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 I176 R1 180 42.9 1710034 96.5% 1650182 119.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NZ_CP009273 1,069,819 T→G L41R (CTG→CGG)  rutR → HTH‑type transcriptional regulator RutR

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092731,069,8190TG100.0% 119.2 / NA 33L41R (CTG→CGG) rutRHTH‑type transcriptional regulator RutR
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base G (15/18);  total (15/18)

GGGGAGAGCGCATGACGCAAGGCGCAGTGAAAACAACGGGTAAACGTTCGCGCGCAGTAAGCGCGAAGAAAAAAGCGATTCTTAGCGCAGCACTGGACACTTTTTCACAATTCGGTTTTCACGGCACAAGGCTGGAGCAGATCGCAGAGTTGGCGGGTGTTTCAAAAACCAATCTGCTGTATTACTTTCCGTCAAAAGAGGCGCTGTATATTGCCGTGCTGCGGCAGATTCTCGATAT  >  NZ_CP009273/1069687‑1069924
                                                                                                                                    |                                                                                                         
ggggAGAGCGCATGACGCAAGGCGCAGTGAAAACAACGGGTAAACGTTCGCGCGCAGTAAGCGCGAAGAAAAAAGCGATTCTTAGCGCAGCACTGGACACTTTTTCACAATTCGGTTTTCACGGCACAAGGCGGGAGCa                                                                                                     <  1:504648/139‑1 (MQ=255)
 gggAGAGCGCATGACGCAAGGCGCAGTGAAAACAACGGGCAAACGTTCGCGCGCAGTAAGCGCGAAGAAAAAAGCGATTCTTAGCGCAGCACTGGACACTTTTTCACAATTCGGTTTTCACGGCACAAGGCGGGAg                                                                                                       >  2:810102/1‑136 (MQ=255)
                         aGTGAAAACAACGGGTAAACGTTCGCGCGCAGTAAGCGCGAAGAAAAAAGCGATTCTTAGCGCAGCACTGGACACTTTTTCACAATTCGGTTTTCACGGCACAAGGCGGGAGc                                                                                                      <  1:124079/113‑1 (MQ=255)
                         aGTGAAAACAACGGGTAAACGTTCGCGCGCAGTAAGCGCGAAGAAAAAAGCGATTCTTAGCGCAGCACTGGACACTTTTTCACAATTCGGTTTTCACGGCACAAGGCGGGAGc                                                                                                      >  2:124079/1‑113 (MQ=255)
                         aGTGAAAACAACGGGTAAACGTTCGCGCGCAGTAAGCGCGAAGAAAAAAGCGATTCTTAGCGCAGCACTGGACACTTTTTCACAATTCGGTTTTCACGGCACAAGGCGGGAGCAGATCGCAGAGTTGGCGGGTGTTTc                                                                             >  2:756739/1‑138 (MQ=255)
                         aGTGAAAACAACGGGTAAACGTTCGCGCGCAGTAAGCGCGAAGAAAAAAGCGATTCTTAGCGCAGCACTGGACACTTTTTCACAATTCGGTTTTCACGGCACAAGGCGGGAGCAGATCGCAGAGTTGGCGGGTGTTTc                                                                             >  2:101217/1‑138 (MQ=255)
                                   acGGGTAAACGTTCGCGCGCAGTAAGCGCGAAGAAAAAATCGATTCTTAGCGCAGCACTGGACACTTTTTCACAATTCGGTTTTCACGGCACAAGGCGGGAGCAGATCGCAGAGTTGGCGGGTGTTTCAAAAACCAATc                                                                  <  2:675847/139‑1 (MQ=255)
                                     gggTAAACGTTCGCGCGCAGTAAGCGCGAAGAAAAAAGCGATTCTTAGCGCAGCACTGGACACTTTTTCACAATTCGGTTTTCACGGCACAAGGCGGGAGCAGATCGCAGAGTTGGCGGGTGTTTCAAAAACCAATctg                                                                >  2:98169/1‑139 (MQ=255)
                                                cgcgcgCAGTAAGCGCGAAGAAAAAAGCGATTCTTAGCGCAGCACTGGACACTTTTTCACAATTCGGTTTTCACGGCACAAGGCGGGAGCa                                                                                                     <  1:640617/91‑1 (MQ=255)
                                                cgcgcgCAGTAAGCGCGAAGAAAAAAGCGATTCTTAGCGCAGCACTGGACACTTTTTCACAATTCGGTTTTCACGGCACAAGGCGGGAGCa                                                                                                     >  2:640617/1‑91 (MQ=255)
