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
A2 F5 I179 R1 182 40.3 1547118 96.8% 1497610 120.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NZ_CP009273 1,036,585 A→G G171G (GGA→GGG)  appA → bifunctional acid phosphatase/4‑phytase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092731,036,5850AG100.0% 22.3 / NA 8G171G (GGA→GGG) appAbifunctional acid phosphatase/4‑phytase
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (5/3);  total (5/3)

CACCTGACTGTGCAATAACCGTACATACCCAGGCAGATACGTCCAGTCCCGATCCGTTATTTAATCCTCTAAAAACTGGCGTTTGCCAACTGGATAACGCGAACGTGACTGACGCGATCCTCAGCAGGGCAGGAGGGTCAATTGCTGACTTTACCGGGCATCGGCAAACGGCGTTTCGCGAACTGGAACGGGTGCTTAATTTTCCGCAATCAAACTTGTGCCTTAAACGTGAGAAACAGGACGAAAGCTGTTCATTAACGCAGGCA  >  NZ_CP009273/1036452‑1036717
                                                                                                                                     |                                                                                                                                    
cACCTGACTGTGCAATAACCGTACATACCCAGGCAGATACGTCCAGTCCCGATCCGTTATTTAATCCTCTAAAAACTGGCGTTTGCCAACTGGATAACGCGAACGTGACTGACGCGATCCTCAGCAGGGCAGGGGGGTc                                                                                                                                 <  2:267109/139‑1 (MQ=255)
      aCTGTGCAATAACCGTACATACCCAGGCAGATACGTCCAGTCCCGATCCGTTATTTAATCCTCTAAAAACTGGCGTTTGCCAACTGGATAACGCGAACGTGACTGACGCGATCCTCAGCAGGGCAGGGGGGTCAATTGc                                                                                                                           <  2:731789/139‑1 (MQ=255)
                                          ccAGTCCCGATCCGTTATTTAATCCTCTAAAAACTGGCGTTTGCCAACTGGATAACGCGAACGTGACTGACGCGATCCTCAGCAGGGCAGGGGGGTCAATTGCTGACTTTACCGGGCATCGGCAAACGGCGTTTcgcg                                                                                        >  2:695146/1‑138 (MQ=255)
                                           cAGTCCCGATCCGTTATTTAATCCTCTAAAAACTGGCGTTTGCCAACTGGATAACGCGAACGTGACTGACGCGATCCTCAGCAGGGCAGGGGGGTCAATTGCTGACTTTACCGGGCATCGGCAAACGGCGTTTCGCGa                                                                                       <  1:114322/138‑1 (MQ=255)
                                                                                                                    aTCCTCAGCAGGGCAGGGGGGTCAATTGCTGACTTTACCGGGCATCGGCAAACGGCGTTTCGCGAACTGGAACGGGTGCTTAATTTTCCGCAATCAAACTTGTGCCTTAAACGTGAGAAACAGGACGAAAGCTGTTCAt             >  2:769030/1‑139 (MQ=255)
                                                                                                                               ggcaggGGGGTCAATTGCTGACTTTACCGGGCATCGGCAAACGGCGTTTCGCGAACTGGAACGGGTGCTTAATTTTCCGCAATCAAACTTGTGCCTTAAACGTGAGAAACAGGACGAAAGCTGTTCATTAACGCAGGCa  >  1:508157/1‑139 (MQ=255)
                                                                                                                               ggcaggGGGGTCAATTGCTGACTTTACCGGGCATCGGCAAACGGCGTTTCGCGAACTGGAACGGGTGCTTAATTTTCCGCAATCAAACTTGTGCCTTAAACGTGAGAAACAGGACGAAAGCTGTTCATTAACGCAGGCa  >  1:629443/1‑139 (MQ=255)
                                                                                                                               ggcaggGGGGTCAATTGCTGACTTTACCGGGCATCGGCAAACGGCGTTTCGCGAACTGGAACGGGTGCTTAATTTTCCGCAATCAAACTTGTGCCTTAAACGTGAGAAACAGGACGAAAGCTGTTCATTAACGCAGGCa  >  2:673249/1‑139 (MQ=255)
                                                                                                                                     |                                                                                                                                    
CACCTGACTGTGCAATAACCGTACATACCCAGGCAGATACGTCCAGTCCCGATCCGTTATTTAATCCTCTAAAAACTGGCGTTTGCCAACTGGATAACGCGAACGTGACTGACGCGATCCTCAGCAGGGCAGGAGGGTCAATTGCTGACTTTACCGGGCATCGGCAAACGGCGTTTCGCGAACTGGAACGGGTGCTTAATTTTCCGCAATCAAACTTGTGCCTTAAACGTGAGAAACAGGACGAAAGCTGTTCATTAACGCAGGCA  >  NZ_CP009273/1036452‑1036717

