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 I171 R2 5 16.1 989330 95.6% 945799 85.1

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
MC JC NZ_CP009273 2,399,465 Δ7 bp coding (650‑656/939 nt) lrhA ← transcriptional regulator LrhA

Missing coverage evidence...
   seq id start end size ←reads reads→ gene description
* * ÷ NZ_CP009273 2399465 2399471 7 13 [0] [0] 13 lrhA transcriptional regulator LrhA

New junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NZ_CP009273 = 23994640 (0.000)13 (0.760) 8/168 0.6 100% coding (657/939 nt) lrhA transcriptional regulator LrhA
?NZ_CP009273 2399472 = 0 (0.000)coding (649/939 nt) lrhA transcriptional regulator LrhA

GATK/CNVnator alignment

BRESEQ :: bam2aln output
GGTCCGGGCTCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGGCGACATAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCATCCAGCAATACAAGAG  >  NZ_CP009273/2399382‑2399558
                                                                                   |                                                                                             
GGTCCGGGCTCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAG‑‑‑‑‑‑‑AAGCCAGTCGCCATGGA                                                                        >  SRR3722043.356089/1‑100 (MQ=60)
                                                    CACTGCCGCACGAACGGCCGGAAGCGTCGAG‑‑‑‑‑‑‑AAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGAT                    <  SRR3722043.23605/100‑1 (MQ=60)
                                                    CACTGCCGCACGAACGGCCGGAAGCGTCGAG‑‑‑‑‑‑‑AAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGAT                    <  SRR3722043.404529/100‑1 (MQ=60)
                                                                    GCCGGAAGCGTCGAG‑‑‑‑‑‑‑AAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCATCCAGCAATACAAG    >  SRR3722043.500174/1‑100 (MQ=60)
                                                                      CGGAAGCGTCGAG‑‑‑‑‑‑‑AAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCATCCAGCAATACAAGAG  <  SRR3722043.102084/100‑1 (MQ=60)
                                                                                   |                                                                                             
GGTCCGGGCTCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGGCGACATAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGATCATCCAGCAATACAAGAG  >  NZ_CP009273/2399382‑2399558

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