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 F2 I75 R1
|
71 |
32.8 |
2150506 |
93.3% |
2006422 |
83.2 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
4,004,376 |
T→C |
intergenic (+16/‑60) |
yigL → / → bioP |
sugar/pyridoxal phosphate phosphatase YigL/biotin transporter |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 4,004,376 | 0 | T | C | 98.0%
| 178.9
/ ‑5.0
| 51 | intergenic (+16/‑60) | yigL/bioP | sugar/pyridoxal phosphate phosphatase YigL/biotin transporter |
| Reads supporting (aligned to +/- strand): ref base T (1/0); new base C (29/20); total (31/20) |
| 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 |
GAGCTGGAAGTGATTGGTACTAATGCCGACGACGCGGTGCCGCATTATCTGCGTAAACTCTATTTATCGTAATCGTTCTTTATTTGGTCAGTTGTCAACCTGATACTTCGCTACAATGGATACCCGTTAATCAAAGAGTTTTCCATTGTGGCGCTACTTATCATCACCACGATT > NZ_CP009273/4004289‑4004462
|
gAGCTGGAAGTGATTGGTACTAATGCCGACGACGCGGTGCCGCATTATCTGCGTAAACTCTATTTATCGTAATCGTTCTTTATTTGGCCa > 1:1066449/1‑90 (MQ=255)
gAGCTGGAAGTGATTGGTACTAATGCCGACGACGCGGTGCCGCATTATCTGCGTAAACTCTATTTATCGTAATCGTTCTTTATTTGGCCa < 2:488873/90‑1 (MQ=255)
gAGCTGGAAGTGATTGGTACTAATGCCGACGACGCGGTGCCGCATTATCTGCGTAAACTCTATTTATCGTAATCGTTCTTTATTTGGCCa < 1:977838/90‑1 (MQ=255)
gAGCTGGAAGTGATTGGTACTAATGCCGACGACGCGGTGCCGCATTATCTGCGTAAACTCTATTTATCGTAATCGTTCTTTATTTGGCCa > 1:880103/1‑90 (MQ=255)
gAAGTGATTGGTACTAATGCCGACGACGCGGTGCCGCATTATCTGCGTAAACTCTATTTATCGTAATCGTTCTTTATTTGGCCAGTTGTc < 2:1066449/90‑1 (MQ=255)
gAAGTGATTGGTACTAATGCCGACGACGCGGTGCCGCATTATCTGCGTAAACTCTATTTATCGTAATCGTTCTTTATTTGGCCAGTTGTc < 1:576571/90‑1 (MQ=255)
gATTGGTACTAATGCCGACGACGCGGTGCCGCATTATCTGCGTAAACTCTATTTATCGTAATCGTTCTTTATTTGGCCAGTTGTCAACCt > 1:124483/1‑90 (MQ=255)
ggTACTAATGCCGACGACGCGGTGCCGCATTATCTGCGTAAACTCTATTTATCGTAATCGTTCTTTATTTGGCCAGTTGTCAACCTGATa > 1:618236/1‑90 (MQ=255)
tAATGCCGACGACGCGGTGCCGCATTATCTGCGTAAACTCTATTTATCGTAATCGTTCTTTATTTGGCCAGTTGTCAACCTGATACTTCg > 1:104454/1‑90 (MQ=255)
