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 |
|
A21 F1 I1 R1
|
16 |
43.9 |
3070277 |
96.2% |
2953606 |
75.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
REL606 |
3,339,489 |
Δ1 bp |
intergenic (+31/‑55) |
fis → / → yhdJ |
DNA‑binding protein Fis/predicted methyltransferase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | REL606 | 3,339,488 | 0 | G | . | 87.5%
| 168.1
/ 24.5
| 49 | intergenic (+30/‑56) | fis/yhdJ | DNA‑binding protein Fis/predicted methyltransferase |
| Reads supporting (aligned to +/- strand): ref base G (1/0); major base . (12/30); minor base A (4/2); total (17/32) |
| Fisher's exact test for biased strand distribution p-value = 8.56e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.76e-01 |
CGTGGTACGCTGCGTAAAAAATTGAAAAAATACGGCATGAACTAATTCAGGTTAGCTAAATGCTTGATTAAAAAGGCGCTACTCGGCATGGGGAAGCGCCTTTTTTATAGGTGTCACAAAGGGAGTGACCATGAGAACAGGATGTGA > REL606/3339414‑3339560
|
cGTGGTACGCTGCGTAAAAAATTGAAAAAATACGGCATGAACTAATTCAGGTTAGCTAAATGCTTGATTAAAAAgc > 2:297744/1‑75 (MQ=255)
tGGTACGCTGCGTAAAAAATTGAAAAAATACGGCATGAACTAATTCAGGTTAGCTAAATGCTTGATTAAAAAgcgc > 1:780583/1‑73 (MQ=255)
tGGTACGCTGCGTAAAAAATTGAAAAAATACGGCATGAACTAATTCAGGTTAGCTAAATGCTTGATTAAAAAgcgc > 1:782322/1‑73 (MQ=255)
gTACGCTGCGTAAAAAATTGAAAAAATNCGGCATGAACTAATTCAGGTTAGCTAAATGCTTGATTAAAAAGGCGCt > 1:1529674/1‑76 (MQ=255)
gTACGCTGCGTAAAAAATCGAAAAAATACGGCATGAACTAATTCAGGTTAGCTAAATGCTTGATTAAAAA‑GCGCTa < 1:270215/76‑1 (MQ=255)
gCTGCGTAAAAAATTGAAAAAATACGGCATGAACTAATTCAGGTTAGCTAAATGCTTGATTAAAAA‑GCGCTACTCg < 1:942522/76‑1 (MQ=255)
tGCGTAAAAAATTGAAAAAATACGGCATGAACTAATTCAGGTTAGCTAAATGCTTGATTAAAAA‑GCGCTACTCGGc < 1:606528/76‑1 (MQ=255)
gTAAAAAATTGAAAAAATACGGCATGAACTAATTCAGGTTAGCTAAATGCTTGATTAAAAA‑GCGCTACTCGGCATg < 1:733410/76‑1 (MQ=255)
tAAAAAATTGAAAAAATACGGCATGAACTAATTCAGGTTAGCTAAATGCTTGATTAAAAA‑GCGCTACTCGGCATgg < 1:1166566/76‑1 (MQ=255)
aaaTTGAAAAAATACGGCATGAACTAATTCAGGTTAGCTAAATGCTTGATTAAAAA‑GCGCTACTCGGCATGGGGaa < 2:1078003/76‑1 (MQ=255)
aaaTTGAAAAAATACGGCATGAACTAATTCAGGTTAGCTAAATGCTTGATTAAAAA‑GCGCTACTCGGCATGGGGaa < 2:611966/76‑1 (MQ=255)
aaaTTGAAAAAATACGGCATGAACTAATTCAGGTTAGCTAAATGCTTGATTAAAAA‑GCGCTACTCGGCATGGGGaa < 1:683553/76‑1 (MQ=255)
