Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,410,859	C→T	L103F (CTC→TTC)	yjfJ →	PspA family protein YjfJ

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,410,859	0	C	T	96.9%	88.2 / ‑3.8	32	L103F (CTC→TTC)	yjfJ	PspA family protein YjfJ
Reads supporting (aligned to +/- strand):  ref base C (0/1);  new base T (21/10);  total (21/11)
Fisher's exact test for biased strand distribution p-value = 3.44e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.30e-01

TCCATTGAAGAAACCCAGGGCGTGCGCATGCTGGAACAGCATATTCGTGACGCTAAAGCTGAACTCGATAAAGCCGGAAAATCTCGCGTTGATCTGCTGGCGCGGGTGAAATTAAGTCACGATAAGCTGAAAGATTTACGTGAGCGCAAAGCCAGTCTGGAAGCCCGTGCGCTGGAAGCGTTAAGCAAGAACGTTAATCCGTCGTTGATTAACGAAGTTGCTGAAGAAATCGCGCGCCTTGAGAATCTCATTACCGCTGAAGAGCAAGTGTTGTCGAATCTGGAAGTCTCCCGTGATGGCGTGGAAAAAGCAGTTACAGCGACAGCGCAGCGTATCGCTCAGT‑TTGAGCAGCAAATGGAAGTCGTTAAAGCCACTGAAGCCATGCAGCGTGCACAACAGGCTGTAACAACCTCTACCGTTGGCGCATCTTCCAGCGTTTCGACAGCGGCAGAATCCTTAAAACGCCTGCAAACGCG  >  NC_000913/4410613‑4411088                                                                                                                                                                                                                                                       |                                                                                                                                                                                                                                       tCCATTGAAGAGACCCAGGGCGTGCGCATGCTGGAACAGCATATTCGTGACGCTAAAGCTGAACTCGATAAAGCCGGAAAATCTCGCGTTGATCTGCTGGCGCGGGTGAAATTAAGTCACGCTAAGCTGAAGGATTTACGTGAGCGCAAAGCCAGTCTGGTAGCCCGTGCGCTGGAAGCGTTAAGCAAGAAAGTTAATACGTCGTTGATTAACGTAGTTGCTGAAGAAATCGCGCGCCTAGAAAAtctctt                                                                                                                                                                                                                                    >  2:101877/1‑249 (MQ=255)    aTTGAAGAAACCCAGGGCGTGCGCATGCTGGAACAGCATATTCGTGACGCTAAAGCTGAACTCGATAAAGCCGGAAAATCTCGCGTTGATCTGCTGGCGCGGGTGAAATTAAGTCACGATAAGCTGAAAGATTTACGTGAGCGCAAAGCCAGTCTGGAAGCCCGTGCGCTGGAAGCGTTAAGCAAGAACGTTAATCCGTCGTTGATTAACGAAGTTGCTGAAGAAATCGCGCGCCTTGAGAATTTCATTAc                                                                                                                                                                                                                                 <  1:325333/251‑1 (MQ=255)               ccAGGGCGTGCGCATGCTGGAACAGCATATTCGTGACGCTAAAGCTGAACGCGATAAAGCCGGAAAATCTCGCGTTGATCTGCTGGCGCGGGTGAAATTAAGTCACGATAAGCTGAAAGATTTACGTGAGCGCAAAGCCAGTCTGGAAGCCCGTGCGCTGGAAGCGTTAAGCAAGAACGTTAATCCGTCGTTGATTAACGAAGTTGCTGAAGAAATCGCGCGCCTTGAGAATTTCATTACCGCTGAAGAGc                                                                                                                                                                                                                      <  1:329255/251‑1 (MQ=255)                             