Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,433,359	T→C	T106A (ACC→GCC)	pinR ←	Rac prophage; putative site‑specific recombinase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,433,359	0	T	C	100.0%	115.6 / NA	52	T106A (ACC→GCC)	pinR	Rac prophage; putative site‑specific recombinase
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (25/27);  total (25/27)

CCAAAACGTTTCCCTGCGCCGCGGGCTCTTACTATCCCGGAATGAGTGCGTTCAAGTAAAAGGTCTCGTTCAAATTCAGCGACTGCTGAAATTACTTGCATCATCATTTTTCCTGTTGGACTGGTCAGGTCAATGCCACCCAATGCTAAGCAATGCACTCTGATACCTGTTTCGGTCAGTTGTTCCACTGTTTTCCTGATATCCATTGCATTACAACCAAGGCGATCCAGTTTTGTCA  >  NC_000913/1433235‑1433472                                                                                                                             |                                                                                                                  ccAAAACGTTTCCCTGCGCCGCGGGCTCTTACTATCCCGGAATGAGTGCGTTCAAGTAAAAGGTCTCGTTCAAATTCAGCGACTGCTGAAATTACTTGCATCATCATTTTTCCTGTTGGACTGGCCAGGTCAATGCCAcc                                                                                                    <  1:231128/140‑1 (MQ=17)   aaaaCGTTTCCCTGCGCCGCGGGCTCTTACTATCCCGGAATGAGTGCGTTCAAGTAAAAGGTCTCGTTCAAATTCAGCGACTGCTGAAATTACTTGCATCATCATTTTTCCTGTTGGACTGGCCAGGTCAATGCCAcccg                                                                                                  <  2:486282/140‑2 (MQ=18)       cGTTTCCCTGCGCCGCGGGCTCTTACTATCCCGGAATGAGTGCGTTCAAGTAAAAGGTCTCGTTCAAATTCAGCGACTGCTGAAATTACTTGCATCATCATTTTTCCTGTTGGACTGGCCAGGTCAATGCCACCCAATGc                                                                                              >  1:1027334/1‑140 (MQ=17)           tCCCTGCGCCGCGGGCTCTTACTATCCCGGAATGAGTGCGTTCAAGTAAAAGGTCTCGTTCAAATTCAGCGACTGCTGAAATTACTTGCATCATCATTTTTCCTGTTGGACTGGCCAGGTCAATGCCACCCAATGCTAAg                                                                                          >  2:1017490/1‑140 (MQ=17)                gcgcCGCGGGCTCTTACTATCCCGGAATGAGTGCGTTCAAGTAAAAGGTCTCGTTCAAATTCAGCGACTGCTGAAATTACTTGCATCATCATTTTTCCTGTTGGACTGGCCAGGTCAATGCCACCCAATGCTAAGCAATg                                                                                     <  1:877618/140‑1 (MQ=17)                 cgccgcGGGCTCTTACTATCCCGGAATGAGTGCGTTCAAGTAAAAGGTCTCGTTCAAATTCAGCGACTGCTGAAATTACTTGCATCATCATTTTTCCTGTTGGACTGGCCAGGTCAATGCCACCCAATGCTAAGCAATGc                                                                                    <  2:778285/140‑1 (MQ=17)                      cgGGCTCTTACTATCCCGGAATGAGTGCGTTCAAGTAAAAGGTCTCGTTCAAATTCAGCGACTGCTGAAATTACTTGCATCATCATTTTTCCTGTTGGACTGGCCAGGTCAATGTCACCCAATGCTAAGCAATGCActct                                                                               >  2:42840/1‑140 (MQ=17)                      cgGGCTCTTACTATCCCGGAATGAGTGCGTTCAAGTAAAAGGTCTCGTTCAAATTCAGCGACTGCTGAAATTACTTGCATCATCATTTTTCCTGTTGGACTGGCCAGGTCAATGCCACCCAATGCTaa                                                                                           >  2:44812/1‑128 (MQ=17)                      