Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	5,650,676	G→T	12.6%	H173N (CAT→AAT) ‡	PP_4959 ←	diguanylate cyclase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	5,650,676	0	G	T	12.6%	146.4 / 11.2	55	H173N (CAT→AAT) ‡	PP_4959	diguanylate cyclase
Reads supporting (aligned to +/- strand):  ref base G (23/25);  new base T (3/4);  total (26/29)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.51e-01

GTAGGCCTTGTAGAAGTCCGACTCGCGCCACAGGCTGGTACTGGTCAGTTGCACAACGTCGAGCAATTGGGTGCCCTGCAGGTGTTGCACCGGTGCCGCCAGCAAACGGGAAATGGCCGGATTGGCAA‑AACGGATGATGCCATGGGCATCAACCACCAGAATGCCTTCGGCGGCATTTTCCAGGATGGACGCATTGAAGGCCCTGGCCGTCTCCAGCTCACGACTCAGCTGCTGCAGCATGCGCCGGTTGCGCTGCTGGTCGAGCAGCGCCTGGACCTTGGGCTTGAG  >  NC_002947/5650533‑5650820                                                                                                                                                 |                                                                                                                                                 gTAGGCCTTGTAGAAGTCCGACTCGCGCCACAGGCTGGTACTGGTCAGTTGCACAACGTCGAGCAATTGGGTGCCCTGCAGGTGTTGCACCGGTGCCGCCAGCAAACGGGAAATGGCCGGATTGGCAA‑AACGGATGATGCCATGGGCAt                                                                                                                                             <  5:51314/149‑1 (MQ=255)    ggCCTTGTATAAGGCCGACTCGCGCCACAGGCTGGTACTGGTCAGTTGCACAACGTCGAGCAATTTGGTGCCCTGCAGGTGTTGCACCGGTGCCGCCAGCAAACGGGAAATGGCCGGATTGGCAA‑AACGGATGATGCCCATGGCATCat                                                                                                                                          <  3:279776/149‑2 (MQ=255)      ccTTGTAGAAGTCCGACTCGCGCCACAGGCTGGTACTGGTCAGTTGCACAACGTCGAGCAATTGGGTGCCCTGCAGGTGTTGCACCGGTGCCGCCAGCAAACGGGAAATGGCCGGATTGGCAA‑AACGGATGATGCCATGGGCATCAac                                                                                                                                         >  5:231293/1‑148 (MQ=255)       cTTGTAGAAGTCCGACTCGCGCCACAGGCTGGTACTGGTCAGTTGCACAACGTCGAGCAATTGGGTGCCCTGCAGGTGTTGCACCGGTGCCGCCAGCAAACGGGAAATGGCCGGATTGGCAA‑AACGGATGATGCCCATGGCATCat                                                                                                                                          <  1:221990/146‑2 (MQ=255)       cTTGTAGAAGTCCGACTCGCGCCACAGGCTGGTACTGGTCAGTTGCACAACGTCGAGCAATTGGGTGCCCTGCAGGTGTTGCACCGGTGCCGCCAGCAAACGGGAAATGGCCGGATTGGCAA‑AACGGATGATGCCCATGGCATCat                                                                                                                                          >  2:221990/1‑145 (MQ=255)       cTTGTAGAAGTCCGACTCGCGCCACAGGCTGGTACTGGTCAGTTGCACAACGACGAGCAATTGCGTGCCCTGCAGGTGTTGCACCGGTGCCGACAGCAAACGGGAAATGGACGCATTGGCAA‑AACGGATGATGCCATGGCCATCAacca                                                                                                                                       >  5:41332/1‑149 (MQ=255)       cTTGTAGAAGTCCGACTCGCGCCACACGCTGGTACTGGTCAGTTGCACAACGTCGAGCAATTGGGTGCCCTGCAGGTGTTGCACCGGTGCCGCCAGCAAACGGGAAATGGCCGGATTGGCAA‑AACGGATGATGCCATGGGCATCAacca                                                                                                                                       >  5:41328/1‑149 (MQ=255)           tAGAAGTCCGACTCGCGCCACAGGCTGGTACTGGTCAGTTGCACAACGTCGAGCAATTGGGTGCCCTGCAGGTGTTGCACCGGTGCCGCCAGCAAACGGGAAATGGCCGGATTGGCAA‑AACGGATGATGCCATGGGCATCAtccgtttt                                                                                                                                   <  5:61583/149‑6 (MQ=255)            aGAAGTCCGACTCGCGCCACAGGCTGGTACTGGTCAGTTGCACAACGTCGAGCAATTGGGTGCCCTGCAGGTGTTGCACCGGTGCCGCCAGCAAACGGGAAATGGCCGGATTGGCAA‑AACGGTTGATGCCCATGGCATCAtccgttttg                                                                                                                                  >  3:229829/1‑143 (MQ=255)             gAAGTCCGACTCGCGCCACAGGCTGGTACTGGTCAGTTGCACAACGTCGAGCAATTGGGTGCCCTGCAGGTGTTGCACCGGTGCCGCCAGCAAACGGGAAATGGCCGGATTGGCAA‑AACGGTTGATGCCCATGGCATCAtccgttttgc                                                                                                                                 <  4:229829/149‑8 (MQ=255)                   cGACTCGCGCCACAGGCTGGTACTGGTCAGTTGCACAACGTCGAGCAATTGGGTGCCCTGCAGGTGTTGCACCGGTGCCGCCAGCAAACGGGAAATGGCCGGATTGGCAA‑AACGGATGATGCCATGGGCATCAACCACCAGAATGCCtt                                                                                                                           >  4:144114/1‑149 (MQ=255)                                  gCTGGTTCTGGTCAGTTGCACAACGTCGAGCTATTGGGTGCCGTGCTGGTGTTGCACCGGTGCCGCCAGCAAACGGGAAATGGCCGGATTGGCAA‑AACGGATGATGCCATGGGCATCAACCACCAGAATGCCTTCGGCGGCATTTTCCa                                                                                                            <  6:41332/149‑1 (MQ=255)                                  gCTGGTACTGGTCAGTTGCACAACGTCGAGCAATTGGGTGCCCTGCAGGTGTTGCACCGGTGCCGCCAGCAAACGGGAAATGGCCGGATTGGCAA‑AACGGATGATGCCATGGGCATCAACCACCAGAATGCCTTCGGCGGCATTTTCCa                                                                                                            <  6:41328/149‑1 (MQ=255)                                     ggTACTGGTCAGTTGCACAACGTCGAGCAATTGGGTGCCCTGCAGGTGTTGCACCGGTGCCGCCAGCAAACGGGAAATGGCCGGATTGGCAA‑AACGGATGATGCCATGGGCATCAACCACCAGAATGCCTTCGGCGGCAGTTTCCAGGa                                                                                                         >  8:282338/1‑149 (MQ=255)                                      gTACTGGTCAGTTGCACAACGTCGAGCAATTGGGTGCCCTGCAGGTGTTGCACCGGTGCCGCCAGCAAACGGGAAATGGCCGGATTGGCAA‑AACGGATGATGCCATGGGCATCAACCACCAGAATGCCTTCGGCGGCATTTTCCAGGAt                                                                                                        >  5:128125/1‑149 (MQ=255)                                       tACTGGTCAGTTGCACAACGTCGAGCAATTGGGTGCCCTGCAGGTGTTGCACCGGTGCCGCCAGCAAACGGGAAATGGCCGGATTGGCAA‑AACGGATGATGCCATGGGCATCAACCACCAGAATGCCTTCGGCGGCATTTTCCAGGATg                                                                                                       <  6:231293/149‑1 (MQ=255)                                            gTCAGTTGCACAACGTCGAGCAATTGGGTGCCCTGCAGGTGTTGCACCGGTGCCGCCAGCAAACGGGAAATGGCCGGATTGGCAA‑AACGGATGATGCCATGGGCATCAaccac                                                                                                                                      <  3:168478/113‑1 (MQ=255)                                            gTCAGTTGCACAACGTCGAGCAATTGGGTGCCCTGCAGGTGTTGCACCGGTGCCGCCAGCAAACGGGAAATGGCCGGATTGGCAA‑AACGGATGATGCCATGGGCATCAaccac                                                                                                                                      >  4:168478/1‑113 (MQ=255)                                            gTCAGTTGCACAACGTCGAGCAATTGGGTGCCCTGCAGGTGTTGCACCGGTGCCGCCAGCAAACGGGAAATGGCCGGATTGGCAA‑AACGGATGATGCCATGGGCATCAACCACCAGAATGCCTTCGGCGGCATTTTCCAGGATGGAc                                                                                                    <  7:138553/147‑1 (MQ=255)                                            gTCAGTTGCACAACGTCGAGCAATTGGGTGCCCTGCAGGTGTTGCACCGGTGCCGCCAGCAAACGGGAAATGGCCGGATTGGCAA‑AACGGATGATGCCATGGGCATCAACCACCAGAATGCCTTCGGCGGCATTTTCCAGGATGGACg                                                                                                   >  8:23844/1‑148 (MQ=255)                                            gTCAGTTGCACAACGTCGAGCAATTGGGTGCCCTGCAGGTGTTGCACCGGTGCCGCCAGCAAACGGGAAATGGCCGGATTGGCAA‑AACGGATGATGCCATGGGCATCAACCACCAGAATGCCTTCGGCGGCATTTTCCAGGATGGACGc                                                                                                  <  1:2557/149‑1 (MQ=255)                                                 ttGCACAACGTCGAGCAATTGGGTGCCCTGCAGGTGTTGCACCGGTGCCGCCAGCAAACGGGAAATGGCCGGATTGGCAA‑AACGGATGATGCCATGGGCATCAACCACCAGAATGCCTTCGGCGGCATTTTCCAGGATGGACGCATTGa                                                                                             <  5:126349/149‑1 (MQ=255)                                                        aCGTCGAGCAATTGGGTGCCCTGCAGGTGTTGCACCGGTGCCGCCAGCAAACGGGAAATGGCCGGATTGGCAA‑AACGGATGATGCCATGGGCATCAACCACCAGAATGCCTTCGGCGGCATTTTCCAGGATGGACGCATTGAAGGCCCt                                                                                      <  8:132657/149‑1 (MQ=255)                                                                            cTGCAGGTGTTGCACCGGTGCCGCCAGCAAACGGGAAATGGCCGGATTGGCAA‑AACGGATGATGCCATGGGCATCAACCACCAGAATGCCTTCGGCGGCATTTTCCAGGATGGACGCATTGAAGGCCCTGGCCGtc                                                                               >  8:259259/1‑136 (MQ=255)                                                                            cTGCAGGTGTTGCACCGGTGCCGCCAGCAAACGGGAAATGGCCGGATTGGCAA‑AACGGATGATGCCATGGGCATCAACCACCAGAATGCCTTCGGCGGCATTTTCCAGGATGGACGCATTGAAGGCCCTGGCCGtc                                                                               <  7:259259/136‑1 (MQ=255)                                                                              gCAGGTGTTGCACCGGTGCCGCCAGCAAACGGGAAATGGCCGGATTGGCAA‑AACGGATGATGCCATGGGCATCAACCACCAGAATGCCTTCGGCGGCATTTTCCAGGATGGACGCATTGAAGGCCCTGGCCGTCTCCAGCTCACGACt                                                                 >  8:15689/1‑148 (MQ=255)                                                                                aGGTGTTGCACCGGTGCCGCCAGCAAACGGGAAATGGCCGGATTGGCAA‑AACGGATGATGCCATGGGCATCAACCACCAGAATGCCTTCGGCGGCATTTTCCAGGATGGACGCATTGAAGGCCCTGGCCGTCTCCAGCTCACGACTCAg                                                              <  