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
A6 F80 I0 R1 1105 125.4 6144758 94.6% 5812941 133.2

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_002947 1,821,017 Δ1 bp 100% coding (738/1422 nt) PP_1624 → group II intron‑encoding maturase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029471,821,0170G.100.0% 12.0 / NA 4coding (738/1422 nt)PP_1624group II intron‑encoding maturase
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base . (2/2);  total (2/2)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

GGGGACGCCGCAAGGCGGCCCGCTCTCGCCGTTGCTGTCGAATATCCTGCTCGACGAACTCGACCGCGAGCTGGAGCGGCGGGGCCATCGCTTCGTACGTTATGCCGATGATGCGAACATCTATGTACGCAGTCCCCGG  >  NC_002947/1820996‑1821134
                     |                                                                                                                     
ggggACGCCGCAAGGCGGCCC‑CTCCTGCCGTgggctgacgacaccgcccgacatgatcccggcttcaaggtagcggcgaataagcctgagtacgcacttgtctttgatccgacgttcgatgca                 <  1:2197093‑M1/123‑93 (MQ=255)
ggggACGCCGCAAGGCGGCCC‑CTCCTGCCGTgggctgacgacaccgcccgacatgatcccggcttcaaggtagcggcgaataagcctgagtacgcacttgtctttgatccgacgttcgatgca                 >  2:2197093‑M1/1‑31 (MQ=255)
   gACGCCGCAAGGCGGCCC‑CTCCTGCCGTgggctgacgacaccgcccgacatgatcccggcttcaaggtagcggcgaataagcctgagtacgcacttgtctttgatccgacgttcgatgcaggccatgaggatgtc  <  1:211019‑M1/135‑108 (MQ=255)
   gACGCCGCAAGGCGGCCC‑CTCCTGCCGTgggctgacgacaccgcccgacatgatcccggcttcaaggtagcggcgaataagcctgagtacgcacttgtctttgatccgacgttcgatgcaggccatgaggatgtc  >  2:211019‑M1/1‑28 (MQ=255)
                     |                                                                                                                     
GGGGACGCCGCAAGGCGGCCCGCTCTCGCCGTTGCTGTCGAATATCCTGCTCGACGAACTCGACCGCGAGCTGGAGCGGCGGGGCCATCGCTTCGTACGTTATGCCGATGATGCGAACATCTATGTACGCAGTCCCCGG  >  NC_002947/1820996‑1821134

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A