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

BRESEQ :: bam2aln output
CTTCGCCGCCGGGCTGGCACCTGACTGTGCAATAACCGTACATACCCAGGCAGATACGTCCAGTCCCGATCCGTTATTTAATCCTCTAAAAACTGGCGTTTGCCAACTGGATAACGCGAACGTGACTGACGCGATCCTCAGCAGGGCAGGAGGGTCAATTGCTGACTTTACCGGGCATCGGCAAACGGCGTTTCGCGAACTGGAACGGGTGCTTAATTTTCCGCAATCAAACTTGTGCCTTAAACGTGAGAAACAGGACGAAAGCTGTTCATTAACGCAGGCATTACCATCGG  >  NZ_CP009273/1036435‑1036727
                                                                                                                                                      |                                                                                                                                              
CTTCGCCGCCGGGCTGGCACCTGACTGTGCAATAACCGTACATACCCAGGCAGATACGTCCAGTCCCGATCCGTTATTTAATCCTCTAAAAACTGGCGTTTGCCAACTGGATAACGCGAACGTGACTGACGCGATCCTCAGCAGGGCAGGG                                                                                                                                                >  SRR3722133.270742/1‑151 (MQ=60)
                                                           CCAGTCCCGATCCGTTATTTAATCCTCTAAAAACTGGCGTTTGCCAACTGGATAACGCGAACGTGACTGACGCGATCCTCAGCAGGGCAGGGGGGTCAATTGCTGACTTTACCGGGCATCGGCAAACGGCGTTTCGCGAACTGGAACGGG                                                                                      <  SRR3722133.115849/150‑1 (MQ=60)
                                                                                                                                     ATCCTCAGCAGGGCAGGGGGGTCAATTGCTGACTTTACCGGGCATCGGCAAACGGCGTTTCGCGAACTGGAACGGGTGCTTAATTTTCCGCAATCAAACTTGTGCCTTAAACGTGAGAAACAGGACGAAAGCTGTTCATTAACGCAGGCAT           >  SRR3722133.514999/1‑151 (MQ=60)
                                                                                                                                     ATCCTCAGCAGGGCAGGGGGGTCAATTGCTGACTTTACCGGGCATCGGCAAACGGCGTTTCGCGAACTGGAACGGGTGCTTAATTTTCCGCAATCAAACTTGTGCCTTAAACGTGAGAAACAGGACGAAAGCTGTTCATTAACGCAGGCAT           >  SRR3722133.637670/1‑151 (MQ=60)
                                                                                                                                          CAGCAGGGCAGGGGGGTCAATTGCTGACTTTACCGGGCATCGGCAAACGGCGTTTCGCGAACTGGAACGGGTGCTTAATTTTCCGCAATCAAACTTGTGCCTTAAACGTGAGAAACAGGACGAAAGCTGTTCATTAACGCAGGCATTACC       >  SRR3722133.654617/1‑150 (MQ=60)
                                                                                                                                               GGGCAGGGGGGTCAATTGCTGACTTTACCGGGCATCGGCAAACGGCGTTTCGCGAACTGGAACGGGTGCTTAATTTTCCGCAATCAAACTTGTGCCTTAAACGTGAGAAACAGGACGAAAGCTGTTCATTAACGCAGGCATTACCATCGG  >  SRR3722133.280741/1‑150 (MQ=60)
                                                                                                                                                      |                                                                                                                                              
CTTCGCCGCCGGGCTGGCACCTGACTGTGCAATAACCGTACATACCCAGGCAGATACGTCCAGTCCCGATCCGTTATTTAATCCTCTAAAAACTGGCGTTTGCCAACTGGATAACGCGAACGTGACTGACGCGATCCTCAGCAGGGCAGGAGGGTCAATTGCTGACTTTACCGGGCATCGGCAAACGGCGTTTCGCGAACTGGAACGGGTGCTTAATTTTCCGCAATCAAACTTGTGCCTTAAACGTGAGAAACAGGACGAAAGCTGTTCATTAACGCAGGCATTACCATCGG  >  NZ_CP009273/1036435‑1036727

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