Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	419,294	A→G	intergenic (+110/‑297)	phoR → / → brnQ	sensor histidine kinase PhoR/branched chain amino acid transporter BrnQ

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	419,294	0	A	G	100.0%	101.0 / NA	29	intergenic (+110/‑297)	phoR/brnQ	sensor histidine kinase PhoR/branched chain amino acid transporter BrnQ
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (16/13);  total (16/13)

ATCGTGAAACATGCTGTGAATCATCACGAAAGTCGCCTGAATATTGAGAGTACAGTAGGAAAAGGAACACGTTTCAGTTTTGTTATCCCGGAACGTTTAATTGCCAAAAACAGCGATTAATCCGCCTTTGTCATCTTTTATTGCCATAAGCCAGTCGATGCTGGCTTATTTTCTTTGCAGTCAAAATACGGGCGTTAGATTTTACAACGATTGGTGATTTTTTGTTCGCATGATTAGCCATGTCTTTTTCACGGAAATAGTGTTTTATACTGGTTGGTGATTTCTTATCGCTATATACCTCTGGTTTTTAGATCCCTCCTTGCTTTAAAACGTTATAAGCGTTTAAATTGCGCTTCAGGTGCTGTCATACTGACTGCATTAACGCGGTAAATCGAAAAACTATTCTTCGCCGCGCCTGGTTGGGAGTATTTCCCGCTAAAATTGTTTAAATATACCGCTGTATCATCCCCA  >  NC_000913/419065‑419535                                                                                                                                                                                                                                      |                                                                                                                                                                                                                                                  aTCGTGAAACATGCTGTGACTCATCACGAAAGTCGCCTGAATATTGAGAGTACAGTAGGAAAAGGAACACGTTTCAGTTTTGTTATCCCGGAACGTTTAATTGCCAAAAACAGCGATTAATCCGCCTTTGTCATCTTTTATTGCCATAAGCCAGTCGATGCTGGCTTATTTTCTTTGCAGTCAAAATACGGGCGTTAGATTTTACAACGATTGGTGATTTTTTGTTCGCGTGATTAGCCATGTCTTTTTc                                                                                                                                                                                                                               >  1:272594/1‑250 (MQ=255)   cgttaaaCATGCTGTGAATCATCACGAAAGTCGCCTGAATATTGAGAGTACAGTAGGAAAAGGAACACGTTTCAGTTGTGTTATCCCGGAACGTTTAATTGCCAAAAACAGCGATTAATCCGCCTTTGTCATCTTTTATTGCCATAAGCCAGTCGATGCTGGCTTATTTTCTTTGCAGTCAAAATACGGGCGTTAGATTTTACAACGATTGGTGATTTTTTGTTCGCGTGATTAGCCATGTCTTTTTCACg                                                                                                                                                                                                                            <  2:200695/247‑1 (MQ=255)        aaCATGCTGTGAATCATCACGAAAGTCGCCTGAATATTGAGAGTACAGTAGGAAAAGGAACACGTTTCAGTTTTGTTATCCCGGAACGTTTAATTGCCAAAAACAGCGATTAATCCGCCTTTGTCATCTTTTATTGCCATAAGCCAGTCGATGCTGGCTTATTTTCTTTGCAGTCAAAATACGGGCGTTAGATTTTACAACGATTGGTGATTTTTTGTTCGCGTGATTAGCCATGTCTTTTTCACGGAAAt                                                                                                                                                                                                                       <  1:41257/251‑1 (MQ=255)          cATGCTGTGAATCATCACGAAAGTCGCCTGAATATTGAGAGTACAGTAGGAAAAGGAACACGTTTCAGTTTTGTTATCCCGGAACGTTTAATTGCCAAAAACAGCGATTAATCCGCCTTTGTCATCTTTTATTGCCATAAGCCAGTCGATGCTGGCTTATTTTCTTTGCAGTCAAAATACGGGCGTTAGATTTTACAACGATTGGTGATTTTTTGTTCGCGTGATTAGCCATGTCTTTTTCACGGAAATAg                                                                                                                                                                                                                     <  1:248767/251‑1 (MQ=255)                          aCGAAAGTCGCCTGAATATTGAGAGTACAGTAGGAAAAGGAACACGTTTCAGTTTTGTTATCCCGGAACGTTTAATTGCCAAAAACAGCGATTAATCCGCCTTTGTCATCTTTTATTGCCATAAGCCAGTCGATGCTGGCTTATTTTCTTTGCAGTCAAAATACGGGCGTTAGATTTTACAACGATTGGTGATTTTTTGTTCGCGTGATTAGCCATGTCTTTTTCACGGAAATAGTGTTTTATACtggttg                                                                                                                                                                                                     <  1:229334/251‑1 (MQ=255)                                  cGCCTGAATATTGAGAGTACAGTAGGAAAAGGAACACGTTTCAGTTTTGTTATCCCGGAACGTTTAATTGCCAAAAACAGCGATTAATCCGCCTTTGTCATCTTTTATTGCCATAAGCCAGTCGATGCTGGCTTATTTTCTTTGCAGTCAAAATACGGGCGTTAGATTTTACAACGATTGGTGATTTTTTGTTCGCGTGATTAGCCATGTCTTTTTCACGGAAATAGTGTTTTATACTGGTTGGTGAttt                                                                                                                                                                                              <  1:252115/250‑1 (MQ=255)                                          tatTGAGAGTACAGTAGGAAAAGGAACACGTTTCAGTTTTGTTATCCCGGAACGTTTAATTGCCAAAAACAGCGATTAATCCGCCTTTGTCATCTTTTATTGCCATAAGCCAGTCGATGCTGGCTTATTTTCTTTGCAGTCAAAATACGGGCGTTAGATTTTACAACGATTGGTGATTTTTTGTTCGCGTGATTAGCCATGTCTTTTTCACGGAAATAGTGTTTTATACTGGTTGGTGATTTCTTATCGCt                                                                                                                                                                                     >  2:236307/1‑251 (MQ=255)                                                        tAGGAAAAGGAACACGTTTAAGTTTTGTTATCCCGGAACGTTTAATTGCCAAAAACAGCGATTAATCCGCCTTTGTCATCTTTTATTGCCATAAGCCAGTCGATGCTGGCTTATTTTCTTTGCAGTCAAAATACGGGCGTTAGATTTTACAACGATTGGTGATTTTTTGTTCGCGTGATTAGCCATGTCTTTTTCACGGAAATAGTGTTTTATACTGGTTGGTGATTTCTTATCGCTATATACCTCTGGtt                                                                                                                                                                       >  2:212202/1‑251 (MQ=255)                                                         aGGAAAAGGAACACGTTTCAGTTTTGTTATCCCGGAACGTTTAATTGCCAAAAACAGCGATTAATCCGCCTTTGTCATCTTTTATTGCCATAAGCCAGTCGATGCTGGCTTATTTTCTTTGCAGTCAAAATACGGGCGTTAGATTTTACAACGATTGGTGATTTTTTGTTCGCGTGATTAGCCATGTCTTTTTCACGGAAATAGTGTTTTATACTGGTTGGTGATTTCTTATCGCTATATACCTCTGGtt                                                                                                                                                                       <  2:171981/250‑1 (MQ=255)                                                             aaaGGAACACGTTTCAGTTTTGTTATCCCGGAACGTTTAATTGCCAAAAACAGCGATTAATCCGCCTTTGTCATCTTTTATTGCCATAAGCCAGTCGATGCTGGCTTATTTTCTTTGCAGTCAAAATACGGGCGTTAGATTTTACAACGATTGGTGATTTTTTGTTCGCGTGATTAGCCATGTCTTTTTCACGGAAATAGTGTTTTATACTGGTTGGTGATTTCTTATCGCTATATACCTCTGGTTTTTAg                                                                                                                                                                  <  1:302706/251‑1 (MQ=255)                                                                                       cccGGAACGTTTAATTGCCAAAAACAGCGATTAATCCGCCTTTGTCATCTTTTATTGCCATAAGCCAGTCGATGCTGGCTTATTTTCTTTGCAGTCAAACTACGGGCGTTAGATTTTACAACGATTGGTGATTTTTTGTTCGCGTGATTAGCCATGTCTTTTTCACGGAAATAGTGTTTTATACTGGTTGGTGATTTCTTATCGCTATATACCTCTGGTTTTTAGATCCCTCCTTGCTTTAAAACGTtat                                                                                                                                         >  2:316226/1‑250 (MQ=255)                                                                                              cGTTTAATTGCCAAAAACAGCGATTAATCCGCCTTTGTCATCTTTTATTGCCATAAGCCAGTCGATGCTGGCTTATTTTCTTTGCAGTCAAAATACGGGCGTTAGATTTTACAACGATTGGTGATTTTTTGTTCGCGTGATTAGCCATGTCTTTTTCACGGAAATAGTGTTTTATACTGGTTGGTGATTTCTTATCGCTATATACCTCTGGTTTTTAGATCCCTCCTTGCTTTAAAACGTTATAAGCGttt                                                                                                                                 >  2:239212/1‑251 (MQ=255)                                                                                               gTTTAATTGCCAAAAACAGCGATTAATCCGCCTTTGTCATCTTTTATTGCCATAAGCCAGTCGATGCTGGCTTATTTTCTTTGCAGTCAAAATACGGGCGTTAGATTTTACAACGATTGGTGATTTTTTGTTCGCGTGATTAGCCATGTCTTTTTCACGGAAATAGTGTTTTATACTGGTTGGTGATTTCTTATCGCTATATACCTCTGGTTTTTAGATCCCTCCTTGCTTTAAAACGTTATAAGCGttt                                                                                                                                 >  1:237095/1‑250 (MQ=255)                                                                                                   aaTTGCCAAAAACAGCGCTTAATCCGCCTTTGTCATCTTTTATTGCCATAAGCCAGTCGATGCTGGCTTATTTTCTTTGCAGTCAAAATACGGGCGTTAGATTTTACAACGATTGGTGATTTTTTGTTCGCGTGATTAGCCATGTCTTTTTCACGGAAATAGTGTTTTATACTGGTTGGTGATTTCTTATCGCTATATACCTCTGGTTTTTAGATCCCTCCTTGCTTTAAAACGTTATAAGCGTTTAAAtt                                                                                                                            >  1:291843/1‑251 (MQ=255)                                                                                                   aaTTGCCAAAAACAGCGATTAATCCGCCTGTGGCATCTTTTATTGCCATAAGCCCGTCGATGCTGGCTTATTTTCTTTGCAGGCAAAAGACGGGCGTTAGATTTTACACCGATTGGTTATTTTTTGTTCGCGTGATTAGCCATGTCTTTTTCACGGAAATAGTGTTTTATACTGGTTGGTCATTTCTTATCGCTATATACCTCTGGTGTTTAGCTCCCTCCGTGCTTGAAGTCGTTATGAGCTTTTaaag                                                                                                                             <  2:215845/250‑2 (MQ=255)                                                                                                   aaTTGCCAAAAACAGAGATTAATCCGCCTTTGTCATCTTTTATTGCCATAAGCCAGTCGATGCTGGCTTATTTTCTTTGCAGTCAAAATACGGGCGTTAGATTTTACAACGATTGGTGATTTTTTGTTCGCGTGATTAGCCATGTCTTTTTCACGGAAATAGTGTTTTATACTGGTTGGTGATTTCTTATCGCTATATACCTCTGGTTTTTAGATCCCTCCTTGCTTTAAAACGTTATAAGCGTTTAAAtt                                                                                                                            >  2:175572/1‑251 (MQ=255)                                                                                                          aaaaaCAGCGATTAATCCGCCTTTGTCATCTTTTATTGCCATAAGCCAGTCGATGCTGGCTTATTTTCTTTGCAGTCAAAATACGGGCGTTAGATTTTACAACGATTGGTGATTTTTTGTTCGCGTGATTAGCCATGTCTTTTTCACGGAAATAGTGTTTTATACTGGTTGGTGATTTCTTATCGCTATATACCTCTGGTTTTTAGATCCCTCCTTGCTTTAAAACGTTATAAGCGTTTAAATTGCGCTTc                                                                                                                     >  1:246505/1‑251 (MQ=255)                                                                                                           