Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,867,455	G→A	Q33* (CAG→TAG)	rpoS ←	RNA polymerase sigma factor RpoS

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,867,455	0	G	A	100.0%	95.4 / NA	34	Q33* (CAG→TAG)	rpoS	RNA polymerase sigma factor RpoS
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (18/16);  total (18/16)

ACGATTGCCATAACGGCGGGCAATTTTTACCACCAGACGCAAGTTACTCTCGATCATCCGGCGGCGAGAGGCGACATCTCCACGCAGTGCGCGACGCGCAAAATAAACTTCTTCTTCGGCCGTTAACAGTGGTGAATAACCAATCTCACCAAGGTAAAGCTGAGTCGCGTCCAACACACGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTGTTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCATTTAAATCATGAACTTTCAGCGTATTCTGACTCATAAGGTGGCTCCTACCCGTGATCCCTTGACGGAACATTCAAGCAAAAGCCTGGTTCCGCCGATTTATCGCTGCGGCAAATAACGCAGCGGGTTTACGGATTTCCCCTTGTAACGAATTTCAAAATGCAAGCGTG  >  NC_000913/2867216‑2867684                                                                                                                                                                                                                                                |                                                                                                                                                                                                                                      aCGATTGCCATAACGGCGGGCAATTTTTACCACCAGACGCAAGTTACTCTCGATCATCCGGCGGCGAGAGGCGACCTCTCCACGCAGTGCGCGACGCGCAAAATAAACTTCTTCTTCGGCCGTTAAAAGTGGTGAATAACCAATCTCACCCAGGTAAAACTGAGTCGCGTCCAACACAAGCTGTGGGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGGTCCTATTCTAATAAgg                                                                                                                                                                                                                            >  1:366429/1‑251 (MQ=255)              cggcggGCAATTTTTACCACCAGACGAAAGTTACTCTCGATCATCCGGCGGAGAGAGGCGACATCTCCACGCAGTGCGCGACGCGCAAAATAAACTTCTTCTTCGGCCGTTAACAGTGGTGAATAACCACTCTCACCAAGGTAAAGATGAGTCGCGTCCAAAACACGCTGTGTGGCTCCCCGCGCAAACCGTTCCTCTTCGGCCAAATCCGTATTCCTGGGTTCCTATTTTACTAAAGCCTTTTCGTCaa                                                                                                                                                                                                                >  2:251468/1‑250 (MQ=255)                 cggGCAATTTTTACCACCAGACGCAAGTTACTCTCGATCATCCGGCGGCGAGAGGCGACATCTCCACGCAGTGCGCGACGCGCAAAATAAACTTCTTCTTCGGCCGTTAACAGTGGTGAATAACCAATCTCACCAAGGTAAAGCTGAGTCGCGTCCAACACACGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTATTCTACTAAGGCCTTTTCGTCAAAAAc                                                                                                                                                                                                            >  1:26508/1‑251 (MQ=255)                           ttACCACCAGACGCAAGTTACTCTCGATCATCCGGCGGCGAGAGGCGACATCTCCACGCAGTGCGCGACGCGCAAAATAAACTTCTTCTTCGGCCGTTAACAGTGGTGAATAACCAATCTCACCAAGGTAAAGCTGAGTCGCGTCCAACACACGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTcc                                                                                                                                                                                                   <  1:251468/250‑1 (MQ=255)                             accaccAGACGCAAGTTACTCTCGATCATCCGGCGGCGAGAGGCGACATCTCCACGCAGTGCGCGACGCGCAAAATAAACTTCTTCTTCGGCCGTTAACAGTGGTGAATAACCAATCTCACCAAGGTAAAGCTGAGTCGCGTCCAACACACGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTATTCTACTAAGGCCTGTTCGGCAAAAACCTCAACTCCGtt                                                                                                                                                                                                >  1:374520/1‑251 (MQ=255)                              ccaccaGACGCAAGTTACTCTCGATCATCCGGCGGCGAGAGGCGACATCTCCACGCAGTGCGCGACGCGCAAAATAAACTTCTTCTTCGGCCGTTAACAGTGGTGAATAACCAATCTCACCAAGGTAAAGCTGAGTCGCGTCCAACACACGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTtc                                                                                                                                                                                               <  1:374444/251‑1 (MQ=255)                                accaGGCGCAAGTTCCTCTCGATCATCCGGCGGCGAGAGGCGACATCGCCACGCAGTGCTCGACTCGCAAAATAAACTTCTTCTGCGGCCGTTAACAGTGGTGAATAACCAATCTCACCAAGGTAAAGCTGAGTCGCGTCCAACACACGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGTCCAAATCGTTATCACTGGGTTCCTATTCTACTAAGGTCTTTTCGTCAAAAACCTCAACTCCGTtctc                                                                                                                                                                                             <  2:48233/251‑1 (MQ=255)                                 cccgACGCAAGTTACTCTCGCTCATCCGGCGGCGAGAGGCGACATCTCCACGCAGAGCGCGACGCGCAAAATAAACTTCTTCTTCGGCCGTTCACAGTGGTGAATAACCAATCTCACCAAGGTAAAGCTGAGTCGCGTCCAACACCCGCTGTGTGGCTCCCTGCGATAACATTTACTCTTCGTCCAAATCGTTATCACTGGGTTCCTATTCTACTAAGTCCTTTTCGTCAAAAACCTCAACTcatttctc                                                                                                                                                                                             >  2:214579/4‑243 (MQ=255)                                  caGACGCAAGTTACTCTCGATCATCCGGCGGCGAGAGGCGACATCTCCACGCAGTGCGCGACGCGCAAAATAAACTGCTTCTTCGGCCGTTAACAGTGGTGAATAACCAATCGCACCAAGGTAAAGCTGAGTCGCGTCCAACACACGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTATTCGACGAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCtcat                                                                                                                                                                                           <  2:148851/251‑1 (MQ=255)                                        cAAGTTACTCTCGATCATCCGGCGGCGAGAGGCGACATCGCCACGCAGTGCGCGACGCGCAAAATAAACTTCTTCTTCGGCCGTTAACAGTGGTGAATAACCAATCTCACCAAGGTAAAGCTGAGTCGCGTCCAACACACGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAAtt                                                                                                                                                                                     <  1:246904/251‑1 (MQ=255)                                         aaGTTACTCTCGATCATCCGGCGGCGAGAGGCGACATCTCCACGCAGTGCGCGACGCGCAAACTAAACTTCTTCTTCGGCCGTTAACAGTGGTGAATAACCAATCTCACCAAGGTAAAGCTGAGTCGCGTCCAACACACGCTGAGTGGCTCCCTGCGATAAAAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTGCCTATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTc                                                                                                                                                                                    >  1:112904/1‑251 (MQ=255)                                               ctctCGATCATCAGGCGGCGAGAGGCGACATCTCCACGCAGTGCGCGACGCGCAAAATAAACTTCTTCTTCGGCCGTTAACAGTGGTGAATAACCAATCTCACCAAGGTAAAGCTGAGTCGCGTCCAACACACGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATc                                                                                                                                                                              >  1:269529/1‑251 (MQ=255)                                                    gATCATCCGGCGGCGAGAGGCGACATCTCCACGCAGTGCGCGACGCGCAAAATAAACTTCTTCTTCGGCCGTTAACAGTGGTGAATAACCAATCTCACCAAGGTAAAGCTGAGCCGCGTCCAACACACGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCAt                                                                                                                                                                         <  1:202583/251‑1 (MQ=255)                                                                 cgAGAGGCGACATCTCCACGCAGTGCGCGACGCGCAAAATAAACTTCTTCTTCGGCCGTTAACAGTGGTGAATAACCAATCACACCAAGGTAAAGCTGAGTCGCGTCCAACACACGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAGTTCCGCATCTTCATTTAAATCATGAAc                                                                                                                                                            <  1:49121/251‑1 (MQ=255)                                                                         gACATCTCCCCGCCGTGCGCGACGCGCAAAATAAACGTCTTCTTCGGCCGTTAACAGTGGTGAATAACCAATCTCACCAAGGTAAAGCTGAGTCGCGTCCAACACACGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCATTTAAATc                                                                                                                                                                  <  2:149448/237‑1 (MQ=255)                                                                         gACATCTCCACGCAGTGCGCGACGCGCAAAATAAACTTCTTCTTCGGCCGTTAACAGTGGTGAATAACCAATCTCACCAAGGTAAAGCTGAGTCGCGTCCAACACACGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCATTTAAATc                                                                                                                                                                  >  1:149448/1‑237 (MQ=255)                                                                                ccACGCAGTGCGCGACGCGCAAAATAAACTTCTTCTTCGGCCGTTAACAGTGGTGAATAACCAATCTCACCAAGGTAAAGCTGAGTCGCGTCCAACACACGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCATTTAAATCATGAACTTTCAGCGTATTCTg                                                                                                                                             <  1:348115/251‑1 (MQ=255)                                                                                                                                              aaTCTCACCAAGGTAAAGCTGAGTCGCGTCCAACACACGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCATTTAAATAATGAACTTTCAGCGTATTCTGACTCATAAGGAGGCTCCTACCCGTGATCACTTGACGGAACATTCAAGCAACAGCCTGGTTcc                                                                               >  1:193360/1‑251 (MQ=255)                                                                                                                                               aTCTCACCAAGGTAAAGCTGAGTCGCGTCCAACACACGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCATTTAAATCATGAACTTTCAGCGTATTCTGACTCATAAGGTGGCTCCTACCCGTGATCCCTTGACGGAACATTCAAGCAAAAGCCTGGTTccg                                                                              >  1:285766/1‑251 (MQ=255)                                                                                                                                                  tcACCAAGGTAAAGCTGAGTCGCGTCCAACACACGCTGTGTGGCTCCCTGCGATACCAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCATTTAAATCATGAACTTTCAGCGTATTCTGACTCATAAGGTGGCTCCTACCCGTGATCCCTTGACGGATCATTCAAGCAAAAGCCTGGTTccgccg                                                                           >  1:166934/1‑251 (MQ=255)                                                                                                                                                     ccAAGGTAAAGCTGAGTCGCGTCCAACACACGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCATTTAAATCATGAACTTTCAGCGTATTCTGACTCATAAGGTGGCTCCTACCCGTGATCCCTTGACGGAACATTCAAGCAAAAGCCTGGTTCCGCCGAtt                                                                        <  1:357887/251‑1 (MQ=255)                                                                                                                                                            aaaGCTGAGTCGCGTCCAACACACGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCATTTAAATCATGAACTTTCAGCGTATTCTGACTCATAAGGTGGCTCCTACCCGTGATCCCTTGACGGAACATTCAAGCAAAAGCCTGGTTCCGCCGATTTATCGc                                                                  <  1:140561/250‑1 (MQ=255)                                                                                                                                                             aaGCTGAGTCGCGTCCAACACACGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCATTTAAATCATGAACTTTCAGCGTATTCTGACTCATAAGGTGGCTCCTACCCGTGATCCCTTGACGGAACATTCAAGCAAAAGCCTGGTTCCGCCGATTTATCGCTg                                                                >  1:186687/1‑251 (MQ=255)                                                                                                                                                                                    gCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCAATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGTATCTTCATTTAAATCATGAACTTTCAGCGTATTCTGACTCATAAGGTGGCTCCTACCCGTGATCCCTTGACGGAACATTCAAGCAAAAGCCTGGTTCCGCCGATTTATCGCTGCGGCAAATAACGCAGCGGGttt                                          >  1:108615/1‑250 (MQ=255)                                                                                                                                                                                      tgtttgGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCCCTGGGTTCCTATTCTACTAAGGCCTTTTCGTCAAAAACCTCACCTCCGTTCTCATCAAATTCCGCATCTTCATTTAAATCATGAACTTTCAGCGTATTCTTACTCATAAGGTGGCTCCTACCCGTGATCCCTTGACGGAACATTCAAGCAAAAGCCTGGTTCCGCCGATTTATCGc                                                                  <  2:163866/220‑1 (MQ=255)                                                                                                                                                                                      tgtgtgGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCATTTAAATCATGAACTTTCAGCGTATTCTGACTCATAAGGTGGCTCCTACCCGTGATCCCTTGACGGAACATTCAAGCAAAAGCCTGGTTCCGCCGATTTATCGc                                                                  >  1:163866/1‑224 (MQ=255)                                                                                                                                                                                      tgtgtgGCACCCTGCGATATCACTGCCCAGTCGGCCAACACTTTATCACTGGGTTCCTATTCTGCTCTGGCCGTATTGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCACTTAATTCATGCACTCTCAGCGTTTTCTGACACATAAGGTGGCTCCTCCCCGTGATCCCTTGACGGAAAATTCAAGCAAAAGCCTGGTTCCGCCGATGTATCTCTGCGGCAAATAACGCAGCGGGTTTAc                                        <  2:295708/250‑1 (MQ=255)                                                                                                                                                                                            gCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTCACTATTCTACTAAGGCCTTTTCGTCAAACACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCATTTCAATCATGAACTTTCAGCGTATTCTGACTCATAAGGAGGCTCCTACCCGTGCTCCCTTGACGGAACATTCAAGCAAAAGCCTGGTTCCGCCGATTTATCGCTGCGGCAAATAACGCCGCGGGTTTACGGATTTc                                 >  1:218372/1‑251 (MQ=255)                                                                                                                                                                                                    cGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCATTTAAATCATGAACTTTCAGCGTATTCTGACTCATAAGGTGGCTCCTACCCGTGATCCCTTGACGGAACATTCAAGCAAAAGCCTGGTTCCGCCGATTTATCGCTGCGGCAAATAACGCAGCGGGTTTACGGATTTCCCCTTGt                          >  1:58258/1‑250 (MQ=255)                                                                                                                                                                                                      aTAACAGTTCCTTTTCGGCCAAATCGTTATCACTGGGTTCCTATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCATTTAAATCATGAACTTTCAGCGTATTCTTACTCATAAGGTGGCTCCTCCCCGTGATCCCTTGCCGGATAATTCAAGCAAAAGCCTGGTCTCGCCGATTTATCGCTGCGGCAAATAACGCAGCGGGTTTACGGATTTCCCCTTGTAAc                       <  1:54792/251‑1 (MQ=255)                                                                                                                                                                                                            gTTCCTCTTCGGCCACATCGTTATCACTGGGTTCCTATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCATTTAAATCATGAACTTTAAGCGTATTCTGACTCATAAGGTGGCTCCTACCCGTGATCCCTTGACGGAACATTCCAGCAAAAGCCTGGTTCCGCCGATTTATCGCTGCGGCAAATAACGCTGCGGGGTTACGGATTTCCCCTTGTAACGAtttt                 >  2:260949/1‑251 (MQ=255)                                                                                                                                                                                                                   ttCGGCCAAATCGTTATCACTGGGTTCCTATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCATTTAAATCATGAACTTTCAGCGTATTCTGACTCATAAGGTGGCTCCTACCCGTGATCCCTTGACGGAACATTCAAGCAAAAGcc                                                                                      <  1:323834/175‑1 (MQ=255)                                                                                                                                                                                                                   ttCGGCCAAATCGTTATCACTGGGTTCCTATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCATTTAAATCATGAACTTTCAGCGTATTCTGACTCATAAGGTGGCTCCTACCCGTGATCCCTTGACGGAACATTCAAGCAAAAGcc                                                                                      >  2:323834/1‑175 (MQ=255)                                                                                                                                                                                                                           aagcGTTATCACGGGGTTCCTATTCTACTAAGGCCTTTTCTTCAAAAACCTCAACTCCGTTCTTATCAAATTCCGCAGCTTCATTTAAATCATGAACTTTCAGCGTATTCTGACTCATAAGGTGGCTCCGACCCGTGATCCCTTGACGGAACATTCAAGCAAAAGCCTGGTTCCGCCGATTTATCGCTGCGGCAAATAACGCAGCGGGTTTACGGATTTCCCCTTGTAACGAATTTCAAAATGCAAGCgtg  <  2:58258/248‑1 (MQ=255)                                                                                                                                                                                                                                                |                                                                                                                                                                                                                                      ACGATTGCCATAACGGCGGGCAATTTTTACCACCAGACGCAAGTTACTCTCGATCATCCGGCGGCGAGAGGCGACATCTCCACGCAGTGCGCGACGCGCAAAATAAACTTCTTCTTCGGCCGTTAACAGTGGTGAATAACCAATCTCACCAAGGTAAAGCTGAGTCGCGTCCAACACACGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTGTTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCATTTAAATCATGAACTTTCAGCGTATTCTGACTCATAAGGTGGCTCCTACCCGTGATCCCTTGACGGAACATTCAAGCAAAAGCCTGGTTCCGCCGATTTATCGCTGCGGCAAATAACGCAGCGGGTTTACGGATTTCCCCTTGTAACGAATTTCAAAATGCAAGCGTG  >  NC_000913/2867216‑2867684

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