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 |
|
A1 F3 I122 R1
|
193 |
20.9 |
1228102 |
94.7% |
1163012 |
84.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
4,573,665 |
T→C |
pseudogene (2914/3513 nt) |
hsdR ← |
type I restriction‑modification system endonuclease |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 4,573,665 | 0 | T | C | 96.8%
| 105.9
/ ‑3.4
| 31 | pseudogene (2914/3513 nt) | hsdR | type I restriction‑modification system endonuclease |
| Reads supporting (aligned to +/- strand): ref base T (1/0); new base C (16/14); total (17/14) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
TCACCGTACAGCGATTTTACACTCACCACTTCATCGTCGATATCGAGGAAGATCGGCGCATCATTCAGGTTGTTGATGTCCGTTTTCAGCTTTTCCAGACGGGCGATAAAGCCAGGCAGTTTGTTAAAGACTTCGGCGCTCCAGTGCGGCCCTTTTTCCCGCAGGCGCG > NZ_CP009273/4573580‑4573748
|
tCACCGTACAGCGATTTTACACTCACCACTTCATCGTCGATATCGAGGAAGATCGGCGCATCATTCAGGTTGTTGATGTCCGTTTCCAGc < 2:204116/90‑1 (MQ=255)
tCACCGTACAGCGATTTTACACTCACCACTTCATCGTCGATATCGAGGAAGATCGGCGCATCATTCAGGTTGTTGATGTCCGTTTCCAGc < 1:557619/90‑1 (MQ=255)
tCACCGTACAGCGATTTTACACTCACCACTTCATCGTCGATATCGAGGAAGATCGGCGCATCATTCAGGTTGTTGATGTCCGTTTCCAGc < 2:411219/90‑1 (MQ=255)
ccGTACAGCGATTTTACACTCACCACTTCATCGTCGATATCGAGGAAGATCGGCGCATCATTCAGGTTGTTGATGTCCGTTTCCAGCttt > 2:44142/1‑90 (MQ=255)
ccGTACAGCGATTTTACACTCACCACTTCATCGTCGATATCGAGGAAGATCGGCACATCATTCAGGTTGTTGATGTCCGTTTCCAGCttt > 2:305049/1‑90 (MQ=255)
acTCACCACTTCATCGTCGATATCGAGGAAGATCGGCGCATCATTCAGGTTGTTGATGTCCGTTTCCAGCTTTTCCAGACGGGCGATaaa > 2:561402/1‑90 (MQ=255)
caccacTTCATCGTCGATATCGAGGAAGATCGGCGCATCATTCAGGTTGTTGATGTCCGTTTTCAGCTTTTCCAGACGGGCGATAAAGcc > 2:339193/1‑90 (MQ=255)
caccacTTCATCGTCGATATCGAGGAAGATCGGCGCATCATTCAGGTTGTTGATGTCCGTTTCCAGCTTTTCCAGACGGGCGATAAAGcc > 1:266006/1‑90 (MQ=255)
caccacTTCATCGTCGATATCGAGGAAGATCGGCGCATCATTCAGGTTGTTGATGTCCGTTTCCAGCTTTTCCAGACGGGCGATAAAGcc > 1:356240/1‑90 (MQ=255)
caccacTTCATCGTCGATATCGAGGAAGATCGGCGCATCATTCAGGTTGTTGATGTCCGTTTCCAGCTTTTCCAGACGGGCGATAAAGcc > 2:123002/1‑90 (MQ=255)
ccacTTCATCGTCGATATCGAGGAAGATCGGCGCATCATTCAGGTTGTTGATGTCCGTTTCCAGCTTTTCCAGACGGGCGATAAAGCCAg < 2:500831/90‑1 (MQ=255)
ttCATCGTCGATATCGAGGAAGATCGGCGCATCATTCAGGTTGTTGATGTCCGTTTCCAGCTTTTCCAGACGGGCGATAAAGCCAGGCAg < 1:87302/90‑1 (MQ=255)
cATCGTCGATATCGAGGAAGATCGGCGCATCATTCAGGTTGTTGATGTCCGTTTCCAGCTTTTCCAGACGGGCGATAAAGCCAGGCAGtt < 2:89268/90‑1 (MQ=255)
cATCGTCGATATCGAGGAAGATCGGCGCATCATTCAGGTTGTTGATGTCCGTTTCCAGCTTTTCCAGACGGGCGATAAAGCCAGGCAGtt < 2:186987/90‑1 (MQ=255)
cATCGTCGATATCGAGGAAGATCGGCGCATCATTCAGGTTGTTGATGTCCGTTTCCAGCTTTTCCAGACGGGCGATAAAGCCAGGCAGtt < 1:359877/90‑1 (MQ=255)
tcgtcgATATCGAGGAAGATCGGCGCATCATTCAGGTTGTTGATGTCCGTTTCCAGCTTTTCCAGACGGGCGATAAAGCCAGGCAGTTTg > 1:37949/1‑90 (MQ=255)
tatCGAGGAAGATCGGCGCATCATTCAGGTTGTTGATGTCCGTTTCCAGCTTTTCCAGACGGGCGATAAAGCCAGGCAGTTTGTTAAAGa > 1:461527/1‑90 (MQ=255)
gAAGATCGGCGCATCATTCAGGTTGTTGATGTCCGTTTCCAGCTTTTCCAGACGGGCGATAAAGCCAGGCAGTTTGTTAAAGACTTCGgc < 1:561402/90‑1 (MQ=255)
gATCGGCGCATCATTCAGGTTGTTGATGTCCGTTTCCAGCTTTTCCAGACGGGCGATAAAGCCAGGCAGTTTGTTAAAGACTTCGGCGCt > 1:120022/1‑90 (MQ=255)
aTCGGCGCATCATTCAGGTTGTTGATGTCCGTTTCCAGCTTTTCCAGACGGGCGATAAAGCCAGGCAGTTTGTTAAAGACTTCGGCGCTc > 2:389874/1‑90 (MQ=255)
ggCGCATCATTCAGGTTGTTGATGTCCGTTTCCAGCTTTTCCAGACGGGCGATAAAGCCAGGCAGtt < 1:333463/67‑1 (MQ=255)
ggCGCATCATTCAGGTTGTTGATGTCCGTTTCCAGCTTTTCCAGACGGGCGATAAAGCCAGGCAGtt > 2:333463/1‑67 (MQ=255)
ggCGCATCATTCAGGTTGTTGATGTCCGTTTCCAGCTTTTCCAGACGGGCGATAAAGCCAGGCAGTTTGTTAAAGACTTCGGCGCTCCAg > 2:119820/1‑90 (MQ=255)
gcATCATTCAGGTTGTTGATGTCCGTTTCCAGCTTTTCCAGACGGGCGATAAAGCCAGGCAGtt > 2:185816/1‑64 (MQ=255)
gcATCATTCAGGTTGTTGATGTCCGTTTCCAGCTTTTCCAGACGGGCGATAAAGCCAGGCAGtt < 1:185816/64‑1 (MQ=255)
catcatTCAGGTTGTTGATGTCCGTTTCCAGCTTTTCCAGACGGGCGATAAAGCCAGGCAGTTTGTTAAAGACTTCGGCGCTCCAGTGCg < 1:88858/90‑1 (MQ=255)
tgttgATGTCCGTTTCCAGCTTTTCCAGACGGGCGATAAAGCCAGGCAGTTTGTTAAAGACTTCGGCGCTCCAGTGCGGCCCTTTTTccc > 1:355304/1‑90 (MQ=255)
gTCCGTTTCCAGCTTTTCCAGACGGGCGATAAAGCCAGGCAGTTTGTTAAAGACTTCGGCGCTCCAGTGCGGCCCTTTTTCCCGCAGgcg < 2:355304/90‑1 (MQ=255)
ccGTTTCCAGCTTTTCCAGACGGGCGATAAAGCCAGGCAGTTTGTTAAAGACTTCGGCGCTCCAGTGCGGCCCTTTTTCCCGCAGGcgcg < 1:87214/90‑1 (MQ=255)
ccGTTTCCAGCTTTTCCAGACGGGCGATAAAGCCAGGCAGTTTGTTAAAGACTTCGGCGCTCCAGTGCGGCCCTTTTTCCCGCAGGcgcg > 1:241177/1‑90 (MQ=255)
ccGTTTCCAGCTTTTCCAGACGGGCGATAAAGCCAGGCAGTTTGTTAAAGACTTCGGCGCTCCAGTGCGGCCCTTTTTCCCGCAGGcgcg > 2:570091/1‑90 (MQ=255)
|
TCACCGTACAGCGATTTTACACTCACCACTTCATCGTCGATATCGAGGAAGATCGGCGCATCATTCAGGTTGTTGATGTCCGTTTTCAGCTTTTCCAGACGGGCGATAAAGCCAGGCAGTTTGTTAAAGACTTCGGCGCTCCAGTGCGGCCCTTTTTCCCGCAGGCGCG > NZ_CP009273/4573580‑4573748
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
TCACCGTACAGCGATTTTACACTCACCACTTCATCGTCGATATCGAGGAAGATCGGCGCATCATTCAGGTTGTTGATGTCCGTTTTCAGCTTTTCCAGACGGGCGATAAAGCCAGGCAGTTTGTTAAAGACTTCGGCGCTCCAGTGCGGCCCTTTTTCCCGCAGGCGCGAGGCGAAGCCGT > NZ_CP009273/4573580‑4573760
|
TCACCGTACAGCGATTTTACACTCACCACTTCATCGTCGATATCGAGGAAGATCGGCGCATCATTCAGGTTGTTGATGTCCGTTTCCAGCTTTTCCAGAC < SRR3721989.569718/100‑1 (MQ=60)