6:128125/149‑1 (MQ=255)                                                                                  gtgtTGCACCGGTGCCGCCAGCAAACGGGAAATGGCCGGATTGGCAA‑AACGGATGATGCCATGGGCATCAACCACCAGAATGCCTTCGGCGGCATTTTCCAGGATGGACGCATTGAAGGCCCTGGCCGTCTCCAGCTCACGACTCAgct                                                            >  1:149338/1‑149 (MQ=255)                                                                                    gtTGCACCGGTGCCGCCAGCAAACGGGAAATGGCCGGATTGGCAA‑AACGGATGATGCCATGGGCATCAACCACCAGAATGCCTTCGGCGGCATTTTCCAGGATGGACGCATTGAAGGCCCTGGCCGTCTCCAGCTCACGACTCAgctgc                                                          >  8:207108/1‑149 (MQ=255)                                                                                     ttGCACCGGTGCCGCCAGCAAACGGGAAATGGCCGGATTGGCAAGAACGGATGATGCCATGGGCATCAACCACCAGAATGCCTTCGGCGGCATTTTCCAGGATGGACGCATTGAAGGCCCTGGCCGTCTCCAGCTCACGACTCAgctgc                                                          >  1:66014/1‑149 (MQ=255)                                                                                        cACCGGTGCCGCCAGCAAACGGGAAATGGCCGGATTGGCAA‑AACGGATGATGCCATGGGCATCAACCACCAGAATGCCTTCGGCGGCATTTTCCAGGATGGACGCATTGAAGGCCCTgg                                                                                    >  2:187489/1‑119 (MQ=255)                                                                                        cACCGGTGCCGCCAGCAAACGGGAAATGGCCGGATTGGCAA‑AACGGATGATGCCATGGGCATCAACCACCAGAATGCCTTCGGCGGCATTTTCCAGGATGGACGCATTGAAGGCCCTgg                                                                                    <  1:187489/119‑1 (MQ=255)                                                                                         aCCGGTGCCGCCAGCAAACGGGAAATGGCCGGATTGGCAA‑AACGGATGATGCCATGGGCATCAACCACCAGAATGCCTTCGGCGGCATTTTCCAGGAt                                                                                                        >  5:93046/1‑98 (MQ=255)                                                                                         aCCGGTGCCGCCAGCAAACGGGAAATGGCCGGATTGGCAA‑AACGGATGATGCCATGGGCATCAACCACCAGAATGCCTTCGGCGGCATTTTCCAGGAt                                                                                                        <  6:93046/98‑1 (MQ=255)                                                                                            ggTGCCGCCAGCAAACGGGAAATGGCCGGATTGGCAA‑AACGGATGATGCCATGGGCATCAACCACCAGAATGCCTTCGGCGGCATTTTCCAGGATGGACGCATTGAAGGCCCTGGCCGTCTCCAGCTCACGACTCAGCTGCTGCAGCAt                                                  <  3:144114/149‑1 (MQ=255)                                                                                                     aGCAAACGGGAAATGGCCGGATTGGCAA‑AACGGATGATGCCATGGGCATCAACCACCAGAATGCCTTCGGCGGCATTTTCCAGGATGGACGCATTGAAGGCCCTGGCCGTCTCCAGCTCACGACTCAGCTGCTGCAGCATGCGCCGGtt                                         <  7:23844/149‑1 (MQ=255)                                                                                                      gCAAACGGGAAATGGCCGGATTGGCAA‑AACGGATGATGCCATGGGCATCAACCACCAGAATGCCTTCGGCGGCATTTTCCAGGATGGACGCATTGAAGGCCCTGGCCGTCTCCAGCTCACGa                                                                   <  1:75957/122‑1 (MQ=255)                                                                                                      gCAAACGGGAAATGGCCGGATTGGCAA‑AACGGATGATGCCATGGGCATCAACCACCAGAATGCCTTCGGCGGCATTTTCCAGGATGGACGCATTGAAGGCCCTGGCCGTCTCCAGCTCACGa                                                                   >  2:75957/1‑122 (MQ=255)                                                                                                            gggAAATGGCCGGATTGGCAA‑AACGGATGATGCCATGGGCATCAACCACCAGAATGCCTTCGGCGGCATTTTCCAGGATGGACGCATTGAAGGCCCTGGCCGTCTCCAGCTCACGACTCAGCTGCTGCAGCATGCGCCGGTTGCgctgc                                  <  7:15689/149‑1 (MQ=255)                                                                                                            gggAAATGGCCGGATTGGCAA‑AACGGATGATGCCATGGGCATCAACCACCAGAATGCCTTCGGCGGCATTTTCCAGGATGGACGCATTGAAGGCCCTGGCCGTCTCCAGCTCACGACTCAGCTGCTGCAGCATGCGCCGGTTGCgctgc                                  >  1:79140/1‑149 (MQ=255)                                                                                                                aaTGGCCGGATTGGCAA‑AACGGATGATGCCATGGGCATCAACCACCAGAATGCCTTCGGCGGCATTTTCCAGGATGGACGCATTGAAGGCCCTGGCCGTCTCCAGCTCACGACTCAGCTGCTGCAGCATGCGCCGGTTGCGCTGCTGGt                              >  6:106228/1‑149 (MQ=255)                                                                                                                      cGGATTGGCAA‑AACGGATGATGCCATGGGCATCAACCACCAGAATGCCTTCGGCGGCATTTTCCAGGATGGACGCATTGAAGGCCCTGGCCGTCTCCAGCTCACGACTCAGCTGCTGCAGCATGCGCCGGTTGCGCTGCTGGTCGagca                        <  2:79140/149‑1 (MQ=255)                                                                                                                                  aaCGGATGATGCCATGGGCATCAACCACCAGAATGCCTTCGGCGGCATTTTCCAGGATGGACGCATTGAAGGCCCTGGCCGTCTCCAGCTCACGACTCAGCTGCTGCAGCATGCGCCGGTTGCGCTGCTGGTCGag                          >  7:150365/1‑136 (MQ=255)                                                                                                                                  aaCGGATGATGCCATGGGCATCAACCACCAGAATGCCTTCGGCGGCATTTTCCAGGATGGACGCATTGAAGGCCCTGGCCGTCTCCAGCTCACGACTCAGCTGCTGCAGCATGCGCCGGTTGCGCTGCTGGTCGag                          <  8:150365/136‑1 (MQ=255)                                                                                                                                   aCGGATGATGCCATGGGCATCAACCACCAGAATGCCTTCGGCGGCATTTTCCAGGATGGACGCATTGAAGGCCCTGGCCGTCTCCAGCTCACGACTCAGCTGCTGCAGCATGCGCCGGTTGCGCTGCTGGTCGAGCAGCGCCTGGACCt            <  4:84021/149‑1 (MQ=255)                                                                                                                                   aCGGATGATGCCATGGGCATCAACCACCAGAATGCCTTCGGCGGCATTTTCCAGGATGGACGCATTGAAGGCCCTGGCCGTCTCCAGCTCACGACTCAGCTGCTGCAGCATGCGCCGGTTGCGCTGCTGGTCGAGCAGCGCCTGGACCt            <  7:282338/149‑1 (MQ=255)                                                                                                                                      gttgatgCCCATGGCATCATCCACCAGAATGCCTTCGGCGGCATTTTCCAGGATGGACGCATTGAAGGCCCTGGCCGTCTCCAGCTCACGACTCAGCTGCTGCAGCATGCGCCGGTTGCGCTGCTGGTCGAGCAGCGCCTg                 <  4:197796/139‑1 (MQ=255)                                                                                                                                      gttgatgCCCATGGCATCATCCACCAGAATGCCTTCGGCGGCATTTTCCAGGATGGACGCATTGAAGGCCCTGGCCGTCTCCAGCTCACGACTCAGCTGCTGCAGCATGCGCCGGTTGCGCTGCTGGTCGAGCAGCGCCTg                 >  3:197796/3‑141 (MQ=255)                                                                                                                                            gCCATGGGCATCAACCACCAGAATGCCTTCGGCGGCATTTTCCAGGATGGACGCATTGAAGGCCCTGGCCGTCTCCAGCTCACGACTCAGCTGCTGCAGCATGCGCCGGTTGCGCTGCTGGTCGAGCAGCGCCTGGACCTTGGGCtt     >  2:310723/1‑147 (MQ=255)                                                                                                                                             ccATGGGCATCAACCACCAGAATGCCTTCGGCGGCATTTTCCAGGATGGACGCATTGAAGGCCCTGGCCGTCTCCAGCTCACGACTCAGCTGCTGCAGCATGCGCCGGTTGCGCTGCTGGTCGAGCAGCGCCTGGACCTTGGGCTTGa   <  7:207108/148‑1 (MQ=255)                                                                                                                                              cATGGGCATCAACCACCAGAATGCCTTCGGCGGCATTTTCCAGGATGGACGCATTGAAGGCCCTGGCCGTCTCCAGCTCACGACTCAGCTGCTGCAGCATGCGCCgg                                           >  4:167158/1‑107 (MQ=255)                                                                                                                                              cATGGGCATCAACCACCAGAATGCCTTCGGCGGCATTTTCCAGGATGGACGCATTGAAGGCCCTGGCCGTCTCCAGCTCACGACTCAGCTGCTGCAGCATGCGCCgg                                           <  3:167158/107‑1 (MQ=255)                                                                                                                                              cATGGGCATCAACCACCAGAATGCCTTCGGCGGCATTTTCCAGGATGGACGCATTGAAGGCCCTGGCCGTCTCCAGCTCACGACTCAGCTGCTGCAGCATGCGCCGGTTGCGCTGCTGGTCGa                           <  7:186427/123‑1 (MQ=255)                                                                                                                                              cATGGGCATCAACCACCAGAATGCCTTCGGCGGCATTTTCCAGGATGGACGCATTGAAGGCCCTGGCCGTCTCCAGCTCACGACTCAGCTGCTGCAGCATGCGCCGGTTGCGCTGCTGGTCGa                           >  8:186427/1‑123 (MQ=255)                                                                                                                                              cATGGGCATCAACCACCAGAATGCCTTCGGCGGCATTTTCCAGGATGGACGCATTGAAGGCCCTGGCCGTCTCCAGCTCACGACTCAGCTGCTGCAGCATGCGCCGGTTGCGCTGCTGGTCGAGCAGCGCCTGGACCTTGGGCTTGAg  >  7:114706/1‑148 (MQ=255)                                                                                                                                                 |                                                                                                                                                 GTAGGCCTTGTAGAAGTCCGACTCGCGCCACAGGCTGGTACTGGTCAGTTGCACAACGTCGAGCAATTGGGTGCCCTGCAGGTGTTGCACCGGTGCCGCCAGCAAACGGGAAATGGCCGGATTGGCAA‑AACGGATGATGCCATGGGCATCAACCACCAGAATGCCTTCGGCGGCATTTTCCAGGATGGACGCATTGAAGGCCCTGGCCGTCTCCAGCTCACGACTCAGCTGCTGCAGCATGCGCCGGTTGCGCTGCTGGTCGAGCAGCGCCTGGACCTTGGGCTTGAG  >  NC_002947/5650533‑5650820

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: ‑