Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	4,235,170	A→T	7.3%	intergenic (‑106/+56)	PP_3711 ← / ← PP_3712	diguanylate cyclase/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	4,235,170	0	A	T	7.3%	159.8 / 3.3	55	intergenic (‑106/+56)	PP_3711/PP_3712	diguanylate cyclase/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (27/24);  new base T (2/2);  total (29/26)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.55e-01

TCAACAGCCGGTACATGATGTCGGGGTTTGCTGCGAGCGACATGAACTTTACCTGAACCTTCGAAGCGCATGAAAAGGGACCCCGGCAAGCGGCGGCCGGG‑TCTTGGAAAGCGATG‑G‑TGGCATTATGCCGCTCGCGAGCATTTTGTGAAGCACATCACAAAAATGGCGCTATCCCTTATCTGGACGAACGAAAGCACCCCGCTCTCAATGGCGGGTGCCGGTCACCAGGAAGTTGAGCAAGTCCGGCTCATCCCCCAGGGCGATAGCCTGCGCCGGCCGCGGCAGGCTCGCCAG  >  NC_002947/4235022‑4235315                                                                                                                                                        |                                                                                                                                                  tCAACAGCCGGTACATGATGTCGGGGTTTGCTGCGAGCGACATGAACTTTACCTGAACCTTCGAAGCGCATGAAAAGGGACCCCGGCAAGCGGCGGCCGGG‑TCTTGGAAAGCGATG‑G‑TGGCATTATGCCGCTCGCGAGCATTTTGTGaa                                                                                                                                                   <  5:88494/149‑1 (MQ=255)     cAGCCGGTACATGATGTCGGGGTTTGCTGCGAGCGACATGAACTTTACCTGAACCTTCGAAGCGCATGAAAAGGGACCCCGGCAAGCGGCGGCCGGG‑TCTTGGAAAGCGATG‑G‑TGGCATTATGCCGCTCGCGAGCATTTTGTGAAGca                                                                                                                                                >  2:196018/1‑148 (MQ=255)      aGCCGGTACATGATGTCGTGGTTTGCTGCGAGCGACATGAACTTTACCTGAACCTTCGAAGCGCATGAAAAGGGACCCCGGCAAGCGGCGGCCGGG‑TCTTGGAAAGCGATG‑G‑TGGCATTATGCCGCTCGCGAGCATTTTGTGAAGcaca                                                                                                                                              <  3:147456/149‑1 (MQ=255)         cGGTACATGATGTCGGGGTTTGCTGCGAGCGACATGAACTTTACCTGAACCTTCGAAGCGCATGAAAAGGGACCCCGGCAAGCGGCGGCCGGG‑TCTTGGAAAGCGATG‑G‑TGGCATTATGCCGCTCGCGAGCATTTTGTGAAGCACATca                                                                                                                                           >  6:22221/1‑149 (MQ=255)                    gTCGGGGTTTGCTGCGAGCGACATGAACTTTACCTGAACCTTCGAAGCGCATGAAAAGGGACCCCGGCAAGCGGCGGCCGGG‑TCTTGGAAAGCGATG‑G‑TGGCATTATGCCGCTCGCGAGCATTTTGTGAAGCACATCACAAAAATGgc                                                                                                                                 <  2:255389/148‑1 (MQ=255)                    gTCGGGGTTTGCTGCGAGCGACAGGAACTTTACCTTAACCTTCTAAGCGAATGAAAAGGGACCCCGGCAAGCGGCGGCCGGG‑TCTTGGAAAGCGATT‑G‑TGGCATTATGCCGCTCGCGAGCATTTTGTGATGTGCTTCACaaaatgctc                                                                                                                                 <  6:243903/148‑6 (MQ=255)                       ggggTTTGCTGCGAGCGACATGAACTTTACCTGAACCTTCGAAGCGCATGAAAAGGGACCCCAGCAAGCGGCGGCCGGG‑TCTTGGAAAGCGATG‑G‑TGGCATTATGCCGCTCGCGAGCATTTTGTGAAGCACATCACAAAAATGGCGCTa                                                                                                                             >  