aaTGCCGACGACGCGGTGCCGCATTATCTGCGTAAACTCTATTTATCGTAATCGTTCTTTATTTGGCCAGTTGTc < 2:217320/75‑1 (MQ=255)
aaTGCCGACGACGCGGTGCCGCATTATCTGCGTAAACTCTATTTATCGTAATCGTTCTTTATTTGGCCAGTTGTc > 1:523326/1‑75 (MQ=255)
aaTGCCGACGACGCGGTGCCGCATTATCTGCGTAAACTCTATTTATCGTAATCGTTCTTTATTTGGCCAGTTGTc > 1:217320/1‑75 (MQ=255)
aaTGCCGACGACGCGGTGCCGCATTATCTGCGTAAACTCTATTTATCGTAATCGTTCTTTATTTGGCCAGTTGTc < 2:523326/75‑1 (MQ=255)
gCCGACGACGCGGTGCCGCATTATCTGCGTAAACTCTATTTATCGTAATCGTTCTTTATTTGGCCAGTTGTCAACCTGATACTTCGCTAc < 1:227567/90‑1 (MQ=255)
cgacgaCGCGGTGCCGCATTATCTGCGTAAACTCTATTTATCGTAATCGTTCTTTATTTGGCCAGTTGTCAACCTGATACTTCGCTACaa > 1:663971/1‑90 (MQ=255)
cgacgaCGCGGTGCCGCATTATCTGCGTAAACTCTATTTATCGTAATCGTTCTTTATTTGGCCAGTTGTCAACCTGATACTTCGCTACaa > 1:741747/1‑90 (MQ=255)
gCCGCATTATCTGCGTAAACTCTATTTATCGTAATCGTTCTTTATTTGGCCAGTTGTCACCCTGATACTTCGCTACAATGGATACCCGtt < 2:502245/90‑1 (MQ=255)
gCATTATCTGCGTAAACTCTATTTATCGTAATCGTTCTTTATTTGGCCAGTTGTCAACCTGATACTTCGCTACAATGGATACCCGTTAAt > 2:999844/1‑90 (MQ=255)
ttATCTGCGTAAACTCTATTTATCGTAATCGTTCTTTATTTGGCCAGTTGTCAACCTGATACTTCGCTACAATGGATACCCGTTAATCaa > 2:755301/1‑90 (MQ=255)
aTCTGCGTAAACTCTATTTATCGTAATCGTTCTTTATTTGGTCAGTTGTCAACCTGATCCTTGGCTAAAATGGATACCCGTTAATCAAag > 2:801987/1‑90 (MQ=255)
aTCTGCGTAAACTCTATTTATCGTAATCGTTCTTTATTTGGCCAGTTGTCAACCTGATACTTCGCTACAATGGATa < 1:674975/76‑1 (MQ=255)
aTCTGCGTAAACTCTATTTATCGTAATCGTTCTTTATTTGGCCAGTTGTCAACCTGATACTTCGCTACAATGGATa > 2:674975/1‑76 (MQ=255)
aTCTGCGTAAACTCTATTTATCGTAATCGTTCTTTATTTGGCCAGTTGTCAACCTGATACTTCGCTACAATGGATACCCGTTAATCAAag > 1:824552/1‑90 (MQ=255)
aTCTGCGTAAACTCTATTTATCGTAATCGTTCTTTATTTGGCCAGTTGTCAACCTGATACTTCGCTACAATGGATACCCGTTAATCAAag < 1:85229/90‑1 (MQ=255)
cTGCGTAAACTCTATTTATCGTAATCGTTCTTTATTTGGCCAGTTGTCAACCTGATACTTCGCTACAATGGATACCCGTTAATCAAagag > 2:962410/1‑90 (MQ=255)
tGCGTAAACTCTATTTATCGTAATCGTTCTTTATTTGGCCAGTTGTCAACCTGATACTTCGCTACAATGGATACCCGTTAATCAAAGAGt > 2:526127/1‑90 (MQ=255)
tGCGTAAACTCTATTTATCGTAATCGTTCTTTATTTGGCCAGTTGTCAACCTGATACTTCGCTACAATGGATACCCGTTAATCAAAGAGt < 2:950012/90‑1 (MQ=255)
