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 |
3,762,741 |
A→T |
K662I (AAA→ATA) |
spoT → |
bifunctional (p)ppGpp synthetase II/ guanosine‑3',5'‑bis pyrophosphate 3'‑pyrophosphohydrolase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | REL606 | 3,762,741 | 0 | A | T | 98.4%
| 226.3
/ ‑4.5
| 61 | K662I (AAA→ATA) | spoT | bifunctional (p)ppGpp synthetase II/ guanosine‑3',5'‑bis pyrophosphate 3'‑pyrophosphohydrolase |
| Reads supporting (aligned to +/- strand): ref base A (0/0); major base T (31/29); minor base G (0/1); total (31/30) |
| Fisher's exact test for biased strand distribution p-value = 4.92e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.69e-01 |
TGCGCTGGCAAACCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGAAAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGAATATCAT > REL606/3762670‑3762810
|
tGCGCTGGCAAACCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGagatagat < 1:329929/76‑1 (MQ=255)
gcTGGCAAACCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGt > 2:944128/1‑76 (MQ=255)
gcTGGCAAACCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGt > 1:769161/1‑76 (MQ=255)
gcTGGCAAACCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGt > 1:1711356/1‑76 (MQ=255)
gcTGGCAAACCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGt > 1:1354063/1‑76 (MQ=255)
cTGGCAAACCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTc < 1:556224/76‑1 (MQ=255)
ggCAAACCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTcgc < 2:878278/76‑1 (MQ=255)
ggCAAACCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTcgc < 2:951454/76‑1 (MQ=255)
gCAAACCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTcgcg > 1:622257/1‑76 (MQ=255)
cAAACCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGt > 1:1410453/1‑76 (MQ=255)
aaaCCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTc > 1:1005011/1‑76 (MQ=255)
aaCCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCt < 1:1734625/76‑1 (MQ=255)
aaCCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCt > 1:1420533/1‑76 (MQ=255)
ccTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTAc < 2:1563381/76‑1 (MQ=255)
cTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACa < 1:822897/76‑1 (MQ=255)
gACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAgc > 2:1232814/1‑76 (MQ=255)
ggcAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCttt < 2:87641/76‑1 (MQ=255)
gcAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTa > 1:1584745/1‑76 (MQ=255)
cAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTAt > 1:146822/1‑76 (MQ=255)
aTTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTc > 1:363092/1‑76 (MQ=255)
caccacGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTg < 1:1143347/76‑1 (MQ=255)
ccacGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGAc > 2:1328340/1‑76 (MQ=255)
cacGACTTCGAATATTCAAAGTTTGAATACGGAAGAGATATATGGTCGCGTCTACAGCGCCTTTATTCGTCTGAcc < 1:402611/76‑1 (MQ=255)
ctgcGAATATTCAAAGGTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCg < 2:560130/73‑1 (MQ=255)
tCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTg < 2:257723/76‑1 (MQ=255)
tCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTg < 2:795104/76‑1 (MQ=255)
tCGAATATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTg > 2:1572745/1‑76 (MQ=255)
aaTATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGAcc < 1:20638/76‑1 (MQ=255)
aaTATTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGAcc > 1:192315/1‑76 (MQ=255)
tatTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCgt > 1:1761573/1‑76 (MQ=255)
atTCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCgtg > 1:930720/1‑76 (MQ=255)
atTCAAAGTTTGAAGACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCgtg < 2:1570175/76‑1 (MQ=255)
atTCAAAGTTTCAAGACCGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGGCCGCTTGTGACCgtg < 2:1570170/76‑1 (MQ=255)
tCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGtgtg < 2:269407/76‑1 (MQ=255)
tCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGtgtg < 2:1420533/76‑1 (MQ=255)
tCAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGtgtg > 1:228271/1‑76 (MQ=255)
cAAAGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGc > 2:796155/1‑76 (MQ=255)
aaaGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCa > 2:1299667/1‑76 (MQ=255)
aaaGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCa > 2:1271427/1‑76 (MQ=255)
aaaGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCa > 2:1623813/1‑76 (MQ=255)
aaaGTTTGAATACGGAAGAGATAGATGGTCGCGTATACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCa > 2:1730956/1‑76 (MQ=255)
aaGTTTGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCAt < 2:480485/76‑1 (MQ=255)
tttGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTg < 1:1280429/76‑1 (MQ=255)
ttGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTgg > 1:1128357/1‑76 (MQ=255)
ttGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTgg < 2:581685/76‑1 (MQ=255)
ttGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTgg < 2:82324/76‑1 (MQ=255)
ttGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTgg < 2:1477748/76‑1 (MQ=255)
tggAATACTGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTgg < 2:498555/74‑1 (MQ=255)
tGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGt > 1:827700/1‑59 (MQ=255)
tGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGt < 2:827700/59‑1 (MQ=255)
tGAATACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGc < 2:679510/76‑1 (MQ=255)
aaTACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGa > 1:396504/1‑76 (MQ=255)
aaTACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGa > 2:1114989/1‑76 (MQ=255)
aTACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGaa > 2:1665711/1‑76 (MQ=255)
tACGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGAat < 1:58584/76‑1 (MQ=255)
cGGAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGAatat > 2:197076/1‑76 (MQ=255)
ggAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGAATATc < 1:1240751/76‑1 (MQ=255)
gAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGAATATCa > 1:795166/1‑76 (MQ=255)
gAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGAATATCa < 1:748689/76‑1 (MQ=255)
gAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGAATATCa < 2:638493/76‑1 (MQ=255)
gAAGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGAATATCa > 1:176367/1‑76 (MQ=255)
gAAGAGAGAGATGGTCGCGTCTACAGAGCCGTGAGTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGAATATCa < 2:638500/76‑1 (MQ=255)
aaGAGATAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGAATATCAt < 1:528397/76‑1 (MQ=255)
|
TGCGCTGGCAAACCTGACGGCGGCAATTAACACCACGACTTCGAATATTCAAAGTTTGAATACGGAAGAGAAAGATGGTCGCGTCTACAGCGCCTTTATTCGTCTGACCGCTCGTGACCGTGTGCATCTGGCGAATATCAT > REL606/3762670‑3762810
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ 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