                                                             cgcgAAGAAAAAAGCGATTCTTAGCGCAGCACTGGACACTTTTTCACAATTCGGTTTTCACGGCACAAGGCGGGAGCAGATCGCAGAGTTGGCGGGTGTTTCAAAAACCAATCTGCTGTATTACTTTCCGTCAAAagag                                        <  1:626622/139‑1 (MQ=255)
                                                              gcgAAGAAAAAAGCGATTCTTAGCGCAGCACTGGACACTTTTTCACAATTCGGTTTTCACGGCACAAGGCGGGAGCAGATCGCAGAGTTGGCGGGTGTTTCAAAAACCAATCTGCTGTATTACTTTCCGTCAAAAGAgg                                       <  1:810102/139‑1 (MQ=255)
                                                               cgAAGAAAAAAGCGATTCTTAGCGCAGCACTGGACACTTTTTCACAATTCGGTTTTCACGGCACAAGGCGGGAGCAGATCGCAGAGTTGGCGGGTGTTTCAAAAACCAATCTGCTGTATTACTTTCCGTCAAAAGAGgc                                      >  1:226234/1‑139 (MQ=255)
                                                               cgAAGAAAAAAGCGATTCTTAGCGCAGCACTGGACACTTTTTCACAATTCGGTTTTCACGGCACAAGGCGGGAGCAGATCGCAGAGTTGGCGGGTGTTTCAAAAACCAATCTGCTGTATTACTTTCCGTCAAAAGAGgc                                      >  1:68192/1‑139 (MQ=255)
                                                                gaagaaAAAAGCGATTCTTAGCGCAGCACTGGACACTTTTTCACAATTCGGTTTTCACGGCACAAGGCGGGAGCAGATCGCAGAGTTGGCGGGTGTTTCAAAAACCAATCTGCTGTATTACTTTCCGTCAAAAGAGgcg                                     <  2:476331/139‑1 (MQ=255)
                                                                gaagaaAAAAGCGATTCTTAGCGCAGCACTGGACACTTTTTCACAATTCGGTTTTCACGGCACAAGGCGGGAGCAGATCGCAGAGTTGGCGGGTGTTTCAAAAACCAATCTGCTGTATTACTTTCCGTCAAAAGAGgcg                                     <  1:541673/139‑1 (MQ=255)
                                                                gaagaaAAAAGCGATTCTTAGCGCAGCACTGGACACTTTTTCACAATTCGGTTTTCACGGCACAAGGCGGGAGCAGATCGCAGAGTTGGCGGGTGTTTCAAAAACCAATCTGCTGTATTACTTTCCGTCAAAAGAGgcg                                     <  1:98169/139‑1 (MQ=255)
                                                                 aagaaAAAAGCGATTCTTAGCGCAGCACTGGACACTTTTTCACAATTCGGTTTTCACGGCACAAGGCGGGAGCAGATCGCAGAGTTGGCGGGTGTTTCAAAAACCAATCTGCTGTATTACTTTCCGTCAAAAGAGgcgc                                    >  2:90012/1‑139 (MQ=255)
                                                                 aagaaAAAAGCGATTCTTAGCGCAGCACTGGACACTTTTTCACAATTCGGTTTTCACGGCACAAGGCGGGAGCAGATCGCAGAGTTGGCGGGTGTTTCAAAAACCAATCTGCTGTATTACTTTCCGTCAAAAGAGgcgc                                    <  2:68192/139‑1 (MQ=255)
                                                                 aagaaAAAAGCGATTCTTAGCGCAGCACTGGACACTTTTTCACAATTCGGTTTTCACGGCACAAGGCGGGAGCAGATCGCAGAGTTGGCGGGTGTTTCAAAAACCAATCTGCTGTATTACTTTCCGTCAAAAGAGgcg                                     <  2:521622/138‑1 (MQ=255)
                                                                 aagaaAAAAGCGATTCTTAGCGCAGCACTGGACACTTTTTCACAATTCGGTTTTCACGGCACAAGGCGGGAGCAGATCGCAGAGTTGGCGGGTGTTTCAAAAACCAATCTGCTGTATTACTTTCCGTCAAAAGAGgcg                                     >  1:521622/1‑138 (MQ=255)
                                                                                               gACACTTTTTCACAATTCGGTTTTCACGGCACAAGGCGGGAGCAGATCGCAGAGTTGGCGGGTGTTTCAAAAACCAATCTGCTGTATTACTTTCCGTCAAAAGAGgcg                                     >  1:672114/1‑108 (MQ=255)
                                                                                               gACACTTTTTCACAATTCGGTTTTCACGGCACAAGGCGGGAGCAGATCGCAGAGTTGGCGGGTGTTTCAAAAACCAATCTGCTGTATTACTTTCCGTCAAAAGAGgcg                                     <  2:672114/108‑1 (MQ=255)
