2680510‑2680645
|
| 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
