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 |
|
A36 F92 I0 R1
|
1778 |
260.6 |
11261716 |
96.7% |
10890079 |
148.3 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
NC_002947 |
1,825,970 |
2 bp→CT |
100% |
coding (742‑743/1422 nt) |
PP_1624 → |
group II intron‑encoding maturase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_002947 | 1,825,970 | 0 | T | C | 100.0%
| 11.3
/ NA
| 5 | S248M (TCG→CTG) | PP_1624 | group II intron‑encoding maturase |
| Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (5/0); total (5/0) |
| Rejected as polymorphism: Frequency below/above cutoff threshold. |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
| * | NC_002947 | 1,825,971 | 0 | C | T | 100.0%
| 10.8
/ NA
| 5 | S248M (TCG→CTG) | PP_1624 | group II intron‑encoding maturase |
| Reads supporting (aligned to +/- strand): ref base C (0/0); new base T (5/0); total (5/0) |
| Rejected as polymorphism: Frequency below/above cutoff threshold. |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
CACGGCAGGAGGGGACGCCGCAAGGCGGC‑‑CCGCTCTCGCCGTTGCTGTCGAATATCCTGCTCGACGAACTCGACCGCGAGCTGGAGCGGCGGGGCCATCGCTTCGTACGTTATGCCGATGATGCGAACATCTATGTACGCAGTCCCCGGGCCGGCGAACGGGTG > NC_002947/1825935‑1826098
||
cACGGCAGGAGGGGACGCCGCAAGGCGGCGTCCCCTCCTGCCGTgggctgacgacaccgcccgacatgatcccggcttcaaggtagcggcgaataagcctgagtacgcactggtctttgatccgacgttcgatgcaggccatgaggatgt > 2:696231‑M1/1‑44 (MQ=255)
gaggGGACGCCGCAAGGCGGC‑‑CC‑CTCCTGCCGTgggctgacgacaccgcccgacatgatcccggcttcaaggtagcggcgaataagcctgagtacgcacttgtctttgatccgacgttcgatgcaggccatgaggatgtcgtgattgacc > 2:4207089‑M1/1‑33 (MQ=255)
ggACGCCGCAAGGCGGC‑‑CC‑CTCCTGCCGTgggctgacgacaccgcccgacatgatcccggcttcaaggtagcggcgaataagcctgagtacgcacttgtctttgatccgacgttcgatgcaggccatgaggatgtcgtgattgacccgat > 2:2172876‑M1/1‑29 (MQ=255)
gACGCCGCAAGGCGGC‑‑CC‑CTCCTGCCGTgggctgacgacaccgcccgacatgatcccggcttcaaggtcgcggcgaataagcctgagtacgcacttgtctttgatccgacggtcgatgcaggccaggaggctgtcgggattgacccgagc > 2:4690301‑M1/1‑28 (MQ=255)
gACGCCGCAAGGCGGC‑‑CC‑CTCCTGCCGTgggctgacgacaccgcccgacatgatcccggcttcaaggtagcggcgaataagcctgagtacgcacttgtctttgatccgacgttcgatgcaggccatgaggatgtcgtgattgacccgatc > 2:2272792‑M1/1‑28 (MQ=255)
||
CACGGCAGGAGGGGACGCCGCAAGGCGGC‑‑CCGCTCTCGCCGTTGCTGTCGAATATCCTGCTCGACGAACTCGACCGCGAGCTGGAGCGGCGGGGCCATCGCTTCGTACGTTATGCCGATGATGCGAACATCTATGTACGCAGTCCCCGGGCCGGCGAACGGGTG > NC_002947/1825935‑1826098
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 11 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