                                                                                                   cTTTTTCACAATTCGGTTTTCACGGCACAAGGCGGGAGCAGATCGCAGAGTTGGCGGGTGTTTCAAAAACCAATCTGCTGTATTACTTTCCGTCAAAAGAGGCGCTGTATATTGCCGTGCTGCGGCAGATTCTCGatat  <  1:90012/139‑1 (MQ=255)
                                                                                                   cTTTTTCACAATTCGGTTTTCACGGCACAAGGCGGGAGCAGATCGCAGAGTTGGCGGGTGTTTCAAAAACCAATCTGCTGTATTACTTTCCGTCAAAAGAGGCGCTGTATATTGCCGTGCTGCGGCAGATTCTCGatat  <  2:486596/139‑1 (MQ=255)
                                                                                                    tttttCACAATTCGGTTTTCACGGCACAAGGCGGGAGCAGATCGCAGAGTTGGCGGGTGTTTCAAAAACCAATCTGCTGTATTACTTTCCGTCAAAagag                                        <  1:714682/100‑1 (MQ=255)
                                                                                                    tttttCACAATTCGGTTTTCACGGCACAAGGCGGGAGCAGATCGCAGAGTTGGCGGGTGTTTCAAAAACCAATCTGCTGTATTACTTTCCGTCAAAagag                                        >  2:714682/1‑100 (MQ=255)
                                                                                                    tttttCACAATTCGGTTTTCACGGCACAAGGCGGGAGCAGATCGCAGAGTTGGCGGGTGTTTCAAAAACCAATCTGCTGTATTACTTTCCGTCAAAAGAGgcg                                     >  1:413973/1‑103 (MQ=255)
                                                                                                    tttttCACAATTCGGTTTTCACGGCACAAGGCGGGAGCAGATCGCAGAGTTGGCGGGTGTTTCAAAAACCAATCTGCTGTATTACTTTCCGTCAAAAGAGgcg                                     <  2:413973/103‑1 (MQ=255)
                                                                                                    tttttCACAATTCGGTTTTCACGGCACAAGGCGGGAGCAGATCGCAGAGTTGGCGGGTGTTTCAAAAACCAATCTGCTGTATTACTTTCCGTCAAAAGAGgcg                                     >  2:172466/1‑103 (MQ=255)
                                                                                                    tttttCACAATTCGGTTTTCACGGCACAAGGCGGGAGCAGATCGCAGAGTTGGCGGGTGTTTCAAAAACCAATCTGCTGTATTACTTTCCGTCAAAAGAGgcg                                     <  1:172466/103‑1 (MQ=255)
                                                                                                                               aaGGCGGGAGCAGATCGCAGAGTTGGCGGGTGTTTCAAAAACCAATCTGCTGTATTACTTTCCGTCAAAagag                                        <  1:60985/73‑1 (MQ=255)
                                                                                                                               aaGGCGGGAGCAGATCGCAGAGTTGGCGGGTGTTTCAAAAACCAATCTGCTGTATTACTTTCCGTCAAAagag                                        >  2:60985/1‑73 (MQ=255)
                                                                                                                                    |                                                                                                         
GGGGAGAGCGCATGACGCAAGGCGCAGTGAAAACAACGGGTAAACGTTCGCGCGCAGTAAGCGCGAAGAAAAAAGCGATTCTTAGCGCAGCACTGGACACTTTTTCACAATTCGGTTTTCACGGCACAAGGCTGGAGCAGATCGCAGAGTTGGCGGGTGTTTCAAAAACCAATCTGCTGTATTACTTTCCGTCAAAAGAGGCGCTGTATATTGCCGTGCTGCGGCAGATTCTCGATAT  >  NZ_CP009273/1069687‑1069924

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

BRESEQ :: bam2aln output
CCAATCTACAAGAGGGGAGAGCGCATGACGCAAGGCGCAGTGAAAACAACGGGTAAACGTTCGCGCGCAGTAAGCGCGAAGAAAAAAGCGATTCTTAGCGCAGCACTGGACACTTTTTCACAATTCGGTTTTCACGGCACAAGGCTGGAGCAGATCGCAGAGTTGGCGGGTGTTTCAAAAACCAATCTGCTGTATTACTTTCCGTCAAAAGAGGCGCTGTATATTGCCGTGCTGCGGCAGATTCTCGATATCTGGCTGGCACCGTTAAAAGCGTTTCGTGAAGATTTCGCCCC  >  NZ_CP009273/1069674‑1069966