tGCTGGAACAGCATATTCGTGACGCTAAAGCTGAACTCGATAAAGCCGGAAAATCTCGCGTTGATCTGCTGGCGCGGGTGAAATTAAGTCACGATACGCTGAAAGATTTACGTGAGCGCAAAGCCAGTCTGGAAGCCCGTGCGCTGGAAGCGTTAAGCAAGAACGTTAATCCGTCGTTGATTAACGAAGTTGCTGAAGAAATCGCGCGCCTTGAGAATTTCATTACCGCTGAAGAGCAAGTGTTGTCGAAt                                                                                                                                                                                                        >  2:119758/1‑251 (MQ=255)                                                 gatgCTAAAGCTGAACTCGATAAAGCCGGAAAATCTCGCGTTGATCTGCTGGCGCGGGGGAAATTAAGTCACGATAAGATGAAAGATTTACGTGAGCGCGAAGACAGTCTGGAAGCCCGTGCGCTGGAAGCGTGAAGCAAGAACGTTAATCAGTCGTTGATTAAAGAAGATTCTGAAGAAATAGTGCGCATAGAAACTTTACTTACCGATGAAGAGCAAGGTTTGTCAAAAATGTAAGTCTCCGGTGATgg                                                                                                                                                                                    >  2:303743/4‑251 (MQ=255)                                                        aaGCTGAACTCGATAAAGCCGGAAAATCTCGCGTTGATCTGCTGGCGCGGGTGAAATTAAGTCACGATAAGCTGAAAGATTTACGTGAGCGCAAAGCCAGTCTGGAAGCCCGTGCGCTGGAAGCGTTAAGCAAGAACGTTAATCCGTCGTTGATTAACGAAGTTGCTGAAGAAATCGCGCGCCTTGAGAATTTCATTACCGCTGAAGAGCAAGTGTTGTCGAATCTGGAAGTCTCCCGTGATGGCGTGGa                                                                                                                                                                              >  1:379927/1‑250 (MQ=255)                                                           cTGAACTCGATAAAGCCGGAAAATCTCGCGTTGATCTGCTGGCGCGGGTGAAATTAAGTCACGATAAGCTGAAAGATTTACGTGAGCGCAAAGCCAGTCTGGAAGCCCGTGCGCTGGAAGCGTTAAGCAAGAACGTTAATCCGTCGTTGATTAACGAAGTTGCTGAAGAAATCGCGCGCCTTGAGAATTTCATTACCGCTGAAGAGCAAGTGTTGTCGAATCTGGAAGTCTCCCGTGATGGCGTGGaaaa                                                                                                                                                                           >  1:185051/1‑250 (MQ=255)                                                               aCTCGATAAAGCCGGAAAATCTAGCGTTGATCTGCTGGCGCGGGTGAAATTAAGTCAAGATAAGCTGAAAGATTTACGTGAGAGCAAAGCCAGTCTGGAAGCCCGAGCGCTGGAAGCGTTAAGCAAGAACGTTAATCCGTCGTTGATTAACGAAGTTGCTGAAGAAATCGAGCGCCTTGAGCATTTCATTACCGCTGAAGAGCCAGTGTTGTCGAATCTGGAAGACTACCGTGGTGGGTTGGAGAAAGCa                                                                                                                                                                       >  2:297875/1‑250 (MQ=255)                                                                        aGCCGGAAAATCTCGCGTTGATCTGCTGGCGCGGGGGAAATTAAGTCACGCTAAGCTGAAAGATTTACGTGAGCGCAAAGCCAGTCTGGAAGCCCGTGCGCTGGAAGCGTTAAGCAAGAACGTTAATCCGGCGTTGATTAACGAAGGTGCTGAAGAAATCGCGCGCCTTGAGAATTTCATTACCGCTGAAGAGCAAGTGTTGTCGACTCTGGAAGTCTCCCGTGATTGCGTGGAAAAAGCAGTTaaagcg                                                                                                                                                              >  2:108004/1‑250 (MQ=255)                                                                          ccGGAAAATCTCGCGTTGATCTGCTGGCGCGGGTGAAATTAAGTCACGATAAGCTGAAAGAGTTACGTGAGCGCAAAGCCAGTCTGGAAGCCCGTGCGCTGGAAGCGTTAAGCAAGAACGTTAATCCGTCGTTGATTAACGAAGTTGCTGAAGAAATCGCGCGCCTTGAGAATTTCATTACCGCTGAAGAGCAAGTGTTGTCGAATCTGGAAGTCTCCCGTGATGGCGTGGAAAAAGCAGTTacagcgaca                                                                                                                                                           <  2:219781/251‑1 (MQ=255)                                                                           cGGAAAATCTCGCGTTGATCTGCTGGCGCGGGTGAAATTAAGTCACGATAAGCTGAAAGATTTACGTGAGCGCCAAGCCAGTCTGGAAGCCCGTGCGCTGGAAGCGTTAAGCAAGAACGTTAATCCGTCGTTGATTAACGAAGTTGCTGAAGAAATCGCGAGCCTTGAGAATTTCTTTACCGCTGAAGAGCAAGTGTAGTCGAATCTGGGAGTCTCCCGTGATGGCGTGGAAACAGCAGTTacagcgaaa                                                                                                                                                           >  2:346894/1‑248 (MQ=255)                                                                           cGGAAAATCTCGCGATGATCTGCTGGCGCGGGTGAAATTAAGTCACGATAAGCTGAAAGATTTACGTGAGCGCAAAGCAAGTCTGGAAGCCCGTGCGCTGGAAGCGTTAAGCAAGAACGTTAATCCGTCGTTGATTAACGCAGTTGCTGAAGAAATCGCGCGCCTTGAGAATTTCATTACCGCTGAAGAGCAAGTGTTGTCGAATCTGGAAGTCTCCCGTGATGGCGTGGAAAAAGCAGTTacagcgac                                                                                                                                                            >  1:228448/1‑249 (MQ=255)                                                                                                    gcgcGGGTGAAATTAAGTCACGATAAGCTGAAAGATTTACGTGAGCGCAAAGCCAGTCTGGAAGCCCGTGCGCTGGAAGCGTTAAGCAAGAACGTTAATCCGTCGTTGATTAACGAAGTTGCTGAAGAAATCGCGCGCCTTGAGAATCTCATTACCGCTGAAGAGCAAGTGTTGTCGAATCTGGAAGTCTCCCGTGATGGCGTGGAAAAAGCAGTTACAGCAACAGCGCAGCGTATCGCTCAGT‑TTGagca                                                                                                                                <  1:65716/251‑1 (MQ=255)                                                                                                                                 gcaaGATTTACGTGAGCGCAAAGCCAGTCTGGACGCCCGTGCGCTGGAAAAGTTAAGCAAGAACGTTAATCCGTCGTTGATTAACGCAGTTGCTGAAGAAATCGCGAGCCTTGAGAATTTCATTACCGATGACGAGCAAGTGTTATCGAATCTGAAAGGCTCACGTGAAGGCGTGGCATAAGCAGTTAAAGCGACGGCACACCGTCTCGCT‑AGTATTGTACAGCAAATGGAAGACGTTAACGCCACTGaa                                                                                                    >  2:287112/3‑250 (MQ=255)                                                                                                                                  aaaGATTTACGTGAGCGCAAAGCCAGTCTGGAAGCCCGTGCGCTGGAAGCGTTAAGCAAGAACGTTAATCCGTCGTTGATTAACGCAGTTGCTGAAGAAATCGCGCGCCTTGAGAATTACATTACCGCTGAAGAGCAAGTGTTGTCGAATCTGGAAGTCTCCCGTGATGGCGTGGAAAAAGCAGTTACAGCGACAGCGCAGCGAATCGCTCAGT‑TTGAGCAGCAAATGGAAGTCGTTAAAGCCCCTGAAGc                                                                                                  >  2:117059/1‑251 (MQ=255)                                                                                                                                              gAGCGCAAAGCCAGTCTGGAAGCCCGTGCGCTGGAAGCGTTAAGCAAGAACGTTAATCCGTCGTTGATTAACGAAGTTGCTGAAGAAATCGCGCGCCTTGAGAATTTCATTACCGCTGAAGAGCAAGTGTTGTCGAATCTGGAAGTCTCCCGTGATGGCGTGGAAAAAGCAGTTACAGCGACAGCGCAGCGTATCGCTCAGT‑TTGAGCAGCAAATGGAAGTCGTTAAAGCCACTGAAGCCATGCAGCGTGc                                                                                      >  1:68701/1‑251 (MQ=255)                                                                                                                                              gAGCGCAAAGCCAGTCTGGAAGCCCGTGCGCTGGAAGCGTTAAGCAAGAACGTTAATCCGTCGTTGATTAACGAAGTTGCTGAAGAAATCGCGCGCCTTGAGAATTTCATTACCGCTGAAGAGCAAGTGTTGTCGAATCTGGAAGTCTCCCGTGATGGCGTGGAAAAAGCAGTTACAGCGACAGCGCAGCGTATCGCTCAGT‑TTGAGCAGCAAATGGAAGTCGTTAAAGCCACTGAAGCCATGCAGCGTGc                                                                                      >  1:177748/1‑251 (MQ=255)                                                                                                                                               aGCGCAAAGCCAGTCTGGAAGCCCGTGCGCTGGAAGCGTTAAGCAAGAACGTTAATCCGTCGTTGATTAACGAAGTTGCTGAAGAAATCGCGCGCCTTGAGAATTTCATTACCGCTGAAGAGCAAGTGTTGTCGAATCTGGCAGTCTCACGTGATGGCGTGGAAAAAGCAGTTACAGCGACAGCGCAGCGTATCGCTCAGT‑TTGAGCAGCAAATGGAAGTCGTTAAAGCCACTGAAGCCATGCAGCGTGc                                                                                      >  2:248977/1‑250 (MQ=255)                                                                                                                                                   cAAAGCCAGTCTGGAAGCCCGTGCGCTGGAAGCGTTAAGCAAGAACGTTAATCCGTCGTTGATTAACGAAGTTGCTGAAGAAATCGCGCGCCTTGAGAATTTCATTACCGCTGAAGAGCAAGTGTTGTCGAATCTGGAAGTCTCCCGTGATGGCGTGGAAAAAGCAGTTACAGCGACAGCGCAGCGTATCGCTCAGT‑TTGAGCAGCAAATGGAAGTCGTTAAAGCCACTGAAGCCATGCAGCGTGCacaac                                                                                 <  1:135991/251‑1 (MQ=255)                                                                                                                                                     attcaaGTCTGGAAGCCCGTGAGTTGGAAGCGTGAAGCAAGTTCGTTACACCGTCGTTGATTTACCAACTCGCTGAAGATATCGCGTGCCTTGAGAATTTCGTTACCGGTGAAGAGCAAGTTTTGTCGAATCTGGATGTATCCCGGGCGGGCGAGGATAAAGCAGTTACAGCGACAGCGCAGCGTATCGCTCAGT‑TGGTGCCGCAAATGGAAGTCGTTAAAGCCACTGAAGACATGCATTGTGCACAACAg                                                                               <  2:23566/246‑1 (MQ=255)                                                                                                                                                                             tGGAAGCGTTAAGCAAGAACGTTAATCCGTCGTTGATTAACGAAGTTGCTGAAGAAATCGCGCGCCTTGAGAATTTCATTACCGCTGAAGAGCAAGTGTTGTCGAATCTGGAAGTCTCCCGTGATGGCGTGGAAAAAGCAGTTACAGCGACAGCGCAGCGTATCGCTCAGT‑TTGAGCAGCAAATGGAAGTCGTTAAAGCCACTGAAGCCATGCAGCGTGCACAACAGGCTGTAACAACCTCTACCGTTGgc                                                       >  1:65964/1‑251 (MQ=255)                                                                                                                                                                              ggAAGCGTTAAGCAAGAACGTTAATCCGTCGTTGATTAACGAAGTTGCTGAAGAAATCGCGCGCCTTGAGAATTTCATTACCGCTGAAGAGCAAGTGTTGTCGAATCTGGAAGTCTCCCGTGATGGCGTGGAAAAAGCAGTTACAGCGACAGCGCAGCGTATCGCTCAGT‑TTGAGCAGCAAATGGAAGTCGTTAAAGCCACTGAAGCCATGCAGCGTGCACAACAGGCTGGAACAACCTCTACCGTTGgc                                                       <  1:60998/250‑1 (MQ=255)                                                                                                                                                                               