8:195936/1‑149 (MQ=255)                                tgcGAGCGACATGAACTTTACCTGAACCTTCGAAGCGCATGAAAAGGGACCCCGGCAAGCGGCGGCCGGG‑TCTTGGAAAGCGATG‑G‑TGGCATTATGCCGCTCGCGAGCATTTTGTGATGTGCTTCACaaaatgc                                                                                                                                   <  6:106434/134‑4 (MQ=255)                                tgcGAGCGACATGAACTTTACCTGAACCTTCGAAGCGCATGAAAAGGGACCCCGGCAAGCGGCGGCCGGG‑TCTTGGAAAGCGATG‑G‑TGGCATTATGCCGCTCGCGAGCATTTTGTGATGTGCTTCACaaaatgc                                                                                                                                   >  5:106434/1‑131 (MQ=255)                                        aCATGAACTTTACCTGAACCTTCGAAGCGCATGAAAAGGGACCCCGGCAAGCGGCGGCCGGG‑TCTTGGAAAGCGATG‑G‑TGGCATTATGCCGCTCGCGAGCATTTTGTGAAGCACATCACAAAAATGGCGCTATCCCTTATCTGGacgaa                                                                                                            <  5:22221/149‑1 (MQ=255)                                           tGACCTTTACCTGAACCTTCGCAGCGCATGAAAAGGGACCCCGGCAAGCGGCGGCCGGG‑TCTTGGAAAGCGATG‑G‑TGGCATTATGCCGCTCGCGAGCATTTTGTGATGCACATCACAAAAATGGCGCTATCCCTTATCTGGacgaacg                                                                                                          >  6:170157/1‑148 (MQ=255)                                              aCTTTACCTGAACCTTCGAAGCGCATGAAAAGGGACCCCGGCAAGCGGCGGCCGGG‑TCTTGGAAAGCGATG‑G‑TGGCATTATGCCGCTCGCGAGCATTTTGTGAAGCACATCACAAAAATGGCGCTATCCCTTATCTGGACGAACGAAAg                                                                                                      <  8:303252/149‑1 (MQ=255)                                              aCTTTAACTTAACCTTTCAACCGCATTAAAATGGACCCCGGCAATCGGCGGCCGGGTTCTTGGAAAGCGATGCGCCATCATTATGCCGCTCGCGAGCATTTTGTGAAGCACATCACAAAAATGGCGCTATCCCTTATCTGGacgaacg                                                                                                          <  1:103503/148‑1 (MQ=255)                                                tttACCTGAACCTTCGAAGCGCATGAAAAGGGACCCCGGCAAGCGGCGGCCGGG‑TCTTGGAAAGCGATG‑G‑TGGCATTATGCCGCTCGCGAGCATTTTGTGAAGCACATCACAAAAATGGCGCTATCCCTTATCTGGACGAACGAAAGCa                                                                                                    >  7:235030/1‑149 (MQ=255)                                                     cTGAACCTTCGAAGCGCATGAAAAGGGACCCCGGCAAGCGGCGGCCGGG‑TCTTGGAAAGCGATG‑G‑TGGCATTATGCCGCTCGCGAGCATTTTGTGAAGCACATCACAAAAATGGCGCTATCCCTTATCTGGACGAACGaaa                                                                                                       >  8:139107/1‑141 (MQ=255)                                                     cTGAACCTTCGAAGCGCATGAAAAGGGACCCCGGCAAGCGGCGGCCGGG‑TCTTGGAAAGCGATG‑G‑TGGCATTATGCCGCTCGCGAGCATTTTGTGAAGCACATCACAAAAATGGCGCTATCCCTTATCTGGACGAACGaaa                                                                                                       <  7:139107/141‑1 (MQ=255)                                                     cTGAACCTTCGAAGCGCATGAAAAGGGACCCCGGCAAGCGGCGGCCGGG‑TCTTGGAAAGCGATG‑G‑TGGCATTATGCCGCTCGCGAGCATTTTGTGAAGCACATCACAAAAATGGCGCTATCCCTTATCTGGACGAACGAAAGCACCCCg                                                                                               >  3:182392/1‑149 (MQ=255)                                                     