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 |
|
A73 F1 I1 R1
|
21 |
62.0 |
3993596 |
96.1% |
3837845 |
76.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
REL606 |
1,573,659 |
A→C |
D39A (GAT→GCT) |
yneC → |
autoinducer‑2 (AI‑2) modifying protein LsrG |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | REL606 | 1,573,659 | 0 | A | C | 91.7%
| 190.3
/ 5.0
| 48 | D39A (GAT→GCT) | yneC | autoinducer‑2 (AI‑2) modifying protein LsrG |
| Reads supporting (aligned to +/- strand): ref base A (1/3); new base C (15/29); total (16/32) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.96e-01 |
GTTGACGAGTTTATCGAAGTTTTTCGCCAGAACCACCTGGGCTCTGTACAGGAAGAAGGCAATTTGCGCTTCGATGTCTTACAGGACCCGGAAGTGAATTCGCGCTTTTATATCTACGAAGCCTATAAAGATGAAGACGCAGTGGC > REL606/1573586‑1573731
|
gTTGACGAGTTTATCGAAGTTTTTCGCCAGAACCACCTGGGCTCTGTACAGGAAGAAGGCAATTTGCGCTTCGCTg < 2:1050701/76‑1 (MQ=255)
tGACGAGTTTATCGAAGTTTTTCGCCAGAACCACCTGGGCTCTGTACAGGAAGAAGGCAATTTGCGCTTCGCTGTc > 1:1093882/1‑76 (MQ=255)
tGACGAGTTTATCGAAGTTTTTCGCCAGAACCACCTGGGCTCTGTACAGGAAGAAGGCAATTTGCGCTTCGCTGTc > 1:655095/1‑76 (MQ=255)
aCGAGTTTATCGAAGTTTTTCGCCAGAACCACCTGGGCTCTGTACAGGAAGAAGGCAATTTGCGCTTCGCTGTCtt < 1:1279123/76‑1 (MQ=255)
aCGAGTTTATCGAAGTTTTTCGCCAGAACCACCTGGGCTCTGTACAGGAAGAAGGCAATTTGCGCTTCGCTGTCtt < 2:352473/76‑1 (MQ=255)
cGAGTTTATCGAAGTTTTTCGCCAGAACCACCTGGGCTCTGTACAGGAAGAAGGCAATTTGCGCTTCGCTGTCTTa < 2:1673027/76‑1 (MQ=255)
gAGTTTATCGAAGTTTTTCGCCAGAACCACCTGGGCTCTGTACAGGAAGAAGGCAATTTGCGCTTCGCTGTCTTAc > 1:731269/1‑76 (MQ=255)
gAGTTTATCGAAGTTTTTCGCCAGAACCACCTGGGCTCTGTACAGGAAGAAGGCAATTTGCGCTTCGATGTCTTAc < 1:739803/76‑1 (MQ=255)
tttATCGAAGTTTTTCGCCAGAACCACCTGGGCTCTGTACAGGAAGAAGGCAATTTGCGCTTCGCTGTCTTACAgg < 1:1476895/76‑1 (MQ=255)
ttATCGAAGTTTTTCGCCAGAACCACCTGGGCTCTGTACAGGAAGAAGGCAATTTGCGCTTCGCTGTCTTACAGGa > 2:1991797/1‑76 (MQ=255)
aTCGAAGTTTTTCGCCAGAACCACCTGGGCTCTGTACAGGAAGAAGGCAATTTGCGCTTCGCTGTCTTACAGGAcc > 1:143451/1‑76 (MQ=255)
aTCGAAGTTTTTCGCCAGAACCACCTGGGCTCTGTACAGGAAGAAGGCAATTTGCGCTTCGCTGTCTTACAGGAcc > 1:442573/1‑76 (MQ=255)
