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 I199 R1
|
220 |
57.5 |
3163680 |
97.0% |
3068769 |
86.1 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NZ_CP009273 |
1,336,062 |
A→G |
intergenic (+78/‑116) |
lapB → / → pyrF |
lipopolysaccharide assembly protein LapB/orotidine‑5'‑phosphate decarboxylase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NZ_CP009273 | 1,336,062 | 0 | A | G | 96.3%
| 79.9
/ ‑3.5
| 27 | intergenic (+78/‑116) | lapB/pyrF | lipopolysaccharide assembly protein LapB/orotidine‑5'‑phosphate decarboxylase |
| Reads supporting (aligned to +/- strand): ref base A (1/0); new base G (17/9); total (18/9) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.89e-01 |
CCTGTAATTTTTAAAAAAAATCCGACTTTAGTTACAACATACTAATTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGAAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATGCTCGCCGTTTACCTG > NZ_CP009273/1335978‑1336135
|
ccTGTAATTTTTAAAAAAAATCCGACTTTAGTTACAACATACTAATTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGGAAAAg > 2:1561105/1‑90 (MQ=255)
ccTGTAATTTTTAAAAAAAATCCGACTTTAGTTACAACATACTAATTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGGAAAAg > 2:1168189/1‑90 (MQ=255)
cTGTAATTTTTAAAAAAAATCCGACTTTAGTTACAACATACTAATTATTAATGTTCCACTGTGCTCCGGCAACGACGGCGCAGGAAAAGc < 1:1467663/90‑1 (MQ=255)
gTAATTTTTAAAAAAAATCCGACTTTAGTTACAACATACTAATTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGGAAAAGCCt < 2:939310/90‑1 (MQ=255)
aTACTAATTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTAtt > 1:1567627/1‑90 (MQ=255)
tACTAATTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTAttt > 1:1359747/1‑90 (MQ=255)
tACTAATTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTAttt > 2:443640/1‑90 (MQ=255)
tACTAATTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTAttt > 2:1516962/1‑90 (MQ=255)
tACTAATTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTAttt > 1:873595/1‑90 (MQ=255)
tACTAATTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTAttt > 1:1553800/1‑90 (MQ=255)
tACTAATTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTAttt > 1:259909/1‑90 (MQ=255)
tACTAATTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGAAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTAttt > 1:55912/1‑90 (MQ=255)
aaTTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGGAAAGGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCAc > 1:1109966/1‑90 (MQ=255)
aaTTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCAc > 2:801043/1‑90 (MQ=255)
attattAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACg < 2:1120193/90‑1 (MQ=255)
attattAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACg < 2:1567627/90‑1 (MQ=255)
aaTGTTCCATTGTGCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGa < 2:470795/90‑1 (MQ=255)
gTTCCATTGTGCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATg > 2:1185986/1‑90 (MQ=255)
gTTCCATTGTGCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATg > 2:683561/1‑90 (MQ=255)
tCCATTGTGCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATGCt > 1:359958/1‑90 (MQ=255)
ccATTGTGCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATGCTc < 1:1570716/90‑1 (MQ=255)
aTTGTGCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATGCTCGc < 1:443640/90‑1 (MQ=255)
aTTGCGCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATGCTCGc < 1:1510284/90‑1 (MQ=255)
gCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTGGAATGCTCGCCGttt > 1:594619/1‑90 (MQ=255)
ccGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATGCTCGCCGTTTAcc < 2:259909/90‑1 (MQ=255)
ccGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATGCTCGCCGTTTAcc > 2:61674/1‑90 (MQ=255)
ggCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATGCTCGCCGTTTACCTg > 2:1136393/1‑90 (MQ=255)
|
CCTGTAATTTTTAAAAAAAATCCGACTTTAGTTACAACATACTAATTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGAAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATGCTCGCCGTTTACCTG > NZ_CP009273/1335978‑1336135
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ 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
GCGGTCTTGATGGCCTGTAATTTTTAAAAAAAATCCGACTTTAGTTACAACATACTAATTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGAAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATGCTCGCCGTTTACCTG > NZ_CP009273/1335965‑1336135
|
GCGGTCTTGATGGCCTGTAATTTTTAAAAAAAATCCGACTTTAGTTACAACATACTAATTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGGAA < SRR3722078.495920/100‑1 (MQ=60)
CTGTAATTTTTAAAAAAAATCCGACTTTAGTTACAACATACTAATTATTAATGTTCCACTGTGCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGG < SRR3722078.1491604/100‑1 (MQ=60)
TAGTTACAACATACTAATTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATT > SRR3722078.1593142/1‑100 (MQ=60)
AGTTACAACATACTAATTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTT > SRR3722078.1381593/1‑100 (MQ=60)
AGTTACAACATACTAATTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTT > SRR3722078.1579102/1‑100 (MQ=60)
AGTTACAACATACTAATTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTT > SRR3722078.263087/1‑100 (MQ=60)
AGTTACAACATACTAATTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTT > SRR3722078.885314/1‑100 (MQ=60)
AGTTACAACATACTAATTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGAAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTT > SRR3722078.56573/1‑100 (MQ=60)
ACAACATACTAATTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGGAAAGGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCAC > SRR3722078.1126903/1‑100 (MQ=60)
TTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATGCT > SRR3722078.364342/1‑100 (MQ=60)
GTTCCATTGTGCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTGGAATGCTCGCCGTTT > SRR3722078.601517/1‑100 (MQ=60)
CCATTGTGCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATGCTCGCCGTTTACC < SRR3722078.1596273/100‑1 (MQ=60)
ATTGTGCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATGCTCGCCGTTTACCTG < SRR3722078.448956/100‑1 (MQ=60)
ATTGCGCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATGCTCGCCGTTTACCTG < SRR3722078.1534918/100‑1 (MQ=60)
|
GCGGTCTTGATGGCCTGTAATTTTTAAAAAAAATCCGACTTTAGTTACAACATACTAATTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGAAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATGCTCGCCGTTTACCTG > NZ_CP009273/1335965‑1336135
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