gCGTAAACTCTATTTATCGTAATCGTTCTTTATTTGGCCAGTTGTCAACCTGATACTTCGCTACAATGGATACCCGTTAATCAAAGAGtt > 2:149436/1‑90 (MQ=255)
cGTAAACTCTATTTATCGTAATCGTTCTTTATTTGGCCAGTTGTCAACCTGATACTTCGCTACAATGGATACCCGTTAATCAAAGAGttt > 1:39028/1‑90 (MQ=255)
gTAAACTCTATTTATCGTAATCGTTCTTTATTTGGACAGTTGTCAACCTGATACTTCGCTACAATGGATACCCGTTAATCAAAGAGtttt > 2:107472/1‑90 (MQ=255)
ctctATTTATCGTAATCGTTCTTTATTTGGCCAGTTGTCAACCTGATACTTCGCTACAATGGATACCCGTTAATCAAAGAGTTTTCCAtt < 1:235039/90‑1 (MQ=255)
tctATTTATCGTAATCGTTCTTTATTTGGCCAGTTGTCAACCTGATACTTCGCTACAATGGATACCCGTTAATCAAAGAGTTTTCCATtg < 1:156736/90‑1 (MQ=255)
tATTTATCGTAATCGTTCTTTATTTGGCCAGTTGTCAACCTGATACTTCGCTACAATGGATACCCGtt < 2:922367/68‑1 (MQ=255)
tATTTATCGTAATCGTTCTTTATTTGGCCAGTTGTCAACCTGATACTTCGCTACAATGGATACCCGtt > 1:922367/1‑68 (MQ=255)
tATTTATCGTAATCGTTCTTTATTTGGCCAGTTGTCAACCTGATACTTCGCTACAATGGATACCCGTTAATCAAAGAGTTTTCCATtgtg > 1:486134/1‑90 (MQ=255)
ttATCGTAATCGTTCTTTATTTGGCCAGTTGTCAACCTGATACTTCGCTACAATGGATACCCGTTAATCAAAGAGTTTTCCATTGTGgcg < 1:749169/90‑1 (MQ=255)
aTCGTAATCGTTCTTTATTTGGCCAGTTGTCAACCTGATACTTCGCTACAATGGATACCCGTTAATCAAAGAGTTTTCCATTGTGTCGCt < 1:624871/90‑1 (MQ=255)
tCGTAATCGTTCTTTATTTGGCCAGTTGTCAACCTGATACTTCGCTACAATGGATACCCGTTAATCAAAGAGTTTTCCATTGTGGCGCTa > 2:675863/1‑90 (MQ=255)
cGTAATCGTTCTTTATTTGGCCAGTTGTCAACCTGATACTTCGCTACAATGGATACCCGTTa < 1:117074/62‑1 (MQ=255)
cGTAATCGTTCTTTATTTGGCCAGTTGTCAACCTGATACTTCGCTACAATGGATACCCGTTa > 2:117074/1‑62 (MQ=255)
cGTAATCGTTCTTTATTTGGCCAGTTGTCAACCTGATACTTCGCTACAATGGATACCCGTTAATCAAAGAGTTTTCCATTGTGGCGCTAc > 1:26883/1‑90 (MQ=255)
cGTAATCGTTCTTTATTTGGCCAGTTGTCAACCTGATACTTCGCTACAATGGATACCCGTTAATCAAAGAGTTTTCCATTGTGGCGCTAc < 2:741747/90‑1 (MQ=255)
tAATCGTTCTTTATTTGGCCGGTTGTCAACCTGATACTTCGCTACAATGGATACCCGTTAATCAAAGAGTTTTCCATTGTGGCGCTACtt > 1:399720/1‑90 (MQ=255)
tAATCGTTCTTTATTTGGCCAGTTGTCAACCTGATACTTCGCTACAATGGATACCCGTTAATCAAAGAGTTTTCCATTGTGGCGCTACtt > 2:386854/1‑90 (MQ=255)
tAATCGTTCTTTATTTGGCCAGTTGTCAACCTGATACTTCGCTACAATGGATACCCGTTAATCAAAGAGTTTTCCATTGTGGCGCTACtt > 2:730006/1‑90 (MQ=255)