aTCGAAGTTTTTCGCCAGAACCACCTGGGCTCTGTACAGGAAGAAGGCAATTTGCGCTTCGCTGTCTTACAGGAcc < 2:383038/76‑1 (MQ=255)
tCGAAGTTTTTCGCCAGAACCACCTGGGCTCTGTACAGGAAGAAGGCAATTTGCGCTTCGCTGTCTTACAGGAccc > 1:783084/1‑76 (MQ=255)
cGAAGTTTTTCGCCAGAACCACCTGGGCTCTGTACAGGAAGAAGGCAATTTGCGCTTCGCTGTCTTACAGGACCCg < 2:1427534/76‑1 (MQ=255)
cGAAGTTTTTCGCCAGAACCACCTGGGCTCTGTACAGGAAGAAGGCAATTTGCGCTTCGCTGTCTTACAGGACCCg > 1:835266/1‑76 (MQ=255)
aGTTTTTCGCCAGAACCACCTGGGCTCTGTACAGGAAGAAGGCAATTTGCGCTTCGCTGTCTTACAGGACCCGGaa < 2:13639/76‑1 (MQ=255)
ttttCGCCAGAACCACCTGGGCTCTGTACAGGAAGAAGGCAATTTGCGCTTCGCTGTCTTACAGGACCCGGAAGTg < 1:1056881/76‑1 (MQ=255)
ttttCGCCAGAACCACCTGGGCTCTGTACAGGAAGAAGGCAATTTGCGCTTCGCTGTCTTACAGGACCCGGAAGTg < 1:425650/76‑1 (MQ=255)
tCGCCAGAACCACCTGGGCTCTGTACAGGAAGAAGGCAATTTGCGCTTCGCTGTCTTACAGGACCCGGAAGTGAAt > 2:1957490/1‑76 (MQ=255)
cGCCAGAACCACCTGGGCTCTGTACAGGAAGAAGGCAATTTGCGCTTCGCTGTCTTACAGGACCCGGAAGTGAAtt > 1:454780/1‑76 (MQ=255)
cGCCAGAACCACCTGGGCTCTGTACAGGAAGAAGGCAATTTGCGCTTCGATGTCTCACAGGACCCGGAAGTGAAtt > 2:538712/1‑76 (MQ=255)
aGAACCACCTGGGCTCTGTACAGGAAGAAGGCAATTTGCGCTTCGCTGTCTTACAGGACCCGGAAGTGAATTcgcg > 2:22745/1‑76 (MQ=255)
accaccTGGGCTCTGTACAGGAAGAAGGCAATTTGCGCTTCGCTGTCTTACAGGACCCGGAAGTGAATTCGCGCtt < 2:1051252/76‑1 (MQ=255)
accaccTGGGCTCTGTACAGGAAGAAGGCAATTTGCGCTTCGCTGTCTTACAGGACCCGGAAGTGAATTCGCGCtt < 2:1873515/76‑1 (MQ=255)
caccTGGGCTCTGTACAGGAAGAAGGCAATTTGCGCTTCGCTGTCTTACAGGACCCGGAAGTGAATTCGCGCtttt < 2:616870/76‑1 (MQ=255)
caccTGGGCTCTGTACAGGAAGAAGGCAATTTGCGCTTCGCTGTCTTACAGGACCCGGAAGTGAATTCGCGCtttt < 2:1269963/76‑1 (MQ=255)
caccTGGGCTCTGTACAGGAAGAAGGCAATTTGCGCTTCGCTGTCTTACAGGACCCGGAAGTGAATTCGCGCtttt > 1:58438/1‑76 (MQ=255)
ccTGGGCTCTGTACAGGAAGAAGGCAATTTGCGCTTCGCTGTCTTACAGGACCCGGAAGTGAATTCGCGCTTTtat < 1:445246/76‑1 (MQ=255)
cTGGGCTCTGTACAGGAAGAAGGCAATTTGCGCTTCGCTGTCTTACAGGACCCGGAAGTGAATTCGCGCTTTtata < 1:331378/76‑1 (MQ=255)
gggCTCTGTACAGGAAGAAGGCAATTTGCGCTTCGCTGTCTTACAGGACCCGGAAGTGAATTCGCGCTTTTatata < 2:1560919/76‑2 (MQ=255)
gCTCTGTACAGGAAGAAGGCAATTTGCGCTTCGCTGTCTTACAGGACCCGGAAGTGAATTCGCGCTTTTATATCTa < 1:1208710/76‑1 (MQ=255)