                                                                                                                                                 |                                                                                                                                                   
CCAATCTACAAGAGGGGAGAGCGCATGACGCAAGGCGCAGTGAAAACAACGGGTAAACGTTCGCGCGCAGTAAGCGCGAAGAAAAAAGCGATTCTTAGCGCAGCACTGGACACTTTTTCACAATTCGGTTTTCACGGCACAAGGCGGGAGC                                                                                                                                                <  SRR3722130.390244/151‑1 (MQ=60)
            gtgtataagagacaGACGCAAGGCGCAGTGAAAACAACGGGTAAACGTTCGCGCGCAGTAAGCGCGAAGAAAAAAGCGATTCTTAGCGCAGCACTGGACACTTTTTCACAATTCGGTTTTCACGGCACAAGGCGGGAGCAGATCGCAGAG                                                                                                                                     <  SRR3722130.125860/136‑1 (MQ=60)
            AGGGGAGAGCGCATGACGCAAGGCGCAGTGAAAACAACGGGTAAACGTTCGCGCGCAGTAAGCGCGAAGAAAAAAGCGATTCTTAGCGCAGCACTGGACACTTTTTCACAATTCGGTTTTCACGGCACAAGGCGGGAGCAGATCGCAGAGT                                                                                                                                    <  SRR3722130.512428/151‑1 (MQ=60)
              tagtctcgtgggctcggagatgtgtataagagacagGGGTAAACGTTCGCGCGCAGTAAGCGCGAAGAAAAAAGCGATTCTTAGCGCAGCACTGGACACTTTTTCACAATTCGGTTTTCACGGCACAAGGCGGGAGCAGATCGCAGAGT                                                                                                                                    <  SRR3722130.650204/113‑1 (MQ=60)
                      GCATGACGCAAGGCGCAGTGAAAACAACGGGTAAACGTTCGCGCGCAGTAAGCGCGAAGAAAAAAGCGATTCTTAGCGCAGCACTGGACACTTTTTCACAATTCGGTTTTCACGGCACAAGGCGGGAGCctgtctcttatacacatctccg                                                                                                                          >  SRR3722130.85430/1‑129 (MQ=60)
                                                                 CGCAGTAAGCGCGAAGAAAAAAGCGATTCTTAGCGCAGCACTGGACACTTTTTCACAATTCGGTTTTCACGGCACAAGGCGGGAGCAGATCGCAGAGTTGGCGGGTGTTTCAAAAACCAATCTGCTGTATTACTTTCCGTCAAAAGAGGCG                                                                               >  SRR3722130.229698/1‑151 (MQ=60)
                                                                 CGCAGTAAGCGCGAAGAAAAAAGCGATTCTTAGCGCAGCACTGGACACTTTTTCACAATTCGGTTTTCACGGCACAAGGCGGGAGCAGATCGCAGAGTTGGCGGGTGTTTCAAAAACCAATCTGCTGTATTACTTTCCGTCAAAAGAGGCG                                                                               >  SRR3722130.69158/1‑151 (MQ=60)
                                                                   CAGTAAGCGCGAAGAAAAAAGCGATTCTTAGCGCAGCACTGGACACTTTTTCACAATTCGGTTTTCACGGCACAAGGCGGGAGCAGATCGCAGAGTTGGCGGGTGTTTCAAAAACCAATCTGCTGTATTACTTTCCGTCAAAAGAGGCGCT                                                                             >  SRR3722130.529621/1‑151 (MQ=60)
                                                                         gtgggctcggagatgtgtataagagacagGCACTGGACACTTTTTCACAATTCGGTTTTCACGGCACAAGGCGGGAGCAGATCGCAGAGTTGGCGGGTGTTTCAAAAACCAATCTGCTGTATTACTTTCCGTCAAAAGAGGCGCTGTATAT                                                                       <  SRR3722130.725238/122‑1 (MQ=60)
                                                                         acggcatacgagattcgccttagtctcgtgggctcggagatgtgtataagagacagTTTCACGGCACAAGGCGGGAGCAGATCGCAGAGTTGGCGGGTGTTTCAAAAACCAATCTGCTGTATTACTTTCCGTCAAAAGAGGCGCTGTATAT                                                                       <  SRR3722130.61819/95‑1 (MQ=60)
