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 I179 R2 4 15.4 992998 94.0% 933418 83.4

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 21 [0] [0] 22 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)21 (1.280) 17/164 0.1 100% 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
CGCAGGTCCGGGCTCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGGCGACATAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGAT  >  NZ_CP009273/2399378‑2399540
                                                                                       |                                                                           
CGCAGGTCCGGGCTCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAG‑‑‑‑‑‑‑AAGCCAGTCGCCA                                                          >  SRR3722052.395233/1‑100 (MQ=60)
 GCAGGTCCGGGCTCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAG‑‑‑‑‑‑‑AAGCCAGTCGCCAT                                                         <  SRR3722052.356178/100‑1 (MQ=60)
    GGTCCGGGCTCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAG‑‑‑‑‑‑‑AAGCCAGTCGCCATGGA                                                      >  SRR3722052.64847/1‑100 (MQ=60)
     GTCCGGGCTCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAG‑‑‑‑‑‑‑AAGCCAGTCGCCATGGAA                                                     >  SRR3722052.219011/1‑100 (MQ=60)
                  ATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAG‑‑‑‑‑‑‑AAGCCAGTCGCCATGGAATATCTGCTTTATT                                        >  SRR3722052.177860/1‑100 (MQ=60)
                                              GACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAG‑‑‑‑‑‑‑AAGCCAGTCGCCATGGAATATCTGCTgtctcttatacacatctccgagcccacgagaca            >  SRR3722052.213231/1‑67 (MQ=60)
                                                  GGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAG‑‑‑‑‑‑‑AAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGC        >  SRR3722052.409765/1‑100 (MQ=60)
                                                        acagGCCGCACGAACGGCCGGAAGCGTCGAG‑‑‑‑‑‑‑AAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGAT  <  SRR3722052.105690/96‑1 (MQ=60)
                                                        CACTGCCGCACGAACGGCCGGAAGCGTCGAG‑‑‑‑‑‑‑AAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGAT  <  SRR3722052.151775/100‑1 (MQ=60)
                                                        CACTGCCGCACGAACGGCCGGAAGCGTCGAG‑‑‑‑‑‑‑AAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGAT  <  SRR3722052.1873/100‑1 (MQ=60)
                                                                                       |                                                                           
CGCAGGTCCGGGCTCATCATCTCAACCGGCCTTGCCGTCACGCCAAGACCGGCTTTCACTGCCGCACGAACGGCCGGAAGCGTCGAGGCGACATAAGCCAGTCGCCATGGAATATCTGCTTTATTAAGCGTCGCCAGCACCATATCGCGAAACGGGCTAGGAT  >  NZ_CP009273/2399378‑2399540

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