tctGTACAGGAAGAAGGCAATTTGCGCTTCGCTGTCTTACAGGACCCGGAAGTGAATTCGCGCTTTTATATCTACg < 2:783084/76‑1 (MQ=255)
tctGTACAGGAAGAAGGCAATTTGCGCTTCGCTGTCTTACAGGACCCGGAAGTGAATTCGCGCTTTTATATCTACg < 1:620320/76‑1 (MQ=255)
tctGTACAGGAAGAAGGCAATTTGCGCTTCGATGTCTTACAGGACCCGGAAGTGAATTCGCGCTTTTATATCTACg < 1:857489/76‑1 (MQ=255)
ctGTACAGGAAGAAGGCAATTTGCGCTTCGCTGTCTTACAGGACCCGGAAGTGAATTCGCGCTTTTATATCTACGa < 2:460947/76‑1 (MQ=255)
aCAGGAAGAAGGCAATTTGCGCTTCGCTGTCTTACAGGACCCGGAAGTGAATTCGCGCTTTTATATCTACGAAGcc > 1:1577228/1‑76 (MQ=255)
cAGGAAGAAGGCAATTTGCGCTTCGCTGTCTTACAGGACCCGGAAGTGAATTCGCGCTTTTATATCTACGAAGCCt < 2:1872622/76‑1 (MQ=255)
cAGGAAGAAGGCAATTTGCGCTTCGCTGTCTTACAGGACCCGGAAGTGAATTCGCGCTTTTATATCTACGAAGCCt < 2:1872636/76‑1 (MQ=255)
ggAAGAAGGCAATTTGCGCTTCGCTGTCTTACAGGACCCGGAAGTGAATTCGCGCTTTTATATCTACGAAGCCtat < 2:1896205/76‑1 (MQ=255)
aagaagGCAATTTGCGCTTCGCTGTCTTACAGGACCCGGAAGTGAATTCGCGCTTTTATATCTACGAAGCCTATaa < 1:1838305/76‑1 (MQ=255)
agaagGCAATTTGCGCTTCGATGTCTTACAGGACCCGGAAGTGAATTCGCGCTTTTATATCTACGAAGCCTATaaa < 2:1744578/76‑1 (MQ=255)
gCAATTTGCGCTTCGCTGTCTTACAGGACCCGGAAGTGAATTCGCGCTTTTATATCTACGAAGCCTATAAAGATGa < 1:853704/76‑1 (MQ=255)
cAATTTGCGCTTCGCTGTCTTACAGGACCCGGAAGTGAATTCGCGCTTTTATATCTACGAAGCCTATAAAGATGaa < 2:139511/76‑1 (MQ=255)
tGCGCTTCGCTGTCTTACAGGACCCGGAAGTGAATTCGCGCTTTTATATCTACGAAGCCTATAAAGATGAAGACGc > 1:303618/1‑76 (MQ=255)
cgcTTCGATGTCTTACAGGACCCGGAAGTGAATTCGCGCTTTTATATCTACGAAGCCTATAAAGATGAAGACGCAg > 1:1947284/1‑76 (MQ=255)
gcTTCGCTGTCTTACAGGACCCGGAAGTGAATTCGCGCTTTTATATCTACGAAGCCTATAAAGATGAAGACGCAGt > 2:1281973/1‑76 (MQ=255)
ttCGCTGTCTTACAGGACCCGGAAGTGAATTCGCGCTTTTATATCTACGAAGCCTATAAAGATGAAGACGCAGTgg < 2:1302492/76‑1 (MQ=255)
tCGCTGTCTTACAGGACCCGGAAGTGAATTCGCGCTTTTATATCTACGAAGCCTATAAAGATGAAGACGCAGTGGc < 2:1137444/76‑1 (MQ=255)
|
GTTGACGAGTTTATCGAAGTTTTTCGCCAGAACCACCTGGGCTCTGTACAGGAAGAAGGCAATTTGCGCTTCGATGTCTTACAGGACCCGGAAGTGAATTCGCGCTTTTATATCTACGAAGCCTATAAAGATGAAGACGCAGTGGC > REL606/1573586‑1573731
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