cgGGCTCTTACTATCCCGGAATGAGTGCGTTCAAGTAAAAGGTCTCGTTCAAATTCAGCGACTGCTGAAATTACTTGCATCATCATTTTTCCTGTTGGACTGGCCAGGTCAATGCCACCCAATGCTaa                                                                                           <  1:44812/128‑1 (MQ=17)                      cgGGCTCTTACTATCCCGGAATGAGTGCGTTCAAGTAAAAGGTCTCGTTCAAATTCAGCGACTGCTGAAATTACTTGCATCATCATTTTTCCTGTTGGACTGGCCAGGTCAATGCCACCCAATGCTAAGCAATGCActct                                                                               >  2:68502/1‑140 (MQ=17)                      cgGGCTCTTACTATCCCGGAATGAGTGCGTTCAAGTAAAAGGTCTCGTTCAAATTCAGCGACTGCTGAAATTACTTGCATCATCATTTTTCCTGTTGGACTGGCCAGGTCAATGCCACCCAATGCTAAGCAATGCActct                                                                               >  2:350790/1‑140 (MQ=17)                      cgGGCTCTTACTATCCCGGAATGAGTGCGTTCAAGTAAAAGGTCTCGTTCAAATTCAGCGACTGCTGAAATTACTTGCATCATCATTTTTCCTGTTGGACTGGCCAGGTCAATGCCACCCAATGCTAAGCAATGCActct                                                                               >  2:255697/1‑140 (MQ=17)                      cgGGCTCTTACTATCCCGGAATGAGTGCGTTCAAGTAAAAGGTCTCGTTCAAATTCAGCGACTGCTGAAATTACTTGCATCATCATTTTTCCTGTTGGACTGGCCAGGTCAATGCCACCCAATGCTAAGCAATGCActct                                                                               <  1:34433/140‑1 (MQ=17)                      cgGGCTCTTACTATCCCGGAATGAGTGCGTTCAAGTAAAAGGTCTCGTTCAAATTCAGCGACTGCTGAAATTACTTGCATCATCATTTTTCCTGTTGGACTGGCCAGGTCAATGCCACCCAATGCTAAGCAATGCActct                                                                               >  1:894678/1‑140 (MQ=17)                                cTATCCCGGAATGAGTGCGTTCAAGTAAAAGGTCTCGTTCAAATTCAGCGACTGCTGAAATTACTTGCATCATCATTTTTCCTGTTGGACTGGCCAGGTCAATGCCACCCAATGCTAAGCAATGCACTCTGATACCTGtt                                                                     <  2:397709/140‑1 (MQ=17)                                   tCCCGGAATGAGTGCGTTCAAGTAAAAGGTCTCGTTCAAATTCAGCGACTGCTGAAATTACTTGCATCATCATTTTTCCTGTTGGACTGGCCAGGTCAATGTCACCCAATGCTAAGCAATGCACTCTGATACCTGTTTCg                                                                  <  1:42840/140‑1 (MQ=12)                                   tCCCGGAATGAGTGCGTTCAAGTAAAAGGTCTCGTTCAAATTCAGCGACTGCTGAAATTACTTGCATCATCATTTTTCCTGTTGGACTGGCCAGGTCAATGCCACCCAATGCTAAGCAATGc                                                                                    >  1:952867/1‑122 (MQ=17)                                   tCCCGGAATGAGTGCGTTCAAGTAAAAGGTCTCGTTCAAATTCAGCGACTGCTGAAATTACTTGCATCATCATTTTTCCTGTTGGACTGGCCAGGTCAATGCCACCCAATGCTAAGCAATGc                                                                                    <  2:952867/122‑1 (MQ=17)                                   tCCCGGAATGAGTGCGTTCAAGTAAAAGGTCTCGTTCAAATTCAGCGACTGCTGAAATTACTTGCATCATCATTTTTCCTGTTGGACTGGCCAGGTCAATGCCACCCAATGCTAAGCAATGCACTCTGATACCTGTTTCg                                                                  >  1:341473/1‑140 (MQ=17)                                   tCCCGGAATGAGTGCGTTCAAGTAAAAGGTCTCGTTCAAATTCAGCGACTGCTGAAATTACTTGCATCATCATTTTTCCTGTTGGACTGGCCAGGTCAATGCCACCCAATGCTAAGCAATGCACTCTGATACCTGTTTCg                                                                  <  1:350790/140‑1 (MQ=17)                                   tCCCGGAATGAGTGCGTTCAAGTAAAAGGTCTCGTTCAAATTCAGCGACTGCTGAAATTACTTGCATCATCATTTTTCCTGTTGGACTGGCCAGGTCAATGCCACCCAATGCTAAGCAATGCACTCTGATACCTGTTTCg                                                                  >  2:919598/1‑140 (MQ=17)                                     ccGGAATGAGTGCGTTCAAGTAAAAGGTCTCGTTCAAATTCAGCGACTGCTGAAATTACTTGCATCATCATTTTTCCTGTTGGACTGGCCAGGTCAATGCCACCCAATGCTAAGCAATGCACTCTGATACCTGTTTCGGt                                                                >  1:764150/1‑140 (MQ=17)                                       ggAATGAGTGCGTTCAAGTAAAAGGTCTCGTTCAAATTCAGCGACTGCTGAAATTACTTGCATCATCATTTTTCCTGTTGGACTGGCCAGGTCAATGCCACCCAATGCTAAGCAATGCACTCTGATAc                                                                          <  1:947325/128‑1 (MQ=17)                                       ggAATGAGTGCGTTCAAGTAAAAGGTCTCGTTCAAATTCAGCGACTGCTGAAATTACTTGCATCATCATTTTTCCTGTTGGACTGGCCAGGTCAATGCCACCCAATGCTAAGCAATGCACTCTGATAc                                                                          >  2:947325/1‑128 (MQ=17)                                         aaTGAGTGCGTTCAAGTAAAAGGTCTCGTTCAAATTCAGCGACTGCTGAAATTACTTGCATCATCATTTTTCCTGTTGGACTGGCCAGGTCAATGCCACCCAATGCTAAGCAATGCACTCTGATACCTGTTTCGGTCAgt                                                            >  2:804995/1‑140 (MQ=17)                                           tGAGTGCGTTCAAGTAAAAGGTCTCGTTCAAATTCAGCGACTGCTGAAATTACTTGCATCATCATTTTTCCTGTTGGACTGGCCAGGTCAATGCCACCCAATGCTAAGCAATGCACTCTGATACCTGTTTCGGTCAgttg                                                          >  2:782921/1‑140 (MQ=17)                                             aGTGCGTTCAAGTAAAAGGTCTCGTTCAAATTCAGCGACTGCTGAAATTACTTGCATCATCATTTTTCCTGTTGGACTGGCCAGGTCAATGCCACCCAATGCTAAGCAATGCACTCTGATACCTGTTTCGGTCAgttgtt                                                        >  2:322945/1‑140 (MQ=17)                                              gTGCGTTCAAGTAAAAGGTCTCGTTCAAATTCAGCGACTGCTGAAATTACTTGCATCATCATTTTTCCTGTTGGACTGGCCAGGTCAATGCCACCCAATGCTAAGCAATGCACTCTGATACCTGTTTCGGTCAGTTGTTc                                                       <  1:919598/140‑1 (MQ=17)                                                gCGTTCAAGTAAAAGGTCTCGTTCAAATTCAGCGACTGCTGAAATTACTTGCATCATCATTTTTCCTGTTGGACTGGCCAGGTCAATGCCACCCAATGCTAAGCAATGCACTCTGATACCTGTTTCGGTCAGTTGTTCCa                                                     <  2:764150/140‑1 (MQ=17)                                                 cGTTCAAGTAAAAGGTCTCGTTCAAATTCAGCGACTGCTGAAATTACTTGCATCATCATTTTTCCTGTTGGACTGGCCAGGTCAATGCCACCCAATGCTAAGCAATGCACTCTGATACCTGTTTCGGTCAGTTGTTCCAc                                                    >  1:503776/1‑140 (MQ=17)                                                 cGTTCAAGTAAAAGGTCTCGTTCAAATTCAGCGACTGCTGAAATTACTTGCATCATCATTTTTCCTGTTGGACTGGCCAGGTCAATGCCACCCAATGCTAAGCAATGCACTCTGATACCTGTTTCGGTCAGTTGTTCCAc                                                    <  2:503776/140‑1 (MQ=17)                                                   