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	94.1%	102.6 / ‑0.2	35	Q33* (CAG→TAG)	rpoS	RNA polymerase sigma factor RpoS
Reads supporting (aligned to +/- strand):  ref base G (1/1);  new base A (13/19);  total (15/20)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.37e-01

CCAGACCACGATTGCCATAACGGCGGGCAATTTTTACCACCAGACGCAAGTTACTCTCGATCATCCGGCGGCGAGAGGCGACATCTCCACGCAGTGCGCGACGCGCAAAATAAACTTCTTCTTCGGCCGTTAACAGTGGTGAATAACCAATCTCACCAAGGTAAAGCTGAGTCGCGTCCAACA‑CACGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTGTTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCATTTAAATCATGAACTTTCAGCGTATTCTGACTCATAAGGTGGCTCCTACCCGTGATCCCTTGACGGAACATTCAAGCAAAAGCCTGGTTCCGCCGATTTATCGCTGCGGCAAATAACGCAGCGGGTTTACGGATTTCCCCTTGTAACGAATTTCAAAATGCAAGCGTGTTGAACTGGTTCCG  >  NC_000913/2867209‑2867698                                                                                                                                                                                                                                                        |                                                                                                                                                                                                                                                    ccAGACCACGATTGCCATAACGGCGGGCAATTTTTACCACCAGACGCAAGTTACTCTCGATCATCCGGCGGCGAGAGGCGACATCTCCACGCAGTGCGCGACGCGCAAAATAAACTTCTTCTTCGGCCGTTAACAGTGGTGAATAACCAATCTCACCAAGGTAAAGCTGAGTCGCGTCCAACA‑CACGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTATTct                                                                                                                                                                                                                                                 <  1:250543/251‑1 (MQ=255)              tccATAACGCCGGGCAATTGTTTCCACAGGACACAAGTTACTCCCGAACATCCGGCGGCGAGAGGCGTCCTTTCCTCGCATTCCGCGACGCGCAAAATAAACCTCTTCTTCGGCGGGTAACAGAGGTGAATAACCAATCTCACCAAGGTAAAGCATTGTTGCGTCCAACA‑CACGCTGTGTGCCTCCCTGCGATAACAGTTCCTTTTCGGCCAAATCGTTATCACTGGGTTCCGATTCTACGAAGGCCttt                                                                                                                                                                                                                                     <  2:290527/249‑1 (MQ=255)              gCCATAACGGCGGGCAATTGTTACCACCAGACGCAAGTTACTCGCGATCATCCGGCGGCGAGAGGCGACATCTCCACGCAGTGCGCGACGCGCAAAATAAACTTCTTCTTCGGCCGGTAACAGTGGTGAATAGCCAATCTCACCAAGGTAAAGCTGAGTCGCGTCCAACA‑CACGCTGTGTGGCGCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTATTCTACGAAGGCCttt                                                                                                                                                                                                                                     <  2:290511/250‑1 (MQ=255)                       gcggGCAATTTTTACCACCAGACGCAAGTTACTCTCGATCATCCGGCGGCGAGAGGCGACATCTCCACGCAGTGCGCGACGCGCAAAATAAACTTCTTCTTCGGCCGTTAACAGTGTTGAATAACCAATCTCACCAAGGTAAATCTGAGTCGCTTCCAACA‑TACGCTGTGTGTCTCCCTTCTATAACAGTTCCTCGTGGGCGAAAGCGTTATCACAGGGTTCCTATTCTACTAAGGCCTTTTCGTCaaaaa                                                                                                                                                                                                                           <  1:186943/251‑1 (MQ=255)                          ggCAATTTTGTCCACCAGACGCAAGATACTCTCGATCATCCGGCGCCGATAGGCGACATCTCCACGCAGTACTCGAAGCGCAAAATAAACTTCTTCTTCGGCCGTTCACAGTGGTGACTAACCAATCTCAACAAGGCAAAGCTGAGTCGCGTC‑AACAACACGCTGTGTGGCTACCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGTGTTCCTATACTACTCAGGCCTTTTTGTCAAAAAcac                                                                                                                                                                                                                        >  2:300386/1‑249 (MQ=255)                                       accaGACGCAAGTTACTCTAGATCATCCGGCGGCGAGAGGCGACATCCCCACGCAGCGAGCGACGCGCAAAATAAACTTATTATTCGGCCGTTAACAGTGGTGAATAACCAATCTCACCAAGGTAAAGCTGAGTCGCGTCCAACA‑CACGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTATTCTACTAAGGCCTTTTCGTCAAAAACCTCACCTCCGTtctc                                                                                                                                                                                                           >  2:273856/1‑251 (MQ=255)                                            aCGCAAGTTACTCTCGATCATCCGGCGGCGAGCCGCGACATCTCCACGCAGTGCGCGACGCGCAAAATAAACTTCTTCTTCGGCAGTTACCAGTGGCGAATAACCAATCTCACCAAGGTAAAGCTGAGTCGCGTCCAACA‑CACGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCtcatca                                                                                                                                                                                                       >  1:449316/1‑250 (MQ=255)                                               