Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000964	1,317,152	+GT	intergenic (+23/+5)	phrA → / ← yjpA	secreted inhibitor of the activity of phosphatase RapA (quorum sensing)/putative enzyme

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000964	1,317,152	1	.	G	100.0%	102.5 / NA	31	intergenic (+23/+5)	phrA/yjpA	secreted inhibitor of the activity of phosphatase RapA (quorum sensing)/putative enzyme
Reads supporting (aligned to +/- strand):  ref base . (0/0);  new base G (17/14);  total (17/14)
*	NC_000964	1,317,152	2	.	T	96.7%	109.2 / ‑4.3	31	intergenic (+23/+5)	phrA/yjpA	secreted inhibitor of the activity of phosphatase RapA (quorum sensing)/putative enzyme
Reads supporting (aligned to +/- strand):  ref base . (0/0);  major base T (15/14);  minor base C (1/0);  total (17/14)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.80e-01

ACAGCCCGAAAAAGCACTTTCATTTTATGAGAAAATGGTGCACGCACAAAAACAAATCCAGAGAGGAGATTGTTTATATGAAATCTAAATGGATGTCAGGTTTGTTGCTCGTTGCGGTCGGGTTCAGCTTTACTCAGGTGATGGTTCATGCAGGTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGGG‑‑CT‑TTTT‑ATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCATGGCCGATTTCCGCTGCCTCTTCCAGTGAATCTGCTTCGATGACATACGCTCCGCCTGTGGCGTCGCTGAATGGCCCAAACATTTTTAAACGTTTTTCTGCCTGTAAACGATCCAGAAATTCATAGTGCCCAGCCACATGCTCCTGATTAAATTTCTCCG  >  NC_000964/1316918‑1317383                                                                                                                                                                                                                                            ||                                                                                                                                                                                                                                          aCAGCCCGAAAAAGCACTTTCATTTTATGAGAAAATGGTGCACGCACAAAAACAAATCCAGAGAGGAGATTGTTTATATGAAATCTAAATGGATGTCAGGTTTGTTGCTCGTTGCGGTCGGGTTCAGCTTTACTCAGGTGATGGTTCATGCAGGTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGGGGTCT‑TTTTTATttctt                                                                                                                                                                                                                            <  2:164260/251‑1 (MQ=255)   aGCCCGAAAAAGCACTTTCATTTTATGAGAAAATGGTGCACGCACAAAAACAAATCCAGAGAGGAGATTGTTTATATGAAATCTAAATGGATGTCAGGTTTGTTGCTCGTTGCGGTCGGGTTCAGCTTTACTCAGGTGATGGTTCATGCAGGTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGGGGTCT‑TTTTTATttcttc                                                                                                                                                                                                                           >  2:60070/1‑250 (MQ=255)      ccGAAAAAGCACTTTCATTTTATGAGAAAATGGTGCACGCACAAAAACAAATCCAGAGAGGAGATTGTTTATATGAAATCTAAATGGATGTCAGGTTTGTTGCTCGTTGCGGTCGGGTTCAGCTTTACTCAGGTGATGGTTCATGCAGGTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGGGGTCT‑TTTTTATTTCTTCAGCt                                                                                                                                                                                                                       >  2:57793/1‑251 (MQ=255)              gCACTTTCATTTTATGAGAAAATGGTGCACGCACAAAAACAAATCCAGAGAGGAGATTGTTTATATGAAATCTAAATGGATGTCAGGTTTGTTGCTCGTTGCGGTCGGGTTCAGCTTTACTCAGGTGATGGTTCATGCAGGTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGGGGTCT‑TTTTTATTTCTTCAGCTTCCATTCt                                                                                                                                                                                                               <  1:57793/251‑1 (MQ=255)                  tttCATTTTATGAGAAAATGGTGCACGCACAAAAACAAATCCAGAGAGGAGATTGTTTATATGAAATCTAAATGGATGTCAGGTTTGTTGCTCGTTGCGGTCGGGTTCAGCTTTACTCAGGTGATGGTTCATGCAGGTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGGGGCCT‑TTTTTATTTCTTCAGCTTCCATTCtttt                                                                                                                                                                                                            >  1:267634/1‑250 (MQ=255)                           aTGAGAAAATGGTGCACGCACAAAAACAAATCCAGAGAGGAGATTGTTTATATGAAATCTAAATGGATGTCAGGTTTGTTGCTCGTTGCGGTCGGGTTCAGCTTTACTCAGGTGATGGTTCATGCAGGTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGGGGTCT‑TTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGc                                                                                                                                                                                                   <  1:344870/250‑1 (MQ=255)                               gaAAATGGTGCACGCACAAAAACAAATCCAGAGAGGAGATTGTTTATATGAAATCTAAATGGATGTCAGGTTTGTTGCTCGTTGCGGTCGGGTTCAGCTTTACTCAGGTGATGGTTCATGCAGGTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGGGGTCT‑TTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTc                                                                                                                                                                                                 >  2:113211/1‑248 (MQ=255)                                     ggTGCTCGCACAAAGACTAATCCAGAGTGGAGCGTGATTAGATGAAATCTAAAAGGATGTCAGGATTGTGGCTAGTTGCGGGCGGGTTTAGCTTTACTCAGGTGATGGTTCATGCAGGTCAAGCATGAAACACAGAATGGAAAACAGGGCATATGGCGGCTTGTAATCAAACATCTTGCATAAAAATATCCCCTTAGGGGTCTGTGTT‑ATTTCTGCAGCGTCCATTcgcttaacggcagttcggaagaac                                                                                                                                                                                         <  2:94619/250‑24 (MQ=255)                                                      aaaTCCAGAGAGGAGATTGTTTATATTAAATCTAAATTGATGTCAGGTTTGTTGCTCGTTGCGGGCGGGTTCAGATTGACTCAGGTGATGGTTTATGCAGGTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGGGGTCT‑TTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCACAGAAGATCCACTTGCCTCCATCGGAt                                                                                                                                                                       <  1:324007/251‑1 (MQ=255)                                                             gagagGAGATTGTTTATATGAAATCTAAATGGATGTCAGGTTTGTTGCTCGTTGCGGTCGGGTTCAGCTTTACTCAGGTGATGGTTCATGCAGGTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGGGGTCT‑TTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCATg                                                                                                                                                                >  1:53691/1‑251 (MQ=255)                                                              agagGAGCTTGTTTATATGAAATCTAAATGGATGTCAGGTTTGTTGCTCGTTGCGGTCGGGTTCAGCTTTACTCAGGCGATGGTTCATGCAGGTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGGGGTCT‑TTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCATgg                                                                                                                                                               >  2:286203/1‑251 (MQ=255)                                                                       tGTTTATATGAAATCTAAATGGATGTCAGGTTTGTTGCTCGTTGCGGTCGGGTTCAGCTTTACTCAGGTGATGGTTCATGCAGGTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGGGGTCT‑TTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCATGGCCGATTTc                                                                                                                                                       <  1:96748/250‑1 (MQ=255)                                                                                gAAATCTAAATGGATGTCAGGTTTGTTGCTCGTTGCGGTCGGGTTCAGCTTTACTCAGGTGATGGTTCATGCAGGTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGGGGTCT‑TTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCATGGCCGATTTCCGCTGCctct                                                                                                                                             >  2:193439/1‑251 (MQ=255)                                                                                       aaaTGGATGTCAGGTTTGTTGCTCGTTGCGGTCGGGTTCAGCTTTACTCAGGTGATGGTTCATGCAGGTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGGGGTCT‑TTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCATGGCCGATTTCCGCTGCCTCTTCCAg                                                                                                                                        <  1:113211/249‑1 (MQ=255)                                                                                        aaTGGATGTCAGGTTTGTTGCTCGTTGCGGTCGGGTTCAGCTTTACTCAGGTGATGGTTCATGCAGGTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGGGGTCT‑TTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCATGGCCGATTTCCGCTGCCTCTTCCAGTGa                                                                                                                                     <  1:286203/251‑1 (MQ=255)                                                                                               gTCAGGTTTGTTGCTCGTTGCGGTCGGGTTCAGCTTTACTCAGGTGATGGTTCATGCAGGTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGGGGGCT‑TTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCATGGCCGATTTCCGCTGCCTCTTCCAGTGAATCTGCt                                                                                                                              >  1:341763/1‑251 (MQ=255)                                                                                                   ggTTTGTTGCTCGTTGCGGTCGGGTTCGGCTTTACTCAGGTGATGGTTCATGCAGGTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGGGGTCT‑TTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCATGGCCGATTTCCGCTGCCTCTTCCAGTGAATCTGCTTCg                                                                                                                           >  2:330995/1‑250 (MQ=255)                                                                                                    gTTTGTTGCTCGTTGCGGTCGGGTTCAGCTTTACTCAGGTGATGGTTCATGCAGGTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGGGGTCT‑TTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCATGGCCGATTTCCGCTGCCTCTTCCAGTGAATCTGCTTCGAt                                                                                                                         >  2:145705/1‑251 (MQ=255)                                                                                                     tttGTTGCTCGTTGCGGTCGGGTTCAGCTTTACTCAGGTGATGGTTCATGCAGGTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGGGGTCT‑TTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCATGGCCGATTTCCGCTGCCTCTTCCAGTGAATCTGCTTCGATg                                                                                                                        >  2:115644/1‑251 (MQ=255)                                                                                                                  gCGGTCGGGTTCAGCTTTACTCAGGTGATGGTTCATGCAGGTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGGGGTCT‑TTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCATGGCCGATTTCCGCTGCCTCTTCCAGTGAATCTGCTTCGATGACATACGCTCCGc                                                                                                           <  2:206306/251‑1 (MQ=255)                                                                                                                         ggTTCAGCTTGACACAGGTGATGGTTCAGGCAGGTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGAAATCAAACATGATGCATAAAAAAAGACCCTTAGGGGTCT‑TTTTTATTTCTTCAGCTTCCATTCGTTTAGCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCATGGCCGATTTCCGCTGCCTCTTCCAGTCAATCTGCTTCGATGACATACGCTCCGCCTGTGGc                                                                                                    <  2:310810/251‑1 (MQ=255)                                                                                                                                   tACTCAGGTGATGGTTCATGCAGGGGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGAACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGGGGTCT‑TTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCATGGCCGATTTCCGCTGCCTCTTCCAGTGATTCTGCTTCGATGACATACGCTCCGCCTGTGGCGTCGATGAAt                                                                                          >  2:284922/1‑251 (MQ=255)                                                                                                                                        aGGTGATGGTTCATGCAGGTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGGGGTCT‑TTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCATGGCCGATTTCCGCTGCCTCTTCCAGTGAATCTGCTTCGATGACATACGCTCCGCCTGTGGCGTCGCTGAATGGccc                                                                                     <  1:68119/251‑1 (MQ=255)                                                                                                                                                        aGGTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGGGGTCT‑TTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCATGGCCGATTTCCGCTGCCTCTTCCAGTGAATCTGCTTCGATGACATACGCTCCGCCTGTGGCGTCGCTGAATGGCCCAAACATTTTTAAACGt                                                                     <  1:193439/251‑1 (MQ=255)                                                                                                                                                                       cacaGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGGGGTCT‑TTTTTATTTCTTCATCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTTCCACCAGCGGATCCGCATGGCCGATTTCCGCTGCCTCTTCCAGTGAATCTGCTTCGATGACATACGCTCCGCCTGTGGCTTCGCTGAATGGCCCAAACATTTTTAAACGTTTTTCTGCCTGTaa                                                       >  2:183604/1‑250 (MQ=255)                                                                                                                                                                          aGAAGGGAAAACATTTCATATTGCGGCACACAATCAAACATGATGCATAAAAAAAGACCCTTAGGGGTCT‑TTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCATGGCCGATTTCCGCTGCCTCTTCCAGTGAATCTGCTTCGATGACATACGCTCCGCCTGTGGCGTCGCTGAATGGCCCAAACATTTTTAAACGTTTTTCTGCCTGTAAACGa                                                   <  1:114968/251‑1 (MQ=255)                                                                                                                                                                           gAAGGGAAAACATTTCATATTTCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGGGGTCTGTTTT‑ATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCATGGCCGATTTCCGCTGCCTCTTCCAGTGAATCTGCTTCGATGACATACGCTCCGCCTGTGGCGTCGCTGAATGGCCCAAACATTTTTAAACGTTTTTCTGCCGGTAAACGAt                                                  <  2:72835/251‑1 (MQ=255)                                                                                                                                                                                  aaaCATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCATTAGGGGTCT‑TTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCATGGCCGATTTCCGCTGCCTCTTCCAGTGAATCTGCTTCGATGACATACGCTCCGCCTGTGGCTTCGCTGAATGGCCCAAACATTTTTAAAAGTTTTTCTGCCTGTAAACGATCCAGaa                                            >  2:14423/1‑250 (MQ=255)                                                                                                                                                                                                        aaaTCAAACATGATGCATAAAAAAAGACCCTTAGGGGTCT‑TTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCATGGCCGATTTCCGCTGCCTCTTCCAGTGAATCTGCTTCGATGACATACGCTCCGCCTGTGGCGTCGCTGAATGGCCCAAACATTTTTAAACGTTTTTCTGCCTGTAAACGATCCAGAAATTCATAGTGCCCAGCCACATGc                     >  2:330182/2‑251 (MQ=255)                                                                                                                                                                                                                      gCATAAAAAAAGACCCTTAGGGGTCT‑TTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCATGGCCGATTTCCGCTGCCTCTTCCAGTGAATCTGCTTCGATGACATACGCTCCGCCTGTGGCGTCGCTGAATGGCCCAAACATTTTTAAACGTTTTTCTGCCTGTAAACGATCCAGAAATTCATAGTGCCCAGCCACATGCTCCTGATTAAAttt       >  1:307197/1‑251 (MQ=255)                                                                                                                                                                                                                           aaaaaaGACCCTTAGGGGTCT‑TTTTTATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCATGGCCGATTTCCGCTGCCTCTTCCAGTGAATCTGCTTCGATGACATACGCTCCGCCTGTGGCGTCGCTGAATGGCCCAAACATTTTTAAACGTTTTTCTGCCTGTAAACGATCCAGAAATTCATAGTGCCCAGCCACATGCTCCTGATTAAATTTCTCCg  >  1:330501/1‑251 (MQ=255)                                                                                                                                                                                                                                            ||                                                                                                                                                                                                                                          ACAGCCCGAAAAAGCACTTTCATTTTATGAGAAAATGGTGCACGCACAAAAACAAATCCAGAGAGGAGATTGTTTATATGAAATCTAAATGGATGTCAGGTTTGTTGCTCGTTGCGGTCGGGTTCAGCTTTACTCAGGTGATGGTTCATGCAGGTGAAACAGCAAACACAGAAGGGAAAACATTTCATATTGCGGCACGCAATCAAACATGATGCATAAAAAAAGACCCTTAGGG‑‑CT‑TTTT‑ATTTCTTCAGCTTCCATTCTTTTATCGTCAGCTCAGAAGATCCACTTGCCACCAGCGGATCCGCATGGCCGATTTCCGCTGCCTCTTCCAGTGAATCTGCTTCGATGACATACGCTCCGCCTGTGGCGTCGCTGAATGGCCCAAACATTTTTAAACGTTTTTCTGCCTGTAAACGATCCAGAAATTCATAGTGCCCAGCCACATGCTCCTGATTAAATTTCTCCG  >  NC_000964/1316918‑1317383

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