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 |
|
A139 F1 I1 R1
|
15 |
48.9 |
3081653 |
97.3% |
2998448 |
76.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
REL606 |
1,689,712 |
(C)6→7 |
intergenic (+360/‑251) |
nth → / → ydgR |
DNA glycosylase and apyrimidinic (AP) lyase (endonuclease III)/putative tripeptide transporter permease |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | REL606 | 1,689,706 | 1 | . | C | 91.5%
| 177.9
/ 8.9
| 47 | intergenic (+354/‑257) | nth/ydgR | DNA glycosylase and apyrimidinic (AP) lyase (endonuclease III)/putative tripeptide transporter permease |
| Reads supporting (aligned to +/- strand): ref base . (3/1); new base C (26/17); total (29/18) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.84e-01 |
TGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑CCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTT > REL606/1689631‑1689775
|
tGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCa < 1:891289/76‑1 (MQ=255)
ggCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑c < 1:1235307/76‑1 (MQ=255)
gCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑cc < 2:575028/76‑1 (MQ=255)
cTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑ccc > 2:59626/1‑76 (MQ=255)
aGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTca < 1:1117385/76‑1 (MQ=255)
aGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTca > 2:1213373/1‑76 (MQ=255)
gAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTcag > 1:841452/1‑76 (MQ=255)
gAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTcag > 1:369306/1‑76 (MQ=255)
gAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTcag < 1:1420161/76‑1 (MQ=255)
aaaCTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTcagt < 1:160916/76‑1 (MQ=255)
aCTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTcagtgc > 2:1204661/1‑76 (MQ=255)
tGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTcagtgcag > 1:125956/1‑76 (MQ=255)
tGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTcagtgcag < 2:1222000/76‑1 (MQ=255)
ggACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTcagtgcagt > 1:487893/1‑76 (MQ=255)
gACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCACCA‑CCCCCCTCTCAGTGCAGTGa > 2:263935/1‑76 (MQ=255)
aCTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGa > 1:1339366/1‑76 (MQ=255)
aCTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGa < 1:1176501/76‑1 (MQ=255)
cTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGaa > 2:927860/1‑76 (MQ=255)
tATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑CCCCCCTCTCAGTGCAGTGaaaa < 1:1045530/76‑1 (MQ=255)
aTCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGaaaa < 1:167655/76‑1 (MQ=255)
aTCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGaaaa > 1:431922/1‑76 (MQ=255)
cACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATc > 1:1223583/1‑76 (MQ=255)
aCTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCCCAGTGCAGCGAAAAAATCt > 2:465398/1‑76 (MQ=255)
aGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGcc > 2:964093/1‑76 (MQ=255)
aGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTAcc > 2:738978/1‑76 (MQ=255)
tAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGttttt > 2:412150/1‑76 (MQ=255)
tAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGttttt > 2:161992/1‑76 (MQ=255)
tAAATAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGttttt < 1:521780/76‑1 (MQ=255)
aaaTAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGattttt > 2:1518781/1‑76 (MQ=255)
aaTAGCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTg < 1:966407/76‑1 (MQ=255)
gCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGaaaa < 2:1330244/76‑1 (MQ=255)
gCAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGaaaa > 1:1209672/1‑76 (MQ=255)
cAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGaaaaa > 2:1539745/1‑76 (MQ=255)
cAGAACATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGaaaaa > 2:351348/1‑76 (MQ=255)
gAACATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAAtt < 1:637274/76‑1 (MQ=255)
aaCATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAAttt < 1:205531/76‑1 (MQ=255)
cATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTaa < 1:1255064/76‑1 (MQ=255)
cATATCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTaa > 2:161144/1‑76 (MQ=255)
tatCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACg > 1:1351876/1‑76 (MQ=255)
tatCGCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACg < 2:434679/76‑1 (MQ=255)
atCGCCGTTAAGCCATCACCCCCCCTCTCAGAGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGc > 1:743180/1‑76 (MQ=255)
gCCGTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTgg > 1:1384708/1‑76 (MQ=255)
ccGTTAAGCCATCACCCCCCCTCTCAGTGCAGGGAAAAAATCTGCCGTTAAGTTTTTTGTAAAATTTAACGCTGGa > 1:284472/1‑76 (MQ=255)
ccGTTAAGCCATCA‑CCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGAt > 2:920809/1‑76 (MQ=255)
gTTAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATa < 1:694600/76‑1 (MQ=255)
ttAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCAGTTACGTTTTTTGAAAAATTTAACGCTGGATaa < 1:386855/76‑1 (MQ=255)
tAAGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAAc > 2:687618/1‑76 (MQ=255)
tAAGCCATCA‑CCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACa > 2:1475577/1‑76 (MQ=255)
aaGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACa < 1:1212139/76‑1 (MQ=255)
aaGCCATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACa > 1:1182153/1‑76 (MQ=255)
ccATCACCCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACAttt < 2:625093/76‑1 (MQ=255)
|
TGGCTATTTTTCAGAAACTGGACTATCTCACTAGTAAAAACGCTAAATAGCAGAACATATCGCCGTTAAGCCATCA‑CCCCCCTCTCAGTGCAGTGAAAAAATCTGCCGTTACGTTTTTTGAAAAATTTAACGCTGGATAACATTT > REL606/1689631‑1689775
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 23 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