aaaGTGAAAAAATACGGCATGAACTAATTCAGGTTAGCTAAATGCTTGATTAAAAA‑GCGCTACTCGNCATGGGGaa < 1:36347/76‑1 (MQ=255)
aTTGAAAAAATACGGCATGAACTAATTCAGGTTAGCTAAATGCTTGATTAAAAA‑GCGCTACTCGGCATGGGGAAgc > 2:512072/1‑76 (MQ=255)
aaaaaaTACGGCATGAACTAATTCAGGTTAGCTAAATGCTTGATTAAAAA‑GCGCTACTCGGCATGGGGAAGCGCCt < 1:442913/76‑1 (MQ=255)
aaaaaTACGGCATGAACTAATTCAGGTTAGCTAAATGCTTGATTAAAAA‑GCGCTACTCGGCATGGGGAAGCGCCtt < 2:583581/76‑1 (MQ=255)
aaaaTACGGCATGAACTAATTCAGGTTAGCTAAATGCTTGATTAAAAA‑GCGCTACTCGGCATGGGGAAGCGCCttt > 2:853027/1‑76 (MQ=255)
aaaaTACGGCATGAACTAATTCAGGTTAGCGAAATGCTTGATTAACAA‑GCGCTACTCGGCATNGGGAAGCGCCttt > 2:1392656/1‑76 (MQ=255)
aaTACGGCATGAACTAATTCAGGTTAGCTAAATGCTTGATTAAAAA‑GCGCTACTCGGCATGGGGAAGCGCCttttt > 2:993374/1‑76 (MQ=255)
aaTACGGCATGAACTAATTCAGGTTAGCTAAATGCTTGATTAAAAA‑GCGCTACTCGGCATGGGGAAGCGCCttttt > 1:209595/1‑76 (MQ=255)
aCGGCATGAACTAATTCAGGTTAGCTAAATGCTTGATTAAAAA‑GCGCTACTCGGCATGGGGAAGCGCCTTTTTtat < 1:167464/76‑1 (MQ=255)
cATGAAGTAATTCAGGTTAGCTAAATGCTTGATTAAAAA‑GCGCTACTCGGCATGGGGAAGCGCCTTTTTTATAGgt < 1:1514842/76‑1 (MQ=255)
cATGAACTAATTCAGGTTAGCGAAATGCTTGATTAAAAA‑GCGCTACTCGGCATTGGGAAGCGCCTTTTTTATAGgt < 2:224897/76‑1 (MQ=255)
tGAACTTATTTAGGTTAGCTATGTGCTTGATTAAAAA‑GCGCTACGCGGCATGGGGAAGCGCCTCCTTTATAGgtgt > 2:914764/1‑76 (MQ=255)
tGAACTAATTCAGGTTAGCTAAATGCTTGATTAAAAA‑GCGCTACTCGGCATGGGGAAGCGCCTTTTTTATAGgtgt < 1:1229439/76‑1 (MQ=255)
cTAATTCAGGTTAGCTAAATGCTTGATTAAAAA‑GCGCTACTCGGCATGGGGAAGCGCCTTTTTTATANGTGTcaca > 1:1350410/1‑76 (MQ=255)
cTAATTCAGGTTAGCTAAATGCTTGATTAAAAA‑GCGCTACTCGGCATGGGGAAGCGCCTTTTTTATAGGTGTcaca < 1:255138/76‑1 (MQ=255)
cTAATTCAGGTTAGCTAAATGCTTGATTAAAAA‑GCGCTACTCGGCATGGGGAAGCGCCTTTTTTATAGGTGTcaca > 1:1481453/1‑76 (MQ=255)
tAATTCAGGTTAGCTAAATGCTTGATTAAAAA‑GCGCTACTCGGCATGGGGAAGCGCCTTTTTTATAGGTGTCACaa < 2:1530816/76‑1 (MQ=255)
tCAGGTTAGCTAAATGCTTGATTAAAAA‑GCGCTACTCGGCATGGGGAAGCGCCTTTTTTATAGGTGTCACAAAggg < 1:1235278/76‑1 (MQ=255)
tCAGGTTAGCTAAATGCTTGATTAAAAA‑GCGCTACTCGGCATGGGGAAGCGCCTTTTTTATAGGTGTCACAAAggg < 2:1100684/76‑1 (MQ=255)
tCAGGTTAGCTAAATGCTTGATTAAAAA‑GCGCTACTCGGCATGGGGAAGCGCCTTTTTTATAGGTGTCACAAAggg < 2:48703/76‑1 (MQ=255)
cAGGTTAGCTAAATGCTTGATTAAACA‑GNGCTACTCGGCCTCGGGAATCGCCTTTTTTATAGGTGTCACAAAGGGa < 1:136544/76‑1 (MQ=255)
cAGGTTAGCTAAATGCTTGATTAAAAA‑GCGCTACTCGGCATGGGGAAGCGCCTTTTTTATAGGTGTCACAAAGGGa < 2:331225/76‑1 (MQ=255)
