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 |
|
A14 F1 I1 R1
|
770 |
68.5 |
3470224 |
91.7% |
3182195 |
103.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
3,804,410 |
C→G |
R236P (CGT→CCT) |
waaS ← |
lipopolysaccharide rhamnose:KdoIII transferase, lipopolysaccharide core biosynthesis protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 3,804,410 | 0 | C | G | 85.7%
| 16.7
/ ‑2.0
| 7 | R236P (CGT→CCT) | waaS | lipopolysaccharide rhamnose:KdoIII transferase, lipopolysaccharide core biosynthesis protein |
| Reads supporting (aligned to +/- strand): ref base C (0/1); new base G (3/3); total (3/4) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.27e-01 |
TTATCCCAATCATCATGACCTATTATAAAAAAGCGAGATTCACTATAGATTTCTGAACCAAATACATTTATATTATTAGTAATTAATTTTTTATTGAAAAATAGTGCCTCAAGTATACGAAGAGTCCAGCCAGATTGGTTTTCTTTGGTTATATCAACAATTATATTAGCATTTAATGTTCTTCTAATATT > NC_000913/3804293‑3804483
|
ttATCCCAATCATCATGACCTATTATAAAAAAGCGAGATTCACTATAGATTTCTGAACCAGATACATTTATATTATTAGTAATTAATTTTTTATTGAAAAATAGTGCCTCAAGTATACGAAGAGTCCAGCCAGATTGGt < 2:1062648/139‑1 (MQ=255)
ttattaGTAATTAATTTTTTATTGAAAAATAGTGCCTCAAGTATAGGAAGAGTCCAGCCAGATTGGTTTTCTTTGGTTATATCAACAATTATATTAGCATTTAATGttctt > 1:1619549/1‑111 (MQ=255)
ttattaGTAATTAATTTTTTATTGAAAAATAGTGCCTCAAGTATAGGAAGAGTCCAGCCAGATTGGTTTTCTTTGGTTATATCAACAATTATATTAGCATTTAATGttctt < 2:1619549/111‑1 (MQ=255)
tttATTGAAAAATAGTGCCTCAAGTATAGGAAGAGTCCAGCCAGATTGGTTTTCTTTGGTTATATCAACAATTATATTAGCATTTAATGTTCTTCTAATAtt < 1:1631124/102‑1 (MQ=255)
tttATTGAAAAATAGTGCCTCAAGTATAGGAAGAGTCCAGCCAGATTGGTTTTCTTTGGTTATATCAACAATTATATTAGCATTTAATGTTCTTCTAATAtt > 2:1631124/1‑102 (MQ=255)
ccTCAAGTATAGGAAGAGTCCAGCCAGATTGGTTTTCTTTg > 1:232854/1‑41 (MQ=255)
ccTCAAGTATAGGAAGAGTCCAGCCAGATTGGTTTTCTTTg < 2:232854/41‑1 (MQ=255)
|
TTATCCCAATCATCATGACCTATTATAAAAAAGCGAGATTCACTATAGATTTCTGAACCAAATACATTTATATTATTAGTAATTAATTTTTTATTGAAAAATAGTGCCTCAAGTATACGAAGAGTCCAGCCAGATTGGTTTTCTTTGGTTATATCAACAATTATATTAGCATTTAATGTTCTTCTAATATT > NC_000913/3804293‑3804483
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