tacgCGTTAAGCAAGAACGTTAATCCGTCGTTGATTAACGAAGTTGCTGAAGAAATCGCGCGCCTTGAGAATTTCATTACCGCTGAAGAGCAAGTGTTGTCGAATCTGGAAGTCTCCCGTGATGGCGTGGAAAAAGCAGTTACAGCGACAGCGCAGAGTATCGCTCAGT‑TTGAGCAGCAAATGAAAGTCGTTAAAGCCACTGAAGCCATGCAGCGTGCACAACAGGCTGTCACAACCTCTACCGTTGacgc                                                     >  2:268605/4‑251 (MQ=255)                                                                                                                                                                                              aaCGTTAATCCGTCGTTGATTAACGAAGTTGCTGAAGAAATCGCGCGCCTTGAGAATTTCATTACCGCTGAAGAGCAAGTGTTGTCGAATCTGGAAGTCTCCCGTGATGGCGTGGAAAAAGCAGTTACAGCGACAGCGCAGCGTATCGCTCAGT‑TTGAGCAGCAAATGGAAGTCGTTAAAGCCACTGAAGCCATGCAGCGTGCACAACAGGCTGTAACAACCTCTACCGTTGGCGCATCTTCCAGCGTTTc                                      <  1:112351/251‑1 (MQ=255)                                                                                                                                                                                                cGTTAATCCGTCGTTGATTAACGAAGTTGCTGAAGAAATCGCGCGCCTTGAGAATTTCATTACCGCTGAAGAGCAAGTGTTGTCGAATCTGGAAGTCTCCCGTGATGGCGTGGAAAAAGCAGTTACAGCGACAGCGCAGCGTATCGCTCAGT‑TTGAGCAGCAAATGGAAGTCGTTAAAGCCACTGAAGCCATGCAGCGTGCGCAACAGGCTGTAACAACCTCTACCGTTGGCGCATCTTCCAGCGTTTCg                                     >  1:226201/1‑250 (MQ=255)                                                                                                                                                                                                 gTTAATCCGTCGTTGATTAACGAAGTTGCTGAAGAAATCGCGCGCCTTGAGAATTTCATTACCGCTGAAGAGCAAGTGTTGTCGAATCTGGAAGTCTCCCGTGATGGCGTGGAAAAAGCAGTTACAGCGACAGCGCAGCGTATCGCTCAGT‑TTGAGCAGCAAATGGAAGTCGTTAAAGCCACTGAAGCCATGCAGCGTGCACAACAGGCTGTAACAACCTCTACCGTTGGCGCATCTTCCAGCGTTTCGAc                                   <  1:119758/251‑1 (MQ=255)                                                                                                                                                                                                       ccGTCGTAGATTAACGAAGTTGATGAAGAAAACGCGCGCCTTGACAATTTCATTACAGCTGAAGAGCAAATGTTGTAGACTATGGAAGTCTCCCATGATGGAGTGGAAAAAGCCGTTACAGCGACAGCGCAGCGTATAGCTCAGT‑TTGAGCAGCAAATGGAAGTCGTTAAAGCAACTGAAGCCATGCAGAGTGCACAACAGGCTGTAAAATCCTCTACCGTTGGAGCATCTTCCAGCGTTTCGACAgacgc                             >  2:328026/1‑247 (MQ=255)                                                                                                                                                                                                          tcgtTGATTAACGAAGTTGCTGAAGAAATCGCGCGCCTTGAGAATTTCATTACCGCTGAAGAGCAAGTGTTGTCGAATCTGGAAGTCTCCCGTGATGGCGTGGAAAAAGCAGTTACAGCGACAGCGCAGCGTATCGCTCAGT‑TTGAGCAGCAAATGGAAGTCGTTAAAGCCACTGAAGCCATGCAGCGTGCACAACAGGCTGTAACAACCTCTACCGTTGGCGCATCTTCCAGCGTTTCGACAGCGGc                             >  1:271939/1‑248 (MQ=255)                                                                                                                                                                                                             ttGATTAACGAAGTTGCTGAAGAAATCGCGCGCCTTGAGAATTTCATTACCGCTGAAGAGCAAGTGTTGTCGAATCTGGAAGTCTCCCGTGATGGCGTGGAAAAAGCAGTTACAGCGACAGCGCAGCGTATCGCTCAGT‑TTGAGCAGCAAATGGAAGTCGTTAAAGCCACTGAAGCCATGCAGCGTGCACAACAGGCTGTAACAACCTCTACCGTTGGCGCATCTTCCAGCGTTTCGACAGCGGCAGAATc                       >  1:321876/1‑251 (MQ=255)                                                                                                                                                                                                                  tAACGAAGTTGCTGAAGAAATCGAGCGCCTTGAGAATTTCATTACCGCTGAAGAGCAAGTGTTGTCGAATCTGGAAGTCTCCCGTGATGGCGTGGAAAAAGCAGTTACAGCGACAGCGCAGCGTATCGCTCAGT‑TTGAGAAGCAGATGGAAGTCGTTAAAGCCACTGAAGCCATGCAGCGAGAACAACAGGCTGGAACAAACTCTACCGTTGGCGCATCTTACAGCGTTTCGACAGCGGCAGAATCCTTa                   >  2:59298/1‑250 (MQ=255)                                                                                                                                                                                                                                aagaaATCGCGCTCCTTGAGAATTTCATTACCGCTGAAGAGCAAGTGTTGTCGAATCTGGAAGTCTCCCGTGATGGCGTGGAAAAAGCAGTTACAGCGACAGCGCAGCGTATCGCTCAGT‑TTGagcag                                                                                                                               <  1:13172/128‑1 (MQ=255)                                                                                                                                                                                                                                aagaaATCGCGCGCCTTGAGAATTTCATTACCGCTGAAGAGCAAGGGTTGTCGAATCTGGAAGTCTCCCGTGATGGCGTGGAAAAAGCAGTTACAGCGACAGCGAAGCGTATCGCTCCGT‑TTGagcag                                                                                                                               >  2:13172/1‑128 (MQ=255)                                                                                                                                                                                                                                  gaaATCGCGCGCCTTGAGAATTACATTACCGCTGAAGAGCAAGTGTTGTCGAATCTGGAAGTCTCCCGTGATGGCGTGGAAAAAGCAGTTACAGCGACAGCGCAGCGTATCGCTCAGT‑TTGAGCAGCAAATGGAAGTCGTTAAAGCCACTGAAGCCATGCAGCGTGCACAACAGGCTGTAACAACCTCTACCGTTGGCGCATCTTCCAGCGTTTCGACAGCGGCAGAATCCTTAAAACGCCTGCAAAcgcg  <  1:117059/251‑1 (MQ=255)                                                                                                                                                                                                                                                       |                                                                                                                                                                                                                                       TCCATTGAAGAAACCCAGGGCGTGCGCATGCTGGAACAGCATATTCGTGACGCTAAAGCTGAACTCGATAAAGCCGGAAAATCTCGCGTTGATCTGCTGGCGCGGGTGAAATTAAGTCACGATAAGCTGAAAGATTTACGTGAGCGCAAAGCCAGTCTGGAAGCCCGTGCGCTGGAAGCGTTAAGCAAGAACGTTAATCCGTCGTTGATTAACGAAGTTGCTGAAGAAATCGCGCGCCTTGAGAATCTCATTACCGCTGAAGAGCAAGTGTTGTCGAATCTGGAAGTCTCCCGTGATGGCGTGGAAAAAGCAGTTACAGCGACAGCGCAGCGTATCGCTCAGT‑TTGAGCAGCAAATGGAAGTCGTTAAAGCCACTGAAGCCATGCAGCGTGCACAACAGGCTGTAACAACCTCTACCGTTGGCGCATCTTCCAGCGTTTCGACAGCGGCAGAATCCTTAAAACGCCTGCAAACGCG  >  NC_000913/4410613‑4411088

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