ttCAAGTAAAAGGTCTCGTTCAAATTCAGCGACTGCTGAAATTACTTGCATCATCATTTTTCCTGTTGGACTGGCCAGGTCAATGCCACCCAATGCTAAGCAATGCACTCTGATACCTGTTCCGGTCAGTTGTTCCACTg                                                  >  1:1068306/1‑140 (MQ=17)                                                     cAAGTAAAAGGTCTCGTTCAAATTCAGCGACTGCTGAAATTACTTGCATCATCATTTTTCCTGTTGGACTGGCCAGGTCAATGCCACCCAATGCTAAGCAATGCACTCTGATACCTGTTTCGGTCAGTTGTTCCACTGtt                                                <  1:782921/140‑1 (MQ=17)                                                      aaGTAAAAGGTCTCGTTCAAATTCAGCGACTGCTGAAATTACTTGCATCATCATTTTTCCTGTTGGACTGGCCAGGTCAATGCCACCCAATGCTAAGCAATGCACTCTGATACCTGTTTCGGTCAGTTGTTCCACTGtt                                                >  1:491062/1‑139 (MQ=17)                                                      aaGTAAAAGGTCTCGTTCAAATTCAGCGACTGCTGAAATTACTTGCATCATCATTTTTCCTGTTGGACTGGCCAGGTCAATGCCACCCAATGCTAAGCAATGCACTCTGATACCTGTTTCGGTCAGTTGTTCCACTGtt                                                <  2:491062/139‑1 (MQ=17)                                                        gTAAAAGGTCTCGTTCAAATTCAGCGACTGCTGAAATTACTTGCATCATCATTTTTCCTGTTGGACTGGCCAGGTCAATGCCACCCAATGCTAAGCAATGCACTCTGATACCTGTTTCGGTCAGTTGTTCCACTGTTTTc                                             <  1:311233/140‑1 (MQ=17)                                                            aaGGTCTCGTTCAAATTCAGCGACTGCTGAAATTACTTGCATCATCATTTTTCCTGTTGGACTGGCCAGGTCAATGCCACCCAATGCTAAGCAATGCACTCTGATACCTGTTTCGGTCAGTTGTTCCACTGttt                                               <  1:107531/134‑1 (MQ=17)                                                            aaGGTCTCGTTCAAATTCAGCGACTGCTGAAATTACTTGCATCATCATTTTTCCTGTTGGACTGGCCAGGTCAATGCCACCCAATGCTAAGCAATGCACTCTGATACCTGTTTCGGTCAGTTGTTCCACTGttt                                               >  2:107531/1‑134 (MQ=17)                                                             aGGTCTCGTTCAAATTCAGCGACTGCTGAAATTACTTGCATCATCATTTTTCCTGTTGGACTGGCCAGGTCAATGCCACCCAATGCTAAGCAATGCACTCTGATACCTGTTTCGGTCAGTTGTTCCACTGTTTTCCTGat                                        <  2:620745/140‑1 (MQ=17)                                                              ggTCTCGTTCAAATTCAGCGACTGCTGAAATTACTTGCATCATCATTTTTCCTGTTGGACTGGCCAGGTCAATGCCACCCAATGCTAAGCAATGCACTCTGATACCTGTTTCGGTCAGTTGTTCCACTGTTTTCCTGata                                       >  2:1010786/1‑140 (MQ=17)                                                                tctcGTTCAAATTCAGCGACTGCTGAAATTACTTGCATCATCATTTTTCCTGTTGGACTGGCCAGGTCAATGCCACCCAATGCTAAGCAATGCACTCTGATACCTGTTTCGGTCAGTTGTTCCACTGTTTTCCTGATATc                                     >  2:474849/1‑140 (MQ=17)                                                                  tcGTTCAAATTCAGCGACTGCTGAAATTACTTGCATCATCATTTTTCCTGTTGGACTGGCCAGGTCAATGCCACCCAATGCTAAGCAATGCACTCTGATACCTGTTTCGGTCAGTTGTTCCACTGTTTTCCTGATATCCa                                   >  2:201834/1‑140 (MQ=17)                                                                   cGTTCAAATTCAGCGACTGCTGAAATTACTTGCATCATCATTTTTCCTGTTGGACTGGCCAGGTCAATGCCACCCAATGCTAAGCAATGCACTCTGATACCTGTTCCGGTCAGTTGTTCCACTGTTTTCCTGATATCCAt                                  <  2:1068306/140‑1 (MQ=12)                                                                    gTTCAAATTCAGCGACTGCTGAAATTACTTGCATCATCATTTTTCCTGTTGGACTGGCCAGGTCAATGCCACCCAATGCTAAGCAATGCACTCTGATACCTGTTTCGGTCAGTTGTTCCACTGTTTTCCTGATATCCAtt                                 <  2:894678/140‑1 (MQ=17)                                                                          aTTCAGCGACTGCTGAAATTACTTGCATCATCATTTTTCCTGTTGGACTGGCCAGGTCAATGCCACCCAATGCTAAGCAATGCACTCTGATACCTGTTTCGGTCAGTTGTTCCACTGTTTTCCt                                           <  1:306989/124‑1 (MQ=17)                                                                          aTTCAGCGACTGCTGAAATTACTTGCATCATCATTTTTCCTGTTGGACTGGCCAGGTCAATGCCACCCAATGCTAAGCAATGCACTCTGATACCTGTTTCGGTCAGTTGTTCCACTGTTTTCCt                                           >  2:306989/1‑124 (MQ=17)                                                                          aTTCAGCGACTGCTGAAATTACTTGCATCATCATTTTTCCTGTTGGACTGGCCAGGTCAATGCCACCCAATGCTAAGCAATGCACTCTGATACCTGTTTCGGTCAGTTGTTCCACTGTTTTCCTGATATCCATTGCATTa                           >  1:193826/1‑140 (MQ=17)                                                                                             tACTTGCATCATCATTTTTCCTGTTGGACTGGCCAGGTCAATGCCACCCAATGCTAAGCAATGCACTCTGATACCTGTTTCGGTCAGTTGTTCCACTGTTTTCCTGATATCCATTGCATTACAACCAAGGCGATCCAGtt        <  1:322945/140‑1 (MQ=17)                                                                                                  gCATCATCATTTTTCCTGTTGGACTGGCCAGGTCAATGCCACCCAATGCTAAGCAATGCACTCTGATACCTGTTTCGGTCAGTTGTTCCACTGTTTTCCTGATATCCATTGCATTACAACCAAGGCGATCCAGTTTTGTc   <  1:804995/140‑1 (MQ=17)                                                                                                   catcatcatTTTTCCTGTTGGACTGGCCAGGTCAATGCCACCCAATGCTAAGCAATGCACTCTGATACCTGTTTCGGTCAGTTGTTCCACTGTTTTCCTGATATCCATTGCATTACAACCAAGGCGATCCAGTTTTGTca  <  1:255697/140‑1 (MQ=17)                                                                                                   catcatcatTTTTCCTGTTGGACTGGCCAGGTCAATGCCACCCAATGCTAAGCAATGCACTCTGATACCTGTTTCGGTCAGTTGTTCCACTGTTTTCCTGATATCCATTGCATTACAACCAAGGCGATCCAGTTTTGTca  <  1:68502/140‑1 (MQ=17)                                                                                                   catcatcatTTTTCCTGTTGGACTGGCCAGGTCAATGCCACCCAATGCTAAGCAATGCACTCTGATACCTGTTTCGGTCAGTTGTTCCACTGTTTTCCTGATATCCATTGCATTACAACCAAGGCGATCCAGTTTTGTca  <  1:1017490/140‑1 (MQ=17)                                                                                                                             |                                                                                                                  CCAAAACGTTTCCCTGCGCCGCGGGCTCTTACTATCCCGGAATGAGTGCGTTCAAGTAAAAGGTCTCGTTCAAATTCAGCGACTGCTGAAATTACTTGCATCATCATTTTTCCTGTTGGACTGGTCAGGTCAATGCCACCCAATGCTAAGCAATGCACTCTGATACCTGTTTCGGTCAGTTGTTCCACTGTTTTCCTGATATCCATTGCATTACAACCAAGGCGATCCAGTTTTGTCA  >  NC_000913/1433235‑1433472

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