tAATCGTTCTTTATTTGGCCAGTTGTCAACCTGATACTTCGCTACAATGGATACCCGTTAATCAAAGAGTTTTCCATTGTGGCGCTACtt > 2:784399/1‑90 (MQ=255)
cGTTCTTTATTTGGCCAGTTGTCAACCTGATACTTCGCTACAATGGATACCCGTTAATCAAAGAGTTTTCCATTGTGGCGCTACTTatca < 2:177521/90‑1 (MQ=255)
ttATTTGGCCAGTTGTCAACCTGATACTTCGCTACAATGGATACCCGTTAATCAAAGAGTTTTCCATTGTGGCGCTACTTATCATcacca > 2:63573/1‑90 (MQ=255)
ttGGCCAGTTGTCAACCTGATACTTCGCTACAATGGATACCCGTTAATCAAAGAGTTTTCCATTGTGGCGCTACTTATCATCACCACGAt < 2:486134/90‑1 (MQ=255)
ttGGCCAGTTGTCAACCTGATACTTCGCTACAATGGATACCCGTTAATCAAAGAGTTTTCCATTGTGGCGCTACTTATCATCACCACGAt > 2:219455/1‑90 (MQ=255)
tGGCCAGTTGTCAACCTGATACTTCGCTACAATGGATACCCGTTAATCAATGATTTTTCCATTGTGGCGCTACTTATCATCACCACGAtt > 2:153291/1‑90 (MQ=255)
|
GAGCTGGAAGTGATTGGTACTAATGCCGACGACGCGGTGCCGCATTATCTGCGTAAACTCTATTTATCGTAATCGTTCTTTATTTGGTCAGTTGTCAACCTGATACTTCGCTACAATGGATACCCGTTAATCAAAGAGTTTTCCATTGTGGCGCTACTTATCATCACCACGATT > NZ_CP009273/4004289‑4004462
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
BRESEQ :: bam2aln output
AATTAGAGGAAGAAAAAATGACAATATTGAATCACACCCTCGGTTTCCCTCGCGTTGGCCTGCGTCGCGAGCTGAAAAAAGCGCAAGAAAGTTATTGGGCGGGGAACTCCACGCGTGAAGAACTGCTGGCGGTAGGGCGTGAATTGCGTGCTCGTCACTGGGATCAACAAAAGCAAGCGGGTATCGACCTGCTGCCGGT > NZ_CP009273/4006396‑4006594
|
tcggagatgtgtataagagacagATATTGAATCACACCCTCGGTTTCCCTCGCGTTGGCCTGCGTCGCGAGCTGAAAAAAGCGCAAGAAAGTTATTGGGG < SRR3722213.1002645/77‑1 (MQ=60)
gctcggagatgtgtataagagacagCGGTTTCCCTCGCGTTGGCCTGCGTCGCGAGCTGAAAAAAGCGCAAGAAAGTTATTGGGGGGGCAACTCCACGCG < SRR3722213.813654/75‑1 (MQ=60)
ATGACAATATTGAATCACACCCTCGGTTTCCCTCGCGTTGGCCTGCGTCGCGAGCTGAAAAAAGCGCAAGAAAGTTATTGGGGGGGGAACTCCACGCGTG > SRR3722213.102459/1‑100 (MQ=60)
ATGACAATATTGAATCACACCCTCGGTTTCCCTCGCGTTGGCCTGCGTCGCGAGCTGAAAAAAGAGCAAGAAAGTTATTGGGGGGGGAACTCCACGCGTG < SRR3722213.676168/100‑1 (MQ=60)
ACAATATTGAATCACACCCTCGGTTTCCCTCGCGTTGGACTGCGTCGAGAGCTGAAAAAAGCGCAAGAAAGTTATTGGGGGGGGAACTCCACGCGTGAAG < SRR3722213.734190/100‑1 (MQ=60)
