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 |
|
A32 F90 I0 R1
|
1898 |
316.0 |
13750914 |
96.0% |
13200877 |
148.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
NC_002947 |
1,825,966 |
Δ1 bp |
100% |
coding (738/1422 nt) |
PP_1624 → |
group II intron‑encoding maturase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_002947 | 1,825,966 | 0 | G | . | 88.9%
| 27.7
/ ‑1.2
| 9 | coding (738/1422 nt) | PP_1624 | group II intron‑encoding maturase |
| Reads supporting (aligned to +/- strand): ref base G (1/0); new base . (6/2); total (7/2) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.73e-01 |
| Rejected as polymorphism: E-value score below prediction cutoff. |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
CGGGATCATGTCGGGCGGTGTCGTCAGCCCACGGCAGGAGGGGACGCCGCAAGGCGGCCCGCTCTCGCCGTTGCTGTCGAATATCCTGCTCGACGAACTCGACCGCGAGCTGGAGCGGCGGGGCCATCGCTTCGTACGTTATGCCGATGATGCGAACATCTATGTACGCAGTCCCCGGGCCGGCGAACGGGTG > NC_002947/1825906‑1826098
|
cGGGATCATGTCGGGCGGTGTCGTCAGCCCACGGCAGGAGGGGACGCCGCAAGGCGGCCCGCTTTCGCCGTtgctgtcgaatatcctgctcgacatgatcccggcttcaaggtagcggcgaataagcctgagtacgcacttatctttgac > 2:6761340‑M1/1‑71 (MQ=255)
aaggcggaggggacgCCGCAAGGCGGCCC‑CTCCTGCCGTgggctgacgacaccgcccgacatgatcccggcttcaaggtagcggcgaataagcctgagtacgcacttgtctttgatccgacgttcgatgcaggccatgaggatgtcgtga < 2:1899671‑M1/145‑112 (MQ=255)
gggACGCCGCAAGGCGGCCC‑CTCCTGCCGTgggctgacgacaccgcccgacatgatcccggcttcaaggtagcggcgaataagcctgagtacgcacttgtctttgatccgacgttcgatgcaggccatgaggatgtcgtgattgacccga > 2:4873168‑M1/1‑30 (MQ=255)
ggACGCCGCAAGGCGGCCC‑CTCCTGCCGTgggctgacgacaccgcccgacatgatcccggcttcaaggtagcggcgaataagcctgagtacgcacttgtctttgatccgacgttcgatgcaggccatgaggatgtcgtgattgacccgat > 1:3163552‑M1/1‑29 (MQ=255)
ggACGCCGCAAGGCGGCCC‑CTCCTGCCGTgggctgacgacaccgcccgacatgatcccggcttcaaggtagcggcgaataagcctgagtacgcacttgtctttgatccgacgttcgatgcaggccatgaggatgtcgtgattgacccgat > 1:4232015‑M1/1‑29 (MQ=255)
ggACGCCGCAAGGCGGCCC‑CTCCTGCCGTgggctgacgacaccgcccgacatgatcccggcttcaaggtagcggcgaataagcctgagtacgcacttgtctttgatccgacgttcgatgcaggccatgaggatgtcgtgattgacccgat > 1:811486‑M1/1‑29 (MQ=255)
gACGCCGCAAGGCGGCCC‑CTCCTGCCGTgggctgacgacaccgcccgacatgatcccggcttcaaggtagcggcgaataagcctgagtacgcacttgtctttgatccgacgttcgatgcaggccatgaggatgtcgtgattgacccgatc > 2:3477570‑M1/1‑28 (MQ=255)
gACGCCGCAAGGCGGCCC‑CTCCTGCCGTgggctgacgacaccgcccgacatgatcccggcttcaaggtagcggcgaataagcctgagtacgcacttgtctt > 1:1238954‑M1/1‑28 (MQ=255)
gACGCCGCAAGGCGGCCC‑CTCCTGCCGTgggctgacgacaccgcccgacatgatcccggcttcaaggtagcggcgaataagcctgagtacgcacttgtctt < 2:1238954‑M1/101‑74 (MQ=255)
|
CGGGATCATGTCGGGCGGTGTCGTCAGCCCACGGCAGGAGGGGACGCCGCAAGGCGGCCCGCTCTCGCCGTTGCTGTCGAATATCCTGCTCGACGAACTCGACCGCGAGCTGGAGCGGCGGGGCCATCGCTTCGTACGTTATGCCGATGATGCGAACATCTATGTACGCAGTCCCCGGGCCGGCGAACGGGTG > NC_002947/1825906‑1826098
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 11 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