cAAGTTCCTCTCGATCAACCGGCGGCGAGAGGCGACATCTCCACGCAGTGCGCGAAGCGCAAAATAAACTGCTTCTTCGGCCGTTAACAGTGGTGAATAACCAATCTCACCAAGGTAAAGCTGAGTCGCGTCCAACA‑CACGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAAtt                                                                                                                                                                                                   <  2:335933/251‑1 (MQ=255)                                                           gATCATCCGGCGGCGAGAGGCGACATCTCCACGCAGTGCGCGACGCGCAAAATAAACTTCTTCTTCGGCCGTTAACAGTGGTGAATAACCAATCTCACCAAGGTAAAGCTGAGTCGCGTCCAACA‑CACGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCAt                                                                                                                                                                                       <  1:157863/251‑1 (MQ=255)                                                                                          cGCAGTGCGCGACGCGCAAAATAAACTTCTTCTTCGGCCGTTAACAGTGGTGAATAACCAATCTCACCAAGGTAAAGCTGAGTCGCGTCTAACA‑CACGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCATTTAAATCATGAACTTTCAGCGTATTCTGACt                                                                                                                                                        <  1:14398/251‑1 (MQ=255)                                                                                            cAGTGCGCGACGCGCAAAATAAACTTCTTCTTCGGCCGTTAACAGGGGTGAATAACCAATCTCACCAAGGAAAAGCTGAGTCGCGTCCAACA‑CACGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTCTTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCCTCTTCATTTAAATCATGAACTTTCAGCGTATTCTGACTc                                                                                                                                                       >  1:390109/1‑250 (MQ=255)                                                                                                 cgcgACGCGCAAAATAAACTTCTTCTTCGGCCGGTAACAGTGGTGAATAACCTATCTCACCAAGGTAAAGCTGAGTCGCGTCCAACA‑CACGCTGTTTGGCTCCCTGCGCTAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCATTTAAATCATGAACTTTCAGCGTATTCTGACTCATAAgg                                                                                                                                                 <  1:395134/251‑1 (MQ=255)                                                                                                    gACGCGCAAAATAAACTTCTTCTTCGGCCGTTAACAGTGGTGAATAACCAACCTCACCACGGTCAAGCTGAGTCGCGTCCAACA‑CCCGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTAGGCCAAATCGTTATCACTGGGTTCCTATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAATTTCCGCATCTTCATTTAAATCATGATCTTTCAGCGTATTCCGACTCATAtggtgg                                                                                                                                              >  2:226317/1‑251 (MQ=255)                                                                                                         gcAAATTAAACTTCTACTTCGGCCGTTAACAGTGGTGAATAACCAATCTCACCAAGGTAAAGCTGAGTCGCGTCCAACA‑CACGATGTGTGGCTCCCTGCGATAACCGTTCCTCTTCGGCCAAATCGTTATAACTGGGTTCCTATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCCTTTAAATCATGAACTTTCAGCGTATTCGGACTCATCAGGCGACTCCt                                                                                                                                         >  2:355925/1‑251 (MQ=255)                                                                                                         gcAAAATAAACTTCTTCTTCGGCCGTTAACAGTGGTGAATAACCAATCTCACCAAGGTAAAGCTGAGTCGCGTCCAACA‑CACGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCATTTAAATCATGAACTTTCAGCGTATTCTGACTCATAAGGTGGCTCCt                                                                                                                                         <  1:184267/251‑1 (MQ=255)                                                                                                            aaaTAAACTTCTTAGTCGGCCGTTCACAGTGGTTAAGAACCAATCTCACCCAGGTAAAGCTGAGTCGCGTCCAACA‑CACGCTGTGTGGCGCCCTGCGATAACAGTGCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTATTCTACTAAGTCCTTGTCGTCAAAAACCACAACTCCGTTCTCAGCAAATTCCGTATCGCCATTGAGATCATGAACGTTCCGCGTATTCTGTGTGATAATGTGGCTCCTAca                                                                                                                                      <  2:446986/251‑2 (MQ=255)                                                                                                                  aCTTCTTCTTCGGCCGTTAACAGTGGTGAATAACCAATCTCACCAAGGTAAAGCTGAGTCGCGTCCAACA‑CACGCTGTGTGTCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCATTTAAATCATGAACTTTCAGCGTATTCTGACTCATAAGGTGGCTCCTACCCGTGAt                                                                                                                                >  2:7977/1‑251 (MQ=255)                                                                                                                      