Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	448,523	Δ1 bp	7.7%	coding (1102/1284 nt)	PP_0369 →	diguanylate cyclase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	448,523	0	G	.	7.7%	165.3 / 6.9	52	coding (1102/1284 nt)	PP_0369	diguanylate cyclase
Reads supporting (aligned to +/- strand):  ref base G (28/20);  new base . (2/2);  total (30/22)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.26e-01

GGTGTTCGCCGGCAAGACCGCCGCGGAATGCGTGCCGCATGTGGAAGCCGTGCGTGAAGTGATCGCCAATTACGTGATGCACCTGCGCGATCAGCACAACCGCCCGCAGGACGATAC‑CGCCGG‑GC‑GCCAGCGCCGG‑GCTGGCAGCGCCGGCGGCACGGTCTCGGTCACCATCAGTATCGGCGTGGCCGAGCGCCAGGCCGATCATCGCAACCCCGAGGCGGTGCTGAAATCCGCCGACCAGGCGCTTTACAGTGCCAAAGGCGCGGGGCGCAATTGTGT  >  NC_002947/448378‑448656                                                                                                                                                      |                                                                                                                                      gccccgcgcctttggcactgtaaagcgcctggtcggcggatttcagcaccgcctcggggttgcgatgatcggcctggcgctcggccacgccgatactgatggtgaccgagaccgTGC‑CGCCGG‑GC‑GCCAGCGCCGG‑GCTGGCAGCGCcg                                                                                                                                    >  4:193474‑M1/115‑149 (MQ=255)  gtgtTCGCCGGCAAGACCGCCGCGGAATGCGTGCCGCATGTGGAAGCCGTGCGTGAAGTGATCGCCAATTACGTGATGCACCTGCGCGATCAGCACAACCGCCCGCAGGACGATAC‑CGCCGG‑GC‑GCCAGCGCCGG‑GCTGGCAGCGCcgg                                                                                                                                   >  8:13462/1‑149 (MQ=255)     ttCGCCGGCAAGACCGCCGCGGAATGCGTGCCGCATGTGGAAGCCGTGCGTGAAGTGATCGCCAATTACGTGATGCACCTGCGCGATCAGCACAACCGCCCGCAGGACGATAC‑CGCCGG‑GC‑GCCAGCGCCGG‑GCTGGCAGCGCcggcgg                                                                                                                                <  1:108497/149‑1 (MQ=255)     ttCGCCGGCAAGACCGCCGCGGAATGCGTGCCGCATGTGGAAGCCGTGCGTGAAGTGATCGCCAATTACGTGATGCACCTGCGCGATCAGCACAACCGCCCGCAGGACGATAC‑CGCCGG‑GC‑GCCAGCGCCGG‑GCTGGCAGCGCcggcgg                                                                                                                                >  8:19020/1‑149 (MQ=255)         ccGGCAAGACCGCCGCGGAATGCGTGCCGCATGTGGAAGCCGTGCGTGAAGTGATCGCCAATTACGTGATGCACCTGCGCGATCAGCACAACCGCCCGCAGGACGATAC‑CGCCGG‑GC‑GCCAGCGCCGG‑GCTGGCAGCGCCGGCGGCACg                                                                                                                            >  5:119402/1‑149 (MQ=255)              aaGACCGCCGCGGAATGCGTGCCGCATGTGGAAGCCGTGCGTGAAGTGATCGCCAATTACGTGATGCACCTGCGCGATCAGCACAACCGCCCGCAGGACGATAC‑CGCCGG‑GC‑GCCAGCGCCGG‑GCTGGCAGCGCCGGCGGCACGGtctc                                                                                                                       >  5:250090/1‑149 (MQ=255)               aGACCGCCGCGGAATGCGTGCCGCATGTGGAAGCCGTGCGTGAAGTGATCGCCAATTACGTGATGCACCTGCGCGATCAGCACAACCGCCCGCAGGACGATAC‑CGCCGG‑GC‑GCCAGCGCCGG‑GCTGGCAGCGCCGGCGGCACGGTCTCg                                                                                                                      <  2:226095/149‑1 (MQ=255)                   cgccgcGGAATGCGTGCCGCATGTGGAAGCCGTGCGTGAAGTGATCGCCAATTACGTGATGCACCTGCGCGATCAGCACAACCGCCCGCAGGACGATAC‑CGCCGG‑GC‑GCCAGCGCCGG‑GCTGGCAGCGCCGGCGGCACGGTCTCGGTCa                                                                                                                  >  5:235096/1‑149 (MQ=255)                               cGTGCCGCATGTGGAAGCCGTGCGTGAAGTGATCGCCAATTACGTGATGCACCTGCGCGATCAGCACAACCGCCCGCAGGACGATAC‑CGCCGG‑GC‑GCCAGCGCCGG‑GCTGGCAGCGCCGGCGGCACGGTCTCGGTCACCATCAGTATc                                                                                                       <  1:62959/148‑1 (MQ=255)                                gTGCCGCATGTGGAAGCCGTGCGTGAAGTGATCGCCAATTACGTGATGCACCTGCGCGATCAGCACAACCGCCCGCAGGACGATAC‑CGCCGG‑GC‑GCCAGCGCCGG‑GCTGGCAGCGCCGGCGGCACGGtctc                                                                                                                       <  5:205601/131‑1 (MQ=255)                                gTGCCGCATGTGGAAGCCGTGCGTGAAGTGATCGCCAATTACGTGATGCACCTGCGCGATCAGCACAACCGCCCGCAGGACGATAC‑CGCCGG‑GC‑GCCAGCGCCGG‑GCTGGCAGCGCCGGCGGCACGGtctc                                                                                                                       >  6:205601/1‑131 (MQ=255)                                 tGCCGCATGTGGAAGCCGTGCGTGAAGTGATCGCCAATTACGTGATGCACCTGCGCGATCAGCACAACCGCCCGCAGGACGATAC‑CGCCGG‑GC‑GCCAGCGCCGG‑GCTