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 |
|
A77 F1 I1 R1
|
21 |
53.0 |
3608474 |
95.6% |
3449701 |
76.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
REL606 |
3,613,043 |
+TT |
intergenic (‑104/+79) |
dctA ← / ← yhjK |
C4‑dicarboxylate transport protein/predicted diguanylate cyclase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | REL606 | 3,613,041 | 1 | . | T | 92.1%
| 140.1
/ 5.6
| 38 | intergenic (‑102/+81) | dctA/yhjK | C4‑dicarboxylate transport protein/predicted diguanylate cyclase |
| Reads supporting (aligned to +/- strand): ref base . (2/1); new base T (17/18); total (19/19) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.60e-01 |
| * | REL606 | 3,613,041 | 2 | . | T | 92.1%
| 138.5
/ 5.6
| 38 | intergenic (‑102/+81) | dctA/yhjK | C4‑dicarboxylate transport protein/predicted diguanylate cyclase |
| Reads supporting (aligned to +/- strand): ref base . (2/1); new base T (17/18); total (19/19) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.93e-01 |
CTTGTAAGGTTATGGGGTACCTGCGGCCTTAAAATAACACCCAGACAACATCACAGAAATGTACCTGGATCATAA‑‑TTGAAACAAAAAGGTTAAAAAGTTTGAGCTGGCTCGCACAAACCAGCACTTTTTAAAGTTTTGTAATCA > REL606/3612967‑3613110
||
cTTGTAAGGTTATGGGGTACCTGCGGCCTTAAAATAACACCCAGACAACATCACAGAAATGTACCTGGATCATAA‑‑t > 1:1335265/1‑76 (MQ=255)
ttGTAAGGTTATGGGGTACCTGCGGCCTTAAAATAACACCCAGACAACATCACAGAAATGTACCTGGATCATAA‑‑tt < 1:1795503/76‑1 (MQ=255)
ttGTAAGGTTATGGGGTACCTGCGGCCTTAAAATAACACCCAGACAACATCACAGAAATGTACCTGGATCATAA‑‑tt > 2:1107717/1‑76 (MQ=255)
ttGTAAGGTTATGGGGTACCTGCGGCCTTAAAATAACACCCAGACAACATCACAGAAATGTACCTGGATCATAA‑‑tt < 1:601271/76‑1 (MQ=255)
tGTAAGGTTATGGGGTACCTGCGGCCTTAAAATAACACCCAGACAACATCACAGAAATGTACCTGGATCATAA‑‑ttt > 1:1465390/1‑75 (MQ=255)
tGTAAGGTTATGGGGTACCTGCGGCCTTAAAATAACACCCAGACAACATCACAGAAATGTACCTGGATCATAA‑‑ttt > 1:773383/1‑75 (MQ=255)
gTAAGGTTATGGGGTACCTGCGGCCTTAAAATAACACCCAGACAACATCACAGAAATGTACCTGGATCATAA‑‑TTGa > 1:154617/1‑76 (MQ=255)
tAAGGTTATGGGGTACCTGCGGCCTTAAAATAACACCCAGACAACATCACAGAAATGTACCTGGATCATAA‑‑ttttg < 2:441422/76‑4 (MQ=255)