cgtcttcGGCCGTTAACAGTGGTGAATAACCAATCTCACCAAGGTAAAGCTGAGTCGCGTCCAACA‑CACGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCATTTAAATCATGAACTTTCAGCGTATTCTGACTCATAAGGTGGCTCCTACCCGTGATCCCt                                                                                                                            <  2:289669/249‑1 (MQ=255)                                                                                                                        tcttcGGCCGTTAACAGTGGTGAATAACCAATCTCACCAAGGTAAAGCGGAGTCGCGTCCAACA‑CACGCTGTGTGGCTCCCTGCTATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTATTCTACTAAGGCCTTTTCGTCAAAAGCCTCAACTCCGTTCTCATCAAATGCCGCATCGTCAGTTAAATCATGAACTTTCAGCGTATGCTGGCTCATAAGGTGGCTCCTACCCGTGATCCCtt                                                                                                                           <  2:214670/250‑1 (MQ=255)                                                                                                                           tcGGCCGTTAACAGTGGTGAATAACCAATCTCACCAAGGTAAAGCTGAGTCGCGTCCAACA‑CACGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCATTTAAATCATGAACTTTCAGCGTATTCTGACTCATAAGGTGGCTCCTACCCGTGATCCCTTg                                                                                                                          <  1:93130/248‑1 (MQ=255)                                                                                                                                   tAACAGTGGTGAATAACCAATCTCACCAAGGTAAAGCTGAGTCGCGTCCAACA‑CACGCTGTGTGGCTCCCTGCGATCACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCACATTCCGCATCTTCATTTAAATCATGAACTTTCAGCGTATTCTGACTCATAAGGTGGCTCCTCCCCGTGATCCCTTGACGGAACATTc                                                                                                               >  2:259950/1‑251 (MQ=255)                                                                                                                                   tAACAGTGGTGAATAACCAATCTCACCAAGGTAAAGCTGAGTCGCGTCCAACA‑CACGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCATTTAAATCATGAACTTTCAGCGTATTCTGACTCATAAGGTGGCTCCTACCCGTGATCCCTTGACGGAACAtt                                                                                                                <  1:29759/250‑1 (MQ=255)                                                                                                                                               aTAACCAATCTCACCAAGGTAAAGCTGAGTCGCGTCCAACA‑CACGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCATTTAAATCATGAACTTTCAGCGTATTCTGACTCATAAGGTGGCTCCTACCCGTGATCCCTTGACGGAACATTCAAGCAAAAGCCt                                                                                                   <  1:313679/251‑1 (MQ=255)                                                                                                                                                                 gTAAAGCTGAGTCGCGTCCAACA‑CACGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCATTTAAATCATGAACTTTCAGCGTATTCTGACTCATAAGGTGGCTCCTACCCGTGATCCCTTGACGGAACATTCAAGCAAAAGCCTGGTTCCGCCGATTTATCg                                                                                 >  2:301741/1‑251 (MQ=255)                                                                                                                                                                  tAAAGCTGAGTCGCGTCCAACA‑CACGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCATTTAAATCATGAACTTTCAGCGTATTCTGACTCATAAGGAGGCTCCTACCCGTGATCCCTTGACGGAACATTCAAGCAAAAGCCTGGTTCCGCCGATTTATCGc                                                                                >  2:282553/1‑251 (MQ=255)                                                                                                                                                                              cgtgtccagcgaactcTGTGTTGCTCCCTGCGATAACAGTTCCTCTTCGTCCAAATCGTTATCACATGGTTCCTATTCTACTAAGTCCTTTTCGTCAAAAACCTCAACGCCGTTGTCATCAAATTCAGAATCTTGATTTAAATCATGAGCTTTCAGGGTATTCTGACTCATAAGGTGGCTCCTACCCGTGATGCCTGTACGGAAGGTTGAAGCAAAATCATTGTTCCGCCGATTTATCGCTGCGGCAAAt                                                                      <  2:258130/235‑1 (MQ=255)                                                                                                                                                                                   cAACA‑CACGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGTGTTCCTATTCTACTAAGGCCTTTTCGTCAAAAACCGCAACTCCGTTCTCATCAAATTCCGCATCTTCATTTAAATCATGAACCTTCAGCGTATTCTGACTCATAAGGTGGCTCCTACCCGTGATCCCTTGACGGAACATTCAAGCAAAAGCCTGGTTCCGCCGATTTATCGCTGCGGCTAATAACGCAg                                                               <  2:145505/251‑1 (MQ=255)                                                                                                                                                                                                                      