aaaaCAGCGATTAATCCGCCTTTGTCATCTTTTATTGCCATAAGCCAGTCGATGCTGGCTTATTTTCTTTGCAGTCAAAATACGGGCGTTAGATTTTACAACGATTGGTGATTTTTTGTTCGCGTGATTAGCCATGTCTTTTTCACGGAAATAGTGTTTTATACTGGTTGGTGATTTCTTATCGCTATATACCTCTGGTTTTTAGATCCCTCCTTGCTTTAAAACGTTATAAGCGTTTAAATTGCGCTTc                                                                                                                     >  1:357048/1‑250 (MQ=255)                                                                                                                           cGCCTTTGTCATCTTTTATTGCCATAAGCCAGTCGATGCTGGCTTATTTTCTTTGCAGTCAAAATACGGGCGTTAGATTTTACAACGATTGGTGATTTTTTGTTCGCGTGATTAGCCATGTCTTTTTCACGGAAATAGTGTTTTATACTGGTTGGTGATTTCTTATCGCTATATACCTCTGGTTTTTAGATCCCTCCTTGCTTTAAAACGTTATAAGCGTTTAAATTGCGCTTCAGGTGCTGTCATactg                                                                                                     >  1:127259/1‑250 (MQ=255)                                                                                                                                          ttATTGCCATAAGCCAGTCGATGCTGGCTTATTTTCTTTGCAGTCAAAATACGGGCGTTAGATTTTACAACGATTGGTGATTTTTTGTTCGCGTGATTAGCCATGTCTTTTTCACGGAAATAGTGTTTTATACTGGTTGGTGATTTCTTATCGCTATATACCTCTGGTTTTTAGATCCCTCCTTGCTTTAAAACGTTATAAGCGTTTAAATTGCGCTTCAGGTGCTGTCATACTGACTGCATTAACGCGGt                                                                                     >  1:25086/1‑251 (MQ=255)                                                                                                                                                        cAGTCGATGCTGGCTTATTTTCTTTGCAGTCAAAATACGGGCGTTAGATTTTACAACGATTGGTGATTTTTTGTTCGCGTGATTAGCCATGTCTTTTTCACGGAAATAGTGTTTTATACTGGTTGGTGATTTCTTATCGCTATATACCTCTGGTTTTTAGATCCCTCCTTGCTTTAAAACGTTATAAGCGTTTAAATTGCGCTTCAGTTGCTGTCATACTGACTGCATTAACGCGGTAAATCGAAAAACt                                                                        >  2:311698/1‑250 (MQ=255)                                                                                                                                                                            tCTTTGCAGTCAAAATACGGGCGTTAGATTTTACAACGATTGGTGATTTTTTGTTCGCGTGATTAGCCATGTCTTTTTCACGGAAATAGTGTTTTATACTGGTTGGTGATTTCTTATCGCTATATACCTCTGGTTTTTAGATCCCTCCTTGCTTTAAAACGTTATAAGCGTTTAAATTGCGCTTCAGGTGCTGTCATACTGACTGCATTAACGCGGTAAATCGAAAAACTATTCTTCGCCGCGCCTGGtt                                                    <  1:236307/250‑1 (MQ=255)                                                                                                                                                                                 gCAGTCAAAATACGGGCGTTAGATTTTACAACGATTGGTGATTTTTTGTGCGCGTGATTAGCCATGTCTTTTTCACGGAAATAGTGTTTTATACTGGTTGGTGATTTCTTATCGCTATATACCTCTGGTTTTTAGATCCCTCCTTGCTTTAAAACGTTATAAGCGTTTAAATTGCGCTTCAGGTGCTGTCATACTGACTGCATTAACGCGGTAAATCGAAAAACTATTCTTCGCCGCGCCTGGTTGGGAg                                               <  1:303985/250‑1 (MQ=255)                                                                                                                                                                                        aaaTACGGGCGTTAGATTTTACAACGATTGGTGATTTTTTGTTCGCGTGATTAGCCATGTCTTTTTCACGGAAATAATGTTTTATACTGGTTGGTGATTTCTTATCGCTATATACCTCTGGTTTTTAGATCCCTCCTTGCTTTAAAACGTTATAAGCGTTTAAATTGCGCTTCAGGTGCTGTCATACTGACTGCATTAACGCGGTAAATCGAAAAACTATTCTTCGCCGCGCCTGGTTGGGAGTATTTccc                                       >  2:172495/1‑251 (MQ=255)                                                                                                                                                                                               