tGGGGTTCCTGCGGCCTTAAAATAACACCCAGACAACATCACAGAAATGTACCTGGATCATAATTTTGAAACaaaa < 2:1287826/76‑1 (MQ=255)
gggTACCTGCGGCCTTAAAATAACACCCAGACAACATCACAGAAATGTACCTGGATCATAATTTTGAAACAAAAAg < 1:1625983/76‑1 (MQ=255)
tgTACCTGCGGCCTTAAAATAACACCCAGACAACATCACAGAAATGTACCTGGATCATAATTTTGAAACAAAAAgg > 2:98498/2‑76 (MQ=255)
tACCTGCGGCCTTAAAATAACACCCAGACAACATCACAGAAATGTACCTGGATCATAATTTTGAAACAAAAAGGtt < 2:1034191/76‑1 (MQ=255)
ccTGCGGCCTTAAAATAACACCCAGACAACATCACAGAAATGTACCTGGATCATAATTTTGAAACAAAAAGGTTaa > 1:693744/1‑76 (MQ=255)
gCGGCCTTAAAATAACACCCAGACAACATCACAGAAATGTACCTGGATCATAATTTTGAAACAAAAAGGTTaaaaa > 2:790014/1‑76 (MQ=255)
cGGCCTTAAAATAACACCCAGACAACATCACAGAAATGTACCTGGATCATAATTTTGAAACAAAAAGGTTAAAAAg > 1:1494617/1‑76 (MQ=255)
gCCTTAAAATAACACCCAGACAACATCACAGAAATGTACCTGGATCATAA‑‑TTGAAACAAAAAGGTTAAAAAGTTTg < 2:1795764/76‑1 (MQ=255)
ccTTAAAATAACACCCAGACAACATCACAGAAATGTACCTGGATCATAATTTTGAAACAAAAAGGTTAAAAAGttt < 1:624849/76‑1 (MQ=255)
cTTAAAATAACACCCAGACAACATCACAGAAATGTACCTGGATCATAATTTTGAAACAAAAAGGTTAAAAAGTTTg < 2:367543/76‑1 (MQ=255)
cTTAAAATAACACCCAGACAACATCACAGAAATGTACCTGGATCATAATTTTGAAACAAAAAGGTTAAAAAGTTTg < 2:1090287/76‑1 (MQ=255)
tAAAATAACACCCAGACAACATCACAGAAATGTACCTGGATCATAATTTTGAAACAAAAAGGTTAAAAAGTTTGAg > 1:1322193/1‑76 (MQ=255)
tAAAATAACACCCAGACAACATCACAGAAATGTACCTGGATCATAATTTTGAAACAAAAAGGTTAAAAAGTTTGAg > 1:1415020/1‑76 (MQ=255)
tAACACCCAGACAACATCACAGAAATGTACCTGGATCATAATTTTGAAACAAAAAGGTTAAAAAGTTTGAGCTGGc > 2:565352/1‑76 (MQ=255)
aaCACCCAGACAACATCACAGAAATGTACCTGGATCATAATTTTGAAACAAAAAGGTTAAAAAGTTTGAGCTGGCt > 1:1282330/1‑76 (MQ=255)
acacCCAGACAACATCACAGAAATGTACCTGGATCATAATTTTGAAACAAAAAGGTTAAAAAGTTTGAGCTGGCTc > 2:971663/1‑76 (MQ=255)
acCCAGACAACATCACAGAAATGTACCTGGATCATAATTTTGAAACAAAAAGGTTAAAAAGTTTGAGCTGGCTCGc < 1:1281266/76‑1 (MQ=255)
acCCAGACAACATCACAGAAATGTACCTGGATCATAATTTTGAAACAAAAAGGTTAAAAAGTTTGAGCTGGCTCGc < 1:80642/76‑1 (MQ=255)
aGACAACATCACAGAAATGTACCTGGATCATAATTTTGAAACAAAAAGGTTAAAAAGTTTGAGCTGGCTCGCACaa < 1:1140780/76‑1 (MQ=255)
gACAACATCACAGAAATGTACCTGGATCATAATTTTGAAACAAAAAGGTTAAAAAGTTTGAGCTGGCTCGCACaaa < 1:685332/76‑1 (MQ=255)