cTGAACCTTCGAAGCGCATGAAAAGGGACCCCGGCAAGCGGCGGCCGGG‑TCTTGGAAAGCGATG‑G‑TGGCATTATGCCGCTCGCGAGCATTTTGTGAAGCACATCACAAAAATGGCGCTATCCCTTATCTGGACGAACGAAAGCACCCCg                                                                                               >  6:153274/1‑149 (MQ=255)                                                     cTGAACCTTCGAAGCGCATGAAAAGGGACCCCGGCAAGCGGCGGCCGGG‑TCTTGGAAAGCGATG‑G‑TGGCATTATGCCGCTCGCGAGCATTTTGTGAAGCACATCACAAAAATGGCGCTATCCCTTATCTGGACGAACGAAAGCACCCCg                                                                                               >  6:29541/1‑149 (MQ=255)                                                       gAACCTTCGAAGCGCATGAAAAGGGACCCCGGCAAGCGGCGGCCGGG‑TCTTGGAAAGCGATG‑G‑TGGCATTATGCCGCTCGCGAGCATTTTGTGAAGCACATCACAAAAATGGCGCTATCCCTTATCTGGACGAACGAAAGCACCCCGct                                                                                             >  3:288912/1‑149 (MQ=255)                                                           cTTCGAAGCGCATGAAAAGGGACCCCGGCAAGCGGCGGCCGGG‑TCTTGGAAAGCGATG‑G‑TGGCATTATGCCGCTCGCGAGCATTTTGTGAAGCACATCACAAAAATGGCGCTATCCCTTATCTGGACGAACGAAAGCACCCCGCtctc                                                                                          >  7:33261/1‑148 (MQ=255)                                                                aaGCGCATGAAAAGGGACCCCGGCAAGCGGCGGCCGGG‑TCTTGGAAAGCGATG‑G‑TGGCATTATGCCGCTCGCGAGCATTTTGTGAAGCACATCACAAAAATGGCGCTATCCCTTATCTGGACGAACGAAAGCACCCCGCTCTCAATGGc                                                                                    >  4:212816/1‑149 (MQ=255)                                                                  gcgcATGAAAAGGGACCCCGGCAAGCGGCGGCCGGG‑TCTTGGAAAGCGATG‑G‑TGGCATTATGCCGCTCGCGAGCATTTTGTGAAGCACATCACAAAAATGGCGCTATCCCTTATCTGGACGAACGAAAGCACCCCGCTCTCAATGGCgg                                                                                  <  4:182392/149‑1 (MQ=255)                                                                    gcATGAAAAGGGACCCCGGCAAGCGGCGGCCGGG‑TCTTGGAAAGCGATG‑G‑TGGCATTATGCCGCTCGCGAGCATTTTGTGAAGCACATCACAAAAATGGCGCTATCCCTTATCTGGACGAACGAAAGCACCCCg                                                                                               >  2:18514/1‑134 (MQ=255)                                                                    gcATGAAAAGGGACCCCGGCAAGCGGCGGCCGGG‑TCTTGGAAAGCGATG‑G‑TGGCATTATGCCGCTCGCGAGCATTTTGTGAAGCACATCACAAAAATGGCGCTATCCCTTATCTGGACGAACGAAAGCACCCCg                                                                                               <  1:18514/134‑1 (MQ=255)                                                                    gcATGAAAAGGGACCCCGGCAAGCGGCGGCCGGG‑TCTTGGAAAGCGATG‑G‑TGGCATTATGCCGCTCGCGAGCATTTTGTGAAGCACATCACAAAAATGGCGCTATCCCTTATCTGGACGAACGAAAGCACCCCGCTCTCAATGGCGGGt                                                                                <  5:153274/149‑1 (MQ=255)                                                                       tGAAAAGGGACCCCGGCAAGCGGCGGCCGGG‑TCTTGGAAAGCGATG‑G‑TGGCATTATGCCGCTCGCGAGCATTTTGTGAAGCACATCACAAAAATGGCGCTATCCCTTATCTGGACGAACGAAAGCACCCCGCTCTCAATGGCGGGTGcc                                                                             >  2:300866/1‑149 (MQ=255)                                                                        