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 I227 R1
|
223 |
21.3 |
1167702 |
97.0% |
1132670 |
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 | 84.6%
| 23.2
/ 0.5
| 13 | intergenic (+78/‑116) | lapB/pyrF | lipopolysaccharide assembly protein LapB/orotidine‑5'‑phosphate decarboxylase |
| Reads supporting (aligned to +/- strand): ref base A (1/1); new base G (8/3); total (9/4) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.72e-01 |
CCTGTAATTTTTAAAAAAAATCCGACTTTAGTTACAACATACTAATTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGAAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATGCTCGCCGTTTACCTGT > NZ_CP009273/1335978‑1336136
|
ccTGTAATTTTTAAAAAAAATCCGACTTTAGTTACAACATACTAATTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGGAAAAg > 2:266940/1‑90 (MQ=255)
tGTAATTTTTAAAAAAAATCCGACTTTAGTTACAACATACTAATTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGGAAAAGcc > 1:317351/1‑90 (MQ=255)
tttttAAAAAAAATCCGACTTTAGTTACAACATACTAATTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCa < 1:239861/90‑1 (MQ=255)
tACTAATTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTAttt > 2:187997/1‑90 (MQ=255)
aaTTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCAc < 2:284866/90‑1 (MQ=255)
tattaATGTTCCATTGTGCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACggg > 1:87358/1‑90 (MQ=255)
ttaATGTTCCATTGTGCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTa > 2:431335/1‑90 (MQ=255)
tCCATTGTGCTCCGGCAACGACGGCGCAGAAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATGCt > 2:378579/1‑90 (MQ=255)
aTTGTGCTCCGGCAACGACGGCGCAGAAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATGCTCGc < 1:378579/90‑1 (MQ=255)
gtgCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATGCTCGCCGt > 1:464586/1‑90 (MQ=255)
ccGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATGCTCGCCGTTTAcc > 1:325374/1‑90 (MQ=255)
ccGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATGCTCGCCGTTTAcc > 1:568364/1‑90 (MQ=255)
gCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATGCTCGCCGTTTACCTGt < 2:9236/90‑1 (MQ=255)
|
CCTGTAATTTTTAAAAAAAATCCGACTTTAGTTACAACATACTAATTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGAAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATGCTCGCCGTTTACCTGT > NZ_CP009273/1335978‑1336136
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 34 ≤ 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 < SRR3722111.287260/100‑1 (MQ=60)
CTTGATGGCCTGTAATTTTTAAAAAAAATCCGACTTTAGTTACAACATACTAATTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGGAAAAGCC > SRR3722111.321540/1‑100 (MQ=60)
TTTTTAAAAAAAATCCGACTTTAGTTACAACATACTAATTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAAT < SRR3722111.242715/100‑1 (MQ=60)
ACATACTAATTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGG > SRR3722111.88430/1‑100 (MQ=60)
ATGTTCCATTGTGCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATGCTCGCCGT > SRR3722111.471663/1‑100 (MQ=60)
CCATTGTGCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATGCTCGCCGTTTACC > SRR3722111.329715/1‑100 (MQ=60)
CCATTGTGCTCCGGCAACGACGGCGCAGGAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATGCTCGCCGTTTACC > SRR3722111.577304/1‑100 (MQ=60)
ATTGTGCTCCGGCAACGACGGCGCAGAAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATGCTCGCCGTTTACCTG < SRR3722111.383998/100‑1 (MQ=60)
|
GCGGTCTTGATGGCCTGTAATTTTTAAAAAAAATCCGACTTTAGTTACAACATACTAATTATTAATGTTCCATTGTGCTCCGGCAACGACGGCGCAGAAAAAGCCTGCCAGGGGAGAAATCGCAACTGTTAATTTTTTATTTCCACGGGTAGAATGCTCGCCGTTTACCTG > NZ_CP009273/1335965‑1336135
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
