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 I228 R1
|
214 |
26.5 |
1448192 |
97.1% |
1406194 |
86.4 |
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 | 90.0%
| 18.9
/ ‑3.0
| 10 | 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 (6/3); total (7/3) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.37e-01 |
CCTGTAATTTTTAAAAAAAATCCGACTTTAGTTACAACATACTAATTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGAAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATGCTCGCCGTTT > NZ_CP009273/1335978‑1336130
|
ccTGTAATTTTTAAAAAAAATCCGACTTTAGTTACAACATACTAATTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGGAAAAg > 1:248520/1‑90 (MQ=255)
cTGTAATTTTTAAAAAAAATCCGACTTTAGTTACAACATACTAATTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGGAAAAGc < 2:481363/90‑1 (MQ=255)
ttaATGTTCCATTGTGCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTa > 2:207878/1‑90 (MQ=255)
taATGTTCCATTGTGCTCCGGCAACGACGGCGCAGGAAAAGCCCGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAg > 1:548067/1‑90 (MQ=255)
tCCATTGTGCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATGCt > 2:197958/1‑90 (MQ=255)
gtgCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATGCTCGCCGt < 2:248520/90‑1 (MQ=255)
gCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATGCTCGc < 1:125412/85‑1 (MQ=255)
gCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATGCTCGc > 2:125412/1‑85 (MQ=255)
gCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATGCTCGCCGttt > 2:136044/1‑90 (MQ=255)
gCTCCGGCAACGACGGCGCAGAAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATGCTCGCCGttt > 2:91406/1‑90 (MQ=255)
|
CCTGTAATTTTTAAAAAAAATCCGACTTTAGTTACAACATACTAATTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGAAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATGCTCGCCGTTT > NZ_CP009273/1335978‑1336130
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 19 ≤ 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
GTCTTGATGGCCTGTAATTTTTAAAAAAAATCCGACTTTAGTTACAACATACTAATTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGAAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATGCTCGCCGTTTACCTG > NZ_CP009273/1335968‑1336135
|
GTCTTGATGGCCTGTAATTTTTAAAAAAAATCCGACTTTAGTTACAACATACTAATTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGGAAAAG > SRR3722112.251459/1‑100 (MQ=60)
TACTAATTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGGAAAAGCCCGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAG > SRR3722112.556329/1‑100 (MQ=60)
ATTGTGCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATGCTCGCCGTTTACCTG < SRR3722112.126968/100‑1 (MQ=60)
|
GTCTTGATGGCCTGTAATTTTTAAAAAAAATCCGACTTTAGTTACAACATACTAATTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGAAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATGCTCGCCGTTTACCTG > NZ_CP009273/1335968‑1336135
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
