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 I1 R1 152 24.9 2083062 91.6% 1908084 109.2

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA AM260479 1,191,771 Δ1 bp coding (5/390 nt) h16_A1095 ← Hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*AM2604791,191,7690C.100.0% 15.9 / NA 5coding (7/390 nt)h16_A1095Hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base . (3/2);  total (3/2)

GCGTCGCGCGGCCTGCGCCGCCTGCAGGCGCGCGGCTTCTTCCTGCACCGCCATGGCCAGCGTTGGCGGCGCGGCGAAGGGCAGGACCGCCGCGCCGGCCCGCTGGCGATCCTCCTCCTGTTGTGCCCGCACGTGCGGCCGCGTGCACCGACTCTGCCAGCGCAGCGGACGGCGCGTAAGCGGGCAGCTCCCGCAGCAGCGCCGAAAGCCGGTCCTTGCCGTCGATAAAGCGGTCGGCCGCGTTCA  >  AM260479/1191644‑1191889
                                                                                                                             |                                                                                                                        
gcgtcgcgCGGCCTGCGCCGCCTGCAGGCGCGCGGCTTCTTCCTGCACCGCCATGGCCAGCGTTGGCGGCGCGGCGAAGGGCAGGACCGCCGCGCCGGCCCGCTGGCGATCCTCCTCCTGTTGTG‑CCGCACGt                                                                                                                  <  2:354703/133‑1 (MQ=255)
                                                                                             gccgGCCCGCTGGCGATCCTCCTCCTGTTGTG‑CCGCACGTGCGGCCGCGTGCACCGACTCTGCCAGCGCAGCGGACGGCGCGTAAGCGGGCAGCTCCCGCAGCAGCGCCGAAAGCCGGTCCTTGCCGTCGATa                     >  2:432118/1‑133 (MQ=255)
                                                                                             gccgGCCCGCTGGCGATCCTCCTCCTGTTGTG‑CCGCACGTGCGGCCGCGTGCACCGACTCTGCCAGCGCAGCGGACGGCGCGTAAGCGGGCAGCTCCCGCAGCAGCGCCGAAAGCCGGTCCTTGCCGTCGATa                     >  2:706962/1‑133 (MQ=255)
                                                                                                               ctcctcctGTTGTG‑CCGCACGTGCGGCCGCGTGCACCGACTCTGCCAGCGCAGCGGACGGCGCGTAAGCGGGCAGCTCCCGCAGCAGCGCCGAAAGCCGGTCCTTGCCGTCGATAAAGCGGTCGGCCGCGTTCa  <  2:34020/134‑1 (MQ=255)
                                                                                                                       gttgtG‑CCGCACGTGCGGCCGCGTGCACCGACTCTGCCAGCGCAGCGGACGGCGCGTAAGCGGGCAGCTCCCGCAGCAGCGCCGAAAGCCGGTCCTTGCCGTCGATAAAGCGGTCgg           >  2:379480/1‑117 (MQ=255)
                                                                                                                             |                                                                                                                        
GCGTCGCGCGGCCTGCGCCGCCTGCAGGCGCGCGGCTTCTTCCTGCACCGCCATGGCCAGCGTTGGCGGCGCGGCGAAGGGCAGGACCGCCGCGCCGGCCCGCTGGCGATCCTCCTCCTGTTGTGCCCGCACGTGCGGCCGCGTGCACCGACTCTGCCAGCGCAGCGGACGGCGCGTAAGCGGGCAGCTCCCGCAGCAGCGCCGAAAGCCGGTCCTTGCCGTCGATAAAGCGGTCGGCCGCGTTCA  >  AM260479/1191644‑1191889

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A