tccgctTCGGCCAAATCGTTATCACTGGGTTCCTATTCTACTAAGGCCTTTGCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCATTTAAATCATGAACTTTCAGCGTATTCTGACTCATAAGGTGGCTCCTACCCGTGATCCCTTGACGGAACATTCAAGCAAAAGCCTGGTTCCGCCGATTTATCGCTGCGGCAAATAACGCAGCGGGTTTACGGATTTCCCCTTGTATCGAATTTc                              <  1:51260/246‑1 (MQ=255)                                                                                                                                                                                                                             cGGCCAAATCGTTATCACTGGGTTCCTATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCATTTAAATCATGAACTTTCAGCGTATTCTGACTCATAAGGTGGCTCCTACCCGTGATCCCTTGACGGAACATTCAAg                                                                                                            <  1:231572/165‑1 (MQ=255)                                                                                                                                                                                                                             cGGCCAAATCGTTATCACTGGGGTCCTATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCATTTAAATCATGAACTTTCAGCGTATTCTGACTCATAAGGTGGCTCCTACCCGTGATCACTTGACGGAACATTCAAg                                                                                                            >  2:231572/1‑165 (MQ=255)                                                                                                                                                                                                                                    aTCGTTATCACTGGGTTCCTATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCATTTAAATCATGAACTTTCAGCGTATTCTGACTCATAAGGTGGCTCCTACCCGTGATCCCTTGACGGAACATTCAAGCAAAAGCCTGGTTCCGCCGATTTATCGCTGCGGCAAATAACGCAGCGGGTTTACGGATTTCCCCTTGTAACGAATTTCAAAATGCAAGCgtgt               >  2:381323/1‑251 (MQ=255)                                                                                                                                                                                                                                      cGTTATCACTGGGTTCCTATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCATTTAAATCATGAACTTTCAGCGTATTCTGACTCATAAGGTGGCTCCTACCCGTGATCCCTTGACGGAACATTCAAGCAAAAGCCTGGTTCCGCCGATTTATCGCTGCGGCAAATAACGCAGCGGGTTTACGGATTTCCCCTTGTAACGAATTTCAAAATGCAAGCGTGTTg             >  1:452281/1‑251 (MQ=255)                                                                                                                                                                                                                                               tGGGTTCCTGTTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCATTTAAATCATGAACTTTCAGCGTATTCTGACTCa                                                                                                                                                      <  2:88745/105‑1 (MQ=255)                                                                                                                                                                                                                                               tGGGTTCCTGTTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCATTTAAATCATGAACTTTCAGCGTATTCTGACTCa                                                                                                                                                      >  1:88745/1‑105 (MQ=255)                                                                                                                                                                                                                                                 ggTTCCTATTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCATTTAAATCATGAACTTTCAGCGTATTCTGACTCATAAGGTGGCTCCTACCCGTGATCCCTTGACGGAACATTCAAGCAAAAGCCTGGTTCCGCCGATTTATCGCTGCGGCAAATAACGCAGCGGGTTTACGGATTTCCCCTTGTAACGAATTTCAAAATGCAAGCGTGTTGAACTGGTTCCg  >  1:147985/1‑251 (MQ=255)                                                                                                                                                                                                                                                        |                                                                                                                                                                                                                                                    CCAGACCACGATTGCCATAACGGCGGGCAATTTTTACCACCAGACGCAAGTTACTCTCGATCATCCGGCGGCGAGAGGCGACATCTCCACGCAGTGCGCGACGCGCAAAATAAACTTCTTCTTCGGCCGTTAACAGTGGTGAATAACCAATCTCACCAAGGTAAAGCTGAGTCGCGTCCAACA‑CACGCTGTGTGGCTCCCTGCGATAACAGTTCCTCTTCGGCCAAATCGTTATCACTGGGTTCCTGTTCTACTAAGGCCTTTTCGTCAAAAACCTCAACTCCGTTCTCATCAAATTCCGCATCTTCATTTAAATCATGAACTTTCAGCGTATTCTGACTCATAAGGTGGCTCCTACCCGTGATCCCTTGACGGAACATTCAAGCAAAAGCCTGGTTCCGCCGATTTATCGCTGCGGCAAATAACGCAGCGGGTTTACGGATTTCCCCTTGTAACGAATTTCAAAATGCAAGCGTGTTGAACTGGTTCCG  >  NC_000913/2867209‑2867698

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