ggCGTTAGATTTTACAACGATTGGTGATTTTTTGTTCGCGTGATTAGCCATGTCTTTTTCACGGAAATAGTGTTTTATACTGGTTGGTGATTTCTTATCGCTATATACCTCTGGTTTTTAGATCCCTCCTTGCTTTAAAACGTTATAAGCGTTTAAATTGCGCTTCAGGTGCTGTCATACTGACTGCATTAACGCGGTAAATCGAAAAACTATTCTTCGCCGCGCCTGGTTGGGAGTATTTCCCGCTaaaa                                <  1:233494/251‑1 (MQ=255)                                                                                                                                                                                                          ttACAACGATTGGTGCTTTTTTGTTCGCGTGATTAGCCATGTCTTTTTCACGGAACTAGTGTTTTATACTGGTTGGTGATTTCTTATCGCTATATACCTCTGGTTTTTAGATCCCTCCTTGCTTTAAAACGTTATAAGCGTTTAAATTGCGCTTCAGGTGCTGTCATACTGACTGCATTAACGCGGTAAATCGAAAAACTATTCTTCGCCGCGCCTGGTTGGGAGTATTTCCCGATAAAATTGTTTAAat                      >  2:311620/1‑250 (MQ=255)                                                                                                                                                                                                            aCAACGATTGGTGATTTTTTGTTCGCGTGATTAGCCATGTCTTTTTCACGGAAATAGTGTTTTATACTGGTTGGTGATTTCTTATCGCTATATACCTCTGGTTTTTAGATCCCTCCTTGCTTTAAAACGTTATAAGCGTTTAAATTGCGCTTCAGGTGCTGTCATACTGACTGCATTAACGCGGTAAATCGAAAAACTATTCTTCGCCGCGCCTGGTTGGGAGTATTTCCCGCTAAAATTGTTTAAatat                    >  2:114048/1‑250 (MQ=255)                                                                                                                                                                                                                         aTTTTTTGTTCGCGTGATTAGCCATGTCTTTTTCACGGAAATAGTGTTTTATACTGGTTGGTGATTTCTTATCGCTATATACCTCTGGTTTTTAGATCCCTCCTTGCTTTAAAACGTTATAAGCGTTTAAATTGCGCTTCAGGTGCTGTCATACTGACTGCATTAACGCGGTAAATCGAAAAACTATTCTTCGCCGCGCCTGGTTGGGAGGATTTCCCGCTAAAATTGTTTAAATATACCGCTGTatcatc      <  1:214621/251‑1 (MQ=255)                                                                                                                                                                                                                              gtGTTCGCGTGATTAGCCATGTCTTTTTCACGGAAATAGTGTTTTATACTGGTTGGTGATTTCTTATCGCTATATACCTCTGGTTTTTAGATCCCTCCTTGCTTTAAAACGTTATAAGCGTTTAAATTGCGCTTCAGGTGCTGTCATACTGACTGCATTAACGCGGTAAATCGAAAAACTATTCTTCGCCGCGCCTGGTTGGGAGTATTTCCCGCTAAAATTGTTTAAATATACCGCTGTATCATCCCCa  <  2:186373/249‑1 (MQ=255)                                                                                                                                                                                                                                      |                                                                                                                                                                                                                                                  ATCGTGAAACATGCTGTGAATCATCACGAAAGTCGCCTGAATATTGAGAGTACAGTAGGAAAAGGAACACGTTTCAGTTTTGTTATCCCGGAACGTTTAATTGCCAAAAACAGCGATTAATCCGCCTTTGTCATCTTTTATTGCCATAAGCCAGTCGATGCTGGCTTATTTTCTTTGCAGTCAAAATACGGGCGTTAGATTTTACAACGATTGGTGATTTTTTGTTCGCATGATTAGCCATGTCTTTTTCACGGAAATAGTGTTTTATACTGGTTGGTGATTTCTTATCGCTATATACCTCTGGTTTTTAGATCCCTCCTTGCTTTAAAACGTTATAAGCGTTTAAATTGCGCTTCAGGTGCTGTCATACTGACTGCATTAACGCGGTAAATCGAAAAACTATTCTTCGCCGCGCCTGGTTGGGAGTATTTCCCGCTAAAATTGTTTAAATATACCGCTGTATCATCCCCA  >  NC_000913/419065‑419535

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