GTATTGAATCACACCCTCGGTTTCCCTCGCGTTGGCCTGCGTCGCGAGCTGAAAAAAGCGCAAGAAAGTTATTGGGGGGGGAACTCCACGCGTGAAGAAC > SRR3722213.632594/1‑100 (MQ=60)
ATATTGAATCACACCCTCGGTTTCCCTCGCGTTGGCCTGCGTCGCGAGCTGAAAAAAGCGCAAGAAAGTTATTGGGGGGGGAACTCCACGCGTGAAGAAC > SRR3722213.1043010/1‑100 (MQ=60)
GAATCACACCCTCGGTTTCCCTCGCGTTGGCCTGCGTCGCGAGCTGAAAAAAGCGCAAGAAAGTTATTGGGGGGGGAACTCCACGCGTGAAGAACTGCTG > SRR3722213.826200/1‑100 (MQ=60)
GAATCACACCCTCGGTTTCCCTCGCGTTGGCCTGCGTCGCGAGCTGAAAAAAGCGCAAGAAAGTTATTGGGGGGGGAACTCCACGCGTGAAGAACTGCTG > SRR3722213.11525/1‑100 (MQ=60)
GAATCACACCCTCGGTTTCCCTCGCGTTGGCCTGCGTCGCGAGCTGAAAAAAGCGCAAGAAAGTTATTGGGGGGGGAACTCCACGCGTGAAGAACTGCTG > SRR3722213.329417/1‑100 (MQ=60)
AATCACACCCTCGGTTTCCCTCGCGTTGGCCTGCGTCGCGAGCTGAAAAAAGCGCAAGAAAGTTATTGGGGGGGGAACTCCACGCGTGAAGAACTGCTGG < SRR3722213.886594/100‑1 (MQ=60)
ACACCCTCGGTTTCCCTCGCGTTGGCCTGCGTCGCGAGCTGAAAAAAGCGCAAGAAAGTTATTGGGGGGGGAACTCCACGCGTGAAGAACTGCTGGCGGT > SRR3722213.755933/1‑100 (MQ=60)
CCCTCGGTTTCCCTCGCGTTGGCCTGCGTCGCGAGCTGAAAAAAGCGCAAGAAAGTTATTGGGGGGGGAACTCCACGCGTGAAGAACTGCTGGCGGTAGG > SRR3722213.351561/1‑100 (MQ=60)
agcTTTCCCTCGCGTTGGCCTGCGTCGCGAGCTGAAAAAAGCGCAAGAAAGTTATTGGGGGGGGAACTCCACGCGTGAAGAACTGCTGGCGGTAGGGCGT < SRR3722213.168804/97‑1 (MQ=60)
CGGTTTCCCTCGCGTTGGCCTGCGTCGCGAGCTGAAAAAAGCGCAAGAAAGTTATTGGGGGGGGAACTCCACGCGTGAAGAACTGCTGGCGGGAGGGCGG > SRR3722213.116661/1‑100 (MQ=60)
agCCCTCGCGTTGGCCTGCGTCGCGAGCTGAAAAAAGCGCAAGAAAGTTATTGGGGGGGGAACTCCACGCGTGAAGAACTGCTGGCGGTAGGGCGTGAAT < SRR3722213.660439/98‑1 (MQ=60)
CCCTCGCGTTGGCCTGCGTCGCGAGCTGAAAAAAGCGCAAGAAAGTTATTGGGGGGGGAACTCCACGCGTGAAGAACTGCTGGCGGTAGGGCGGGAATTG > SRR3722213.268282/1‑100 (MQ=60)
CTCGCGTTGGCCTGCGTCGCGAGCTGAAAAAAGCGCAAGAAAGTTATTGGGGGGGGAACTCCACGCGTGAAGAACTGCTGGCGGTAGGGCGTGAATTGCG < SRR3722213.518441/100‑1 (MQ=60)
GCGTTGGCCTGCGTCGCGAGCTGAAAAAAGCGCAAGAAAGTTATTGGGGGGGGAACTCCACGCGTGAAGAACTGCTGGCGGTAGGGGGTGAATctgtctc > SRR3722213.567575/1‑93 (MQ=60)
CTGCGTCGCGAGCTGAAAAAAGCGCAAGAAAGTTATTGGGGGGGGAACTCCACGCGTGAAGAACTGCTGGCGGTAGGGCGTGAATTGCGTGCTCGTCACT > SRR3722213.1086453/1‑100 (MQ=60)