acaacaTCACAGAAATGTACCTGGATCATAATTTTGAAACAAAAAGGTTAAAAAGTTTGAGCTGGCTCGCACAAAc < 1:369010/76‑1 (MQ=255)
acaacaTCACAGAAATGTACCTGGATCATAATTTTGAAACAAAAAGGTTAAAAAGTTTGAGCTGGCTCGCACAAAc < 1:1247166/76‑1 (MQ=255)
caacaTCACAGAAATGTACCTGGATCATAATTTTGAAACAAAAAGGTTAAAAAGTTTGAGCTGGCTCGCACAAAcc < 2:1297575/76‑1 (MQ=255)
acaTCACAGAAATGTACCTGGATCATAATTTTGAAACAAAAAGGTTAAAAAGTTTGAGCTGGCTCGCACAAACCAg < 2:780000/76‑1 (MQ=255)
tCACAGAAATGTACCTGGATCATAATTTTGAAACAAAAAGGTTAAAAAGTTTGAGCTGGCTCGCACAAACCAGCAc < 1:183137/76‑1 (MQ=255)
acaGAAATGTACCTGGATCATAATTTTGAAACAAAAAGGTTAAAAAGTTTGAGCTGGCTCGCACAAACCAGCACtt > 1:1540123/1‑76 (MQ=255)
caGAAATGTACCTGGATCATAATTTTGAAACAAAAAGGTTAAAAAGTTTGAGCTGGCTCGCACAAACCAGCACttt > 2:1492691/1‑76 (MQ=255)
caGAAATGTACCTGGATCATAATTTTGAAACAAAAAGGTTAAAAAGTTTGAGCTGGCTCGCACAAACCAGCACttt < 2:60927/76‑1 (MQ=255)
aGAAATGTACCTGGATCATAATTTTGAAACAAAAAGGTTAAAAAGTTTGAGCTGGCTCGCACAAACCAGCACtttt > 2:1174780/1‑76 (MQ=255)
aGAAATGTACCTGGATCATAATTTTGAAACAAAAAGGTTAAAAAGTTTGAGCTGGCTCGCACAAACCAGCACtttt < 2:1042136/76‑1 (MQ=255)
aaaTGTACCTGGATCATAATTTTGAAACAAAAAGGTTAAAAAGTTTGAGCTGGCTCGCACAAACCAGCACTTTTTa > 1:252053/1‑76 (MQ=255)
aaTGTACCTGGATCATAATTTTGAAACAAAAAGGTTAAAAAGTTTGAGCTGGCTCGCACAAACCAGCCCTTTTTaa < 1:116341/76‑1 (MQ=255)
tGTACCTGGATCATAATTTTGAAACAAAAAGGTTAAAAAGTTTGAGCTGGCTCGCACAAACCAGCACTTTTTAAAg > 1:1089943/1‑76 (MQ=255)
gTACCTGGATCATAATTTTGAAACAAAAAGGTTAAAAAGTTTGAGCTGGCTCGCACAAACCAGCACTTTTTAAAGt > 1:950712/1‑76 (MQ=255)
ggATCATAATTTTGAAACAAAAAGGTTAAAAAGTTTGAGCTGGCTCGCACAAACCAGCACTTTTTAAAGTTTTGTa > 1:1431641/1‑76 (MQ=255)
ggATCATAATTTTGAAACAAAAAGGTTAAAAAGTTTGAGCTGGCTCGCACAAACCAGCACTTTTTAAAGTTTTGTa < 1:565352/76‑1 (MQ=255)
ggATCATAATTTTGAAACAAAAAGGTTAAAAAGTTTGAGCTGGCTCGCACAAACCAGCACTTTTTAAAGTTTTGTa > 1:1172569/1‑76 (MQ=255)
aTCATAA‑‑TTGAAACAAAAAGGTCAAAAAGTTTGAGCTGGCTCGCACAAACCAGCACTTTTTAAAGTTTTGTAATCa > 1:1432261/1‑76 (MQ=255)
||
CTTGTAAGGTTATGGGGTACCTGCGGCCTTAAAATAACACCCAGACAACATCACAGAAATGTACCTGGATCATAA‑‑TTGAAACAAAAAGGTTAAAAAGTTTGAGCTGGCTCGCACAAACCAGCACTTTTTAAAGTTTTGTAATCA > REL606/3612967‑3613110
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
