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 F1 I2 R1
|
1624 |
250.6 |
12620048 |
98.0% |
12367647 |
93.0 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
NC_000913 |
1,096,622 |
(G)7→8 |
intergenic (+570/+166) |
ycdU → / ← serX |
hypothetical protein/tRNA‑Ser |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 1,096,615 | 1 | . | G | 92.3%
| 23.0
/ ‑4.5
| 13 | intergenic (+563/+173) | ycdU/serX | hypothetical protein/tRNA‑Ser |
| Reads supporting (aligned to +/- strand): ref base . (0/0); major base G (3/9); minor base T (1/0); total (4/9) |
| Fisher's exact test for biased strand distribution p-value = 3.08e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
TTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑GGGGGGGATTGACTCGCTTCG > NC_000913/1096536‑1096636
|
ttCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGATTGa < 1:2628199/93‑1 (MQ=0)
ctcATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGATTGACt < 1:3512996/93‑1 (MQ=12)
ctcATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGCACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGATTGACt < 1:5257119/93‑1 (MQ=255)
tcATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGATTGACtc < 2:534658/93‑1 (MQ=16)
tcATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGCACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGATGGGGGGGATTGACtc > 1:2031840/1‑93 (MQ=255)
tcATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGCACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGATTGACtc > 2:1060798/1‑93 (MQ=255)
tcATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGCACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGATTGACtc > 2:5953516/1‑93 (MQ=255)
cATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGATTGACtcg < 1:5797494/93‑1 (MQ=16)
aTCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGCACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGATTGACtcgc > 1:3304444/1‑93 (MQ=255)
tCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGGTTGACtcgct > 2:4065382/1‑93 (MQ=255)
tCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGCACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGATTGACtcgct < 2:5154619/93‑1 (MQ=255)
ccccccGGTGTGTGCAATATACGAAAAAAAAGCCCGCACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGATTGACtcgctt < 1:226022/93‑1 (MQ=255)
ccccccGGTGTGTGCAATATACGAAAAAAAAGCCCGCACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGATTGACtcgctt < 1:3334761/93‑1 (MQ=255)
cccccGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGATTGACtcgcttc > 1:310016/1‑93 (MQ=12)
cccccGGGGTGTGCAATATACGAAAAAAAACCCCGTCCTTTCGTACGACCTCTTCTTTAAATATGGCGGTGAGGGGGGGGATTGACtcgcttc < 1:1845208/93‑1 (MQ=11)
ccccGGTGTGTGCAATATACGAAAAAAAAGCCCGCACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGGATTGACtcgcttcg > 2:1345872/1‑93 (MQ=255)
|
TTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑GGGGGGGATTGACTCGCTTCG > NC_000913/1096536‑1096636
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