                                                                         GCGCGAAGAAAAAAGCGATTCTTAGCGCAGCACTGGACACTTTTTCACAATTCGGTTTTCACGGCACAAGGCGGGAGCAGATCGCAGAGTTGGCGGGTGTTTCAAAAACCAATCTGCTGTATTACTTTCCGTCAAAAGAGGCGCTGTATAT                                                                       <  SRR3722130.636013/151‑1 (MQ=60)
                                                                          CGCGAAGAAAAAAGCGATTCTTAGCGCAGCACTGGACACTTTTTCACAATTCGGTTTTCACGGCACAAGGCGGGAGCAGATCGCAGAGTTGGCGGGTGTTTCAAAAACCAATCTGCTGTATTACTTTCCGTCAAAAGAGGCGCTGTATATT                                                                      <  SRR3722130.821908/151‑1 (MQ=60)
                                                                            gctcggaggatgtgtataagagacagGCACTGGACACTTTTTCACAATTCGGTTTTCACGGCACAAGGCGGGAGCAGATCGCAGAGTTGGCGGGTGTTTCAAAAACCAATCTGCTGTATTACTTTCCGTCAAAAGAGGCGCTGTATATTGC                                                                    <  SRR3722130.175058/125‑1 (MQ=60)
                                                                            CGAAGAAAAAAGCGATTCTTAGCGCAGCACTGGACACTTTTTCACAATTCGGTTTTCACGGCACAAGGCGGGAGCAGATCGCAGAGTTGGCGGGTGTTTCAAAAACCAATCTGCTGTATTACTTTCCGTCAAAAGAGGCGCTGTATATTGC                                                                    <  SRR3722130.549898/151‑1 (MQ=60)
                                                                            CGAAGAAAAAAGCGATTCTTAGCGCAGCACTGGACACTTTTTCACAATTCGGTTTTCACGGCACAAGGCGGGAGCAGATCGCAGAGTTGGCGGGTGTTTCAAAAACCAATCTGCTGTATTACTTTCCGTCAAAAGAGGCGCTGTATATTGC                                                                    <  SRR3722130.99564/151‑1 (MQ=60)
                                                                                                 GCGCAGCACTGGACACTTTTTCACAATTCGGTTTTCACGGCACAAGGCGGGAGCAGATCGCAGAGTTGGCGGGTGTTTCAAAAACCAATCTGCTGTATTACTTTCCGTCAAAAGAGGCGCTGTATATTGCCtgtctcttatacacatctcc                                               >  SRR3722130.682102/1‑131 (MQ=60)
                                                                                                      GCACTGGACACTTTTTCACAATTCGGTTTTCACGGCACAAGGCGGGAGCAGATCGCAGAGTTGGCGGGTGTTTCAAAAACCAATCTGCTGTATTACTTTCCGTCAAAAGAGGCGCTGTATATTGCCtgtctcttatacacatctccgagcc                                          >  SRR3722130.420524/1‑126 (MQ=60)
                                                                                                               ACTTTTTCACAATTCGGTTTTCACGGCACAAGGCGGGAGCAGATCGCAGAGTTGGCGGGTGTTTCAAAAACCAATCTGCTGTATTACTTTCCGTCAAAAGAGGCGCTGTATATTGCCGTGCTGCGGCAGATTCTCGATATCTGGCTGGCAC                                 <  SRR3722130.91271/151‑1 (MQ=60)
                                                                                                                                              GGCGGGAGCAGATCGCAGAGTTGGCGGGTGTTTCAAAAACCAATCTGCTGTATTACTTTCCGTCAAAAGAGGCGCTGTATATTGCCGTGCTGCGGCAGATTCTCGATATCTGGCTGGCACCGTTAAAAGCGTTTCGTGAAGATTTCGCCCC  >  SRR3722130.294655/1‑151 (MQ=60)
                                                                                                                                                 |                                                                                                                                                   
CCAATCTACAAGAGGGGAGAGCGCATGACGCAAGGCGCAGTGAAAACAACGGGTAAACGTTCGCGCGCAGTAAGCGCGAAGAAAAAAGCGATTCTTAGCGCAGCACTGGACACTTTTTCACAATTCGGTTTTCACGGCACAAGGCTGGAGCAGATCGCAGAGTTGGCGGGTGTTTCAAAAACCAATCTGCTGTATTACTTTCCGTCAAAAGAGGCGCTGTATATTGCCGTGCTGCGGCAGATTCTCGATATCTGGCTGGCACCGTTAAAAGCGTTTCGTGAAGATTTCGCCCC  >  NZ_CP009273/1069674‑1069966

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