ATTTTACACTCACCACTTCATCGTCGATATCGAGGAAGATCGGCGCATCATTCAGGTTGTTGATGTCCGTTTCCAGCTTTTCCAGACGGGCGATAAAGCC > SRR3721989.270723/1‑100 (MQ=60)
ATTTTACACTCACCACTTCATCGTCGATATCGAGGAAGATCGGCGCATCATTCAGGTTGTTGATGTCCGTTTCCAGCTTTTCCAGACGGGCGATAAAGCC > SRR3721989.363078/1‑100 (MQ=60)
CACCACTTCATCGTCGATATCGAGGAAGATCGGCGCATCATTCAGGTTGTTGATGTCCGTTTCCAGCTTTTCCAGACGGGCGATAAAGCCAGGCAGTTTG > SRR3721989.38607/1‑100 (MQ=60)
TTCATCGTCGATATCGAGGAAGATCGGCGCATCATTCAGGTTGTTGATGTCCGTTTCCAGCTTTTCCAGACGGGCGATAAAGCCAGGCAGTTTGTTAAAG < SRR3721989.88872/100‑1 (MQ=60)
TCATCGTCGATATCGAGGAAGATCGGCGCATCATTCAGGTTGTTGATGTCCGTTTCCAGCTTTTCCAGACGGGCGATAAAGCCAGGCAGTTTGTTAAAGA > SRR3721989.471209/1‑100 (MQ=60)
tgtgtataagagacAGGAAGATCGGCGCATCATTCAGGTTGTTGATGTCCGTTTCCAGCTTTTCCAGACGGGCGATAAAGCCAGGCAGTTTGTTAAAGAC < SRR3721989.189220/86‑1 (MQ=60)
gtataagagacagGAGGAAGATCGGCGCATCATTCAGGTTGTTGATGTCCGTTTCCAGCTTTTCCAGACGGGCGATAAAGCCAGGCAGTTTGTTAAAGAC < SRR3721989.339836/87‑1 (MQ=60)
CATCGTCGATATCGAGGAAGATCGGCGCATCATTCAGGTTGTTGATGTCCGTTTCCAGCTTTTCCAGACGGGCGATAAAGCCAGGCAGTTTGTTAAAGAC < SRR3721989.366830/100‑1 (MQ=60)
TATCGAGGAAGATCGGCGCATCATTCAGGTTGTTGATGTCCGTTTCCAGCTTTTCCAGACGGGCGATAAAGCCAGGCAGTTTGTTAAAGACTTCGGCGCT > SRR3721989.122215/1‑100 (MQ=60)
GAAGATCGGCGCATCATTCAGGTTGTTGATGTCCGTTTCCAGCTTTTCCAGACGGGCGATAAAGCCAGGCAGTTTGTTAAAGACTTCGGCGCTCCAGTGC < SRR3721989.573579/100‑1 (MQ=60)
CATCATTCAGGTTGTTGATGTCCGTTTCCAGCTTTTCCAGACGGGCGATAAAGCCAGGCAGTTTGTTAAAGACTTCGGCGCTCCAGTGCGGCCCTTTTTC < SRR3721989.90469/100‑1 (MQ=60)
TCATTCAGGTTGTTGATGTCCGTTTCCAGCTTTTCCAGACGGGCGATAAAGCCAGGCAGTTTGTTAAAGACTTCGGCGCTCCAGTGCGGCCCTTTTTCCC > SRR3721989.362116/1‑100 (MQ=60)
TTGTTGATGTCCGTTTCCAGCTTTTCCAGACGGGCGATAAAGCCAGGCAGTTTGTTAAAGACTTCGGCGCTCCAGTGCGGCCCTTTTTCCCGCAGGCGCG > SRR3721989.245487/1‑100 (MQ=60)
CCGTTTCCAGCTTTTCCAGACGGGCGATAAAGCCAGGCAGTTTGTTAAAGACTTCGGCGCTCCAGTGCGGCCCTTTTTCCCGCAGGCGCGAGGCGAAGCC < SRR3721989.88784/100‑1 (MQ=60)
GTTTCCAGCTTTTCCAGACGGGCGATAAAGCCAGGCAGTTTGTTAAAGACTTCGGCGCTCCAGTGCGGCCCTTTTTCCCGCAGGCGCGAGGCGAAGCCGT > SRR3721989.262569/1‑100 (MQ=60)
GTTTCCAGCTTTTCCAGACGGGCGATAAAGCCAGGCAGTTTGTTAAAGACTTCGGCGCTCCAGTGCGGCCCTTTTTCCCGCAGGCGCGAGGCGAAGCCGT > SRR3721989.58845/1‑100 (MQ=60)
|
TCACCGTACAGCGATTTTACACTCACCACTTCATCGTCGATATCGAGGAAGATCGGCGCATCATTCAGGTTGTTGATGTCCGTTTTCAGCTTTTCCAGACGGGCGATAAAGCCAGGCAGTTTGTTAAAGACTTCGGCGCTCCAGTGCGGCCCTTTTTCCCGCAGGCGCGAGGCGAAGCCGT > NZ_CP009273/4573580‑4573760
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