gAAAAGGGACCCCGGCAAGCGGCGGCCGGG‑TCTTGGAAAGCGATG‑G‑TGGCATTATGCCGCTCGCGAGCATTTTGTGAAGCACATCACAAAAATGGCGCTATCCCTTATCTGGACGAACGAAAGCACCCCGCTCTCAATGGCGGGTGCCg                                                                            >  2:35808/1‑149 (MQ=255)                                                                         aaaaGGGACCCCGGCAAGCGGCGGCCGGG‑TCTTGGAAAGCGATG‑G‑TGGCATTATGCCGCTCGCGAGCATTTTGTGAAGCACATCACAAAAATGGCGCTATCCCTTATCTGGACGAACGAAAGCACCCCGCTCTCAATGGCGGGTGCCg                                                                            <  5:29541/148‑1 (MQ=255)                                                                             gggACCCCGGCAAGCGGCGGCCGGG‑TCTTGGAAAGCGATG‑G‑TGGCATTATGCCGCTCGCGAGCATTTTGTGAAGCACATCACAAAAATGGCGCTATCCCTTATCTGGACGAACGAAAGCACCCCGCTCTCAATGGCGGGTGCCGGTCAc                                                                       <  1:196018/149‑1 (MQ=255)                                                                                   ccGGCAAGCGGCGGCCGGG‑TCTTGGAAAGCGATG‑G‑TGGCATTATGCCGCTCGCGAGCATTTTGTGAAGCACATCACAAAAATGGCGCTATCCCTTATCTGGACGAACGAAAGCACCCCGCTCTCAATGGCGGGTGCCGGTCACCAGGaa                                                                 <  3:212816/149‑1 (MQ=255)                                                                                      gCAAGCGGCGGCCGGG‑TCTTGGAAAGCGATG‑G‑TGGCATTATGCCGCTCGCGAGCATTTTGTGAAGCACATCNCAAAAATGGCGCTATCCCTTATCTGGACGAACGAAAGCACCCCGCTCTCAATGGCGGGTGCCGGTCACCAGGAAGtt                                                              <  1:104930/149‑1 (MQ=255)                                                                                      gCAAGCGGCGGCCGGG‑TCTTGGAAAGCGATG‑G‑TGGCATTATGCCGCTCGCGAGCATTTTGTGAAGCACATCACAAAAATGGCGCTATCCCTTATCTGGACGAACGAAAGCACCCCGCTCTCAATGGCGGGTGCCGGTCACCAGGAAGtt                                                              <  1:300866/149‑1 (MQ=255)                                                                                         aGCGGCGGCCGGG‑TCTTGGAAAGCGATG‑G‑TGGCATTATGCCGCTCGCGAGCATTTTGTGAAGCACATCACAAAAATGGCGCTATCCCTTATCTGGACGAACGAAAGCACCCCGCTCTCAATGGCGGGTGCCGGTCACCAGGAAGTTGAg                                                           <  8:33261/149‑1 (MQ=255)                                                                                           cggcggCCGGG‑TCTTGGAAAGCGATG‑G‑TGGCATTATGCCGCTCGCGAGCATTTTGTGAAGCACATCACAAAAATGGCGCTATCCCTTATCTGGACGAACGAAAGCACCCCGCTCTCAATGGCGGGTGCCGGTCACCAGGAAGTTGAGc                                                          >  3:30521/1‑148 (MQ=255)                                                                                             gcggcCGGG‑TCTTGGAAAGCGATG‑G‑TGGCATTATGCCGCTCGCGAGCATTTTGTGAAGCACATCACAAAAATGGCGCTATCCCTTATCTGGACGAACGAAAGCACCCCGCTCTCAATGGCGGGTGCCGGTCACCAGGAAGTTGAGCAAg                                                       >  4:126451/1‑149 (MQ=255)                                                                                                   ggg‑TCTTGGAAAGCGATG‑G‑TGGCATTATGCCGCTCGCGAGCATTTTGTGAAGCACATCACAAAAATGGCGCTATCCCTTATCTGGACGAACGAAAGCACCCCGCTCTCAATGGCGGGTGCCGGTCACCAGGAAGTTGAGCAAGTCCGGc                                                 <  3:126451/149‑1 (MQ=255)                                                                                                   ggg‑TCTTGGAAAGCGATG‑G‑TGGCATTATGCCGCTCGCGAGCATTTTGTGAAGCACATCACAAAAATGGCGCTATCCCTTATCTGGACGAACGAAAGCACCCCGCTCTCAATGGCGGGTGCCGGTCACCAGGAAGTTGAGCAAGTCCGGc                                                 <  7:195936/149‑1 (MQ=255)                                                                                                     g‑TCTTGGAAAGCGATG‑G‑TGGCATTATGCCGCTCGCGAGCATTTTGTGAAGCACATCACAAAAATGGCGCTATCCCTTATCTGGACGAACGAAAGCACCCCGCTCTCAATGGCGGGTGCCGGTCACCAGGAAGTTGAGCAAGTCCGGCt                                                >  8:12649/1‑148 (MQ=255)                                                                                                            gAAAGCGATG‑G‑TGGCATTATGCCGCTCGCGAGCATTTTGTGAAGCACATCACAAAAATGGCGCTATCCCTTATCTGGACGAACGAAAGCACCCCGCTCTCAATGGCGGGTGCCGGTCACCAGGAAGTTGAGCAAGTCCGGCTCATcccc                                         <  4:30521/149‑1 (MQ=255)                                                                                                             aaaGCGATG‑G‑TGGCATTATGCCGCTCGCGAGCATTTTGTGAAGCACATCACAAAAATGGCGCTATCCCTTATCTGGACGAACGAAAGCACCCCGCTCTCAATGGCGGGTGCCGGTCACCAGGAAGTTGAGCAAGTCCGGCTCATcccc                                         >  3:163762/1‑148 (MQ=255)                                                                                                              aaGCGATG‑G‑TGGCATTATGCCGCTCGCGAGCATTTTGTGAAGCACATCACAAAAATGGCGCTATCCCTTATCTGGacgaacga                                                                                                         <  6:17589/83‑1 (MQ=255)                                                                                                              aaGCGATG‑G‑TGGCATTATGCCGCTCGCGAGCATTTTGTGAAGCACATCACAAAAATGGCGCTATCCCTTATCTGGacgaacga                                                                                                         >  5:17589/1‑83 (MQ=255)                                                                                                               aGCGATG‑G‑TGGCATTATGCCGCTCGCGAGCATTTTGTGAAGCACATCACAAAAATGGCGCTATCCCTTATCTGGACGAACGAAAGCACCCCGCTCTCAATGGCGGGTGCCGGTCACCAGGaa                                                                 >  8:267583/1‑122 (MQ=255)                                                                                                               aGCGATG‑G‑TGGCATTATGCCGCTCGCGAGCATTTTGTGAAGCACATCACAAAAATGGCGCTATCCCTTATCTGGACGAACGAAAGCACCCCGCTCTCAATGGCGGGTGCCGGTCACCAGGaa                                                                 <  7:267583/122‑1 (MQ=255)                                                                                                                gCGATG‑G‑TGGCATTATGCCGCTCGCGAGCATTTTGTGAAGCACATCACAAAAATGGCGCTATCCCTTATCTGGACGAACGAAAGCACCCCGCTCTCAATGGCGGGTGCCGGTCACCAGGAAGTTGAGCAAGTCCGGCTCATCCCCCAgg                                     >  5:221074/1‑149 (MQ=255)                                                                                                                       g‑tggCATTATGCCGCTCGCGAGCATTTTGTGAAGCACATCACAAAAATGGCGCTATcc                                                                                                                          >  4:208072/1‑58 (MQ=255)                                                                                                                             aTTATGCCGCTCGCGAGCATTTTGTGAAGCACATCACAAAAATGGCGCTATCCCTTATCTGGACGAACGAAAGCACCCCGCTCTCAATGGCGGGTGCCGGTCACCAGGAAGTTGAGCAAGTCCGGCTCATCCCCCAGGGCGATAGCCTg                          >  3:82673/1‑149 (MQ=255)                                                                                                                              ttATGCCGCTCGCGAGCATTTTGTGAAGCACATCACAAAAATGGCGCTATCCCTTATCTGGACGAACGAAAGCACCCCGCTCTCAATGGCGGGTGCCGGTCACCAGGAAGTTGAGCAAGTCCGGCTCATCCCCCa                                       >  5:327894/1‑135 (MQ=255)                                                                                                                              ttATGCCGCTCGCGAGCATTTTGTGAAGCACATCACAAAAATGGCGCTATCCCTTATCTGGACGAACGAAAGCACCCCGCTCTCAATGGCGGGTGCCGGTCACCAGGAAGTTGAGCAAGTCCGGCTCATCCCCCa                                       <  6:327894/135‑1 (MQ=255)                                                                                                                                  gCCACTCGCGAGCATTTTGTGAAGCACATCACAAAAATGGCGCTATCCCTTATCTGGACGAACGAAAGCACCCCGCTCTCAATGGCGGGTGCCGGTCACCAGGAAGTTGAGCAAGTCCGGCTCATCCCCCAggg                                    <  8:108842/134‑1 (MQ=255)                                                                                                                                  gCCACTCGCGAGCATTTTGTGAAGCACATCACAAAAATGGCGCTATCCCTTATCTGGACGAACGAAAGCACCCCGCTCTCAATGGCGGGTGCCGGTCACCAGGAAGTTGAGCAAGTCCGGCTCATCCCCCAggg                                    >  7:108842/1‑134 (MQ=255)                                                                                                                                         gcgAGCATTTTGTGAAGCACATCACAAAAATGGCGCTATCCCTTATCTGGACGAACGAAAGCACCCCGCTCTCAATGGCGGGTGCCGGTCACCAGGAAGtt                                                              <  6:162925/101‑1 (MQ=255)                                                                                                                                         gcgAGCATTTTGTGAAGCACATCACAAAAATGGCGCTATCCCTTATCTGGACGAACGAAAGCACCCCGCTCTCAATGGCGGGTGCCGGTCACCAGGAAGtt                                                              >  5:162925/1‑101 (MQ=255)                                                                                                                                                     tgAAGCACATCACAAAAATGGCGCTATCCCTTATCTGGACGAACGAAAGCACCCCGCTCTCAATGGCGGGTGCCGGTCACCAGGAAGTTGAGCAAGTCCGGCTCATCCCCCAGGGCGATAGCCTGCGCCGGCCGCGGCAGGCTCGCCAg  <  7:12649/149‑1 (MQ=255)                                                                                                                                                     tgAAGCACATCACAAAAATGGCGCTATCCCTTATCTGGACGAACGAAAGCACCCCGCTCTCAATGGCGGGTGCCGGTCACCAGGAAGTTGAGCAAGTCCGGCTCATCCCCCAGGGCCATAGCCTGCGCCGGCCGCGGCAGGCTCGCCAg  >  5:224655/1‑149 (MQ=255)                                                                                                                                                        |                                                                                                                                                  TCAACAGCCGGTACATGATGTCGGGGTTTGCTGCGAGCGACATGAACTTTACCTGAACCTTCGAAGCGCATGAAAAGGGACCCCGGCAAGCGGCGGCCGGG‑TCTTGGAAAGCGATG‑G‑TGGCATTATGCCGCTCGCGAGCATTTTGTGAAGCACATCACAAAAATGGCGCTATCCCTTATCTGGACGAACGAAAGCACCCCGCTCTCAATGGCGGGTGCCGGTCACCAGGAAGTTGAGCAAGTCCGGCTCATCCCCCAGGGCGATAGCCTGCGCCGGCCGCGGCAGGCTCGCCAG  >  NC_002947/4235022‑4235315

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