GCGTCGCGAGCTGAAAAAAGCGCAAGAAAGTTATTGGGGGGGGAACTCCACGCGTGAAGAACTGCTGGCGGTAGGTCGTGAATTGCGTGCTCGTCACTGG > SRR3722213.40065/1‑100 (MQ=60)
GTCGCGAGCTGAAAAAAGCGCAAGAAAGTTATTGGGGGGGGAACTCCACGCGTGAAGAACTGCTGGCGGTAGGGCGTGAATTGCGTGCTCGTCACTGGGA < SRR3722213.547514/100‑1 (MQ=60)
GAGCTGAAAAAAGCGCAAGAAAGTTATTGGGGGGGGAACTCCACGCGTGAAGAACTGCTGGCGGTAGGGCGTGAATTGCGTGCTCGTCACTGGGATCAAC < SRR3722213.265504/100‑1 (MQ=60)
GAGCTGAAAAAAGCGCAAGAAAGTTATTGGGGGGGGAACTCCACGCGTGAAGAACTGCTGGCGGTAGGGCGTGAATTGCGTGCTCGTCACTGGGATCAAC < SRR3722213.478055/100‑1 (MQ=60)
GAGCTGAAAAAAGCGCAAGAAAGTTATTGGGGGGGGAACTCCACGCGTGAAGAACTGCTGGCGGTAGGGCGTGAATTGCGTGCTCGTCACTGGGATCAAC < SRR3722213.1095877/100‑1 (MQ=60)
GCGCAAGAAAGTTATTGGGGGGGGAACTCCACGCGTGAAGAACTGCTGGCGGTAGGGCGTGAATTGCGTGCTCGTCACTGGGATCAACAAAAGCAAGCGG > SRR3722213.479587/1‑100 (MQ=60)
GCAAGAAAGTTATCGGGGGGGGACCTCCACGCGTGAAGAACTGCTGGCGGTAGGGCGTGAATTGCGTGCTCGTCACTGGGATCAACAAAAGCAAGCGGGT < SRR3722213.541506/100‑1 (MQ=60)
AGAAAGTTATTGGGGGGGGAACTCCACGCGTGAAGAACTGCTGGCGGTAGGGCGTGAATctgtctcttatacacatctccgagcccacgagacccgttat > SRR3722213.672267/1‑59 (MQ=60)
AAGTTATTGGGGGGGGAACTCCACGCGTGAAGAACTGCTGGCGGTAGGGCGTGAATTGCGTGCTCGTCACTGGGATCAACAAAAGCAAGCGGGTATCGAC < SRR3722213.73805/100‑1 (MQ=60)
GGGGGGGGAACTCCACGCGTGAAGAACTGCTGGCGGTAGGGCGTGAATTGCGTGCTCGTCACTGGGActgtctcttatacacatctccgagcccacgaga > SRR3722213.37643/1‑67 (MQ=60)
GGGGGGGGAACTCCACGCGTGAAGAACTGCTGGCGGTAGGGCGTGAATTGCGTGCTCGTCACTGGGATCAACAAAAGCAAGCGGGTATCtgtctcttata > SRR3722213.208773/1‑89 (MQ=60)
GGGGGAACTCCACGCGTGAAGAACTGCTGGCGGTAGGGCGTGAATTGCGTGCTCGTCACTGGGATCAACAAAAGCAAGCGGGTATCGACCTGCTGCCGGT < SRR3722213.874733/100‑1 (MQ=60)
|
AATTAGAGGAAGAAAAAATGACAATATTGAATCACACCCTCGGTTTCCCTCGCGTTGGCCTGCGTCGCGAGCTGAAAAAAGCGCAAGAAAGTTATTGGGCGGGGAACTCCACGCGTGAAGAACTGCTGGCGGTAGGGCGTGAATTGCGTGCTCGTCACTGGGATCAACAAAAGCAAGCGGGTATCGACCTGCTGCCGGT > NZ_CP009273/4006396‑4006594
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