ttAGCTAAATGCTTGATTAAAAA‑GCGCTACTCGGCATGGGGAAGCGCCTTTTTTATAGGTGTCACAAAGGGAGTGa > 1:702485/1‑76 (MQ=255)
tAGCTAAATGCTTGATTAAAAA‑GCGCTACTCGGNATGGGGAAGCGCCTTTTTTATANGTGTCACATANGGAGTGAc > 2:1279578/1‑76 (MQ=255)
aGCTAAATGCTTGATTAAAAA‑GCGCTACTCGGCATGGGGAAGCGCCTTTTTTATAGGTGTCACAAAGGGAGTGAcc < 2:1008814/76‑1 (MQ=255)
aGCTAAATGCTTGATTAAAAA‑GCGCTACTCGGCATGGGGAAGCGCCTTTTTTATAGGTGTCACAAAGGGAGTGAcc < 2:185838/76‑1 (MQ=255)
cTAAATGCTTGATTAAAAA‑GCGCTACTCGGCATGGGGAAGCGCCTTTTTTATAGGTGTCACAAAGGGAGTGACCAt < 1:1060753/76‑1 (MQ=255)
cTAAATGCTTGATTAAAAA‑GCGCTACTCGGCATGGGGAAGCGCCTTTTTTATAGGTGTCACAAAGGGAGTGACCAt < 2:134815/76‑1 (MQ=255)
cTAAATGCTTGATTAAAAA‑GCGCTACTCGGCATGGGGAAGCGCCTTTTTTATAGGTGTCACAAAGGGAGTGACCAt < 1:864307/76‑1 (MQ=255)
aTGCTTGATTAAAAA‑GCGCTACTCGGCATGGGGAAGCGCCTTTTTTATAGGTGTCACAAAGGGAGTGACCATgaga < 2:1215913/76‑1 (MQ=255)
tGCTTGATTAAAAA‑GCGCTACTCGGCATGGGGAAGCGCCTTTTTTATAGGTGTCACAAAGGGAGTGACCATGAGaa > 1:469346/1‑76 (MQ=255)
tGCTTGATTAAAAA‑GCGCTACTCGGCATGGGGAAGCGCCTTTTTTATAGGTGTCACAAAGAGAGTGACCATGAGaa > 2:51476/1‑76 (MQ=255)
cTTGATTAAAAA‑GCGCTACTCGGCATGGGGAAGCGCCTTTTTTATAGGTGTCACAAAGGGAGTGACCATGAGAACa < 2:1164537/76‑1 (MQ=255)
gATTAAAAA‑GCGCTACTCGGCATGGGGAAGCGCCTTTTTTATAGGTGTCACAAAGGGAGTGACCATGAGAACAGGa < 1:382095/76‑1 (MQ=255)
ttaaaaAGCGCTGCTCGGCATGGGGAAGCGCCTTTTTTATAGGTGTCACAAAGGGAGTGACCATGAGAACAGGAtg < 2:1152953/74‑1 (MQ=255)
ttaaaaAGCGCTACTCGGCATGGGGAAGCGCCTTTTTTATAGGTGTCACAAAGGGAGTGACCATGAGAACAGGAtg < 2:1152970/74‑1 (MQ=255)
taaaaAGCGCTACTCGGCATGGGGAAGCGCCTTTTTTATAGGTGTCACAAGGGGAGTGACCATGAGAACAGGAtgt > 1:458548/2‑76 (MQ=255)
aaaaAGCGCTACTCGGCATGGGGAAGCGCCTTTTTTATAGGTGTCACAAAGGGAGTGACCATGAGAACAGGAtgtg > 2:544943/1‑76 (MQ=255)
aaaaAGCGCTACTCGGCATGGGGAAGCGCCTTTTTTATAGGTGTCACAAAGGGAGTGACCATGAGAACAGGAtgtg > 2:698887/1‑76 (MQ=255)
aaaaAGCGCTACTCGGCATGAGGAAGCGCCTTTTTTATAGGTGTCACAAAGGGAGTGACCATGAGAACAGGAtgtg > 2:480422/1‑76 (MQ=255)
aaaaGCGCTACTCGGCATGGGGAAGCGCCTTTNTTATAGGTGTCACAAAGGGAGTGACCATGAGAACAGGATNTGa > 2:1434817/1‑76 (MQ=255)
|
CGTGGTACGCTGCGTAAAAAATTGAAAAAATACGGCATGAACTAATTCAGGTTAGCTAAATGCTTGATTAAAAAGGCGCTACTCGGCATGGGGAAGCGCCTTTTTTATAGGTGTCACAAAGGGAGTGACCATGAGAACAGGATGTGA > REL606/3339414‑3339560
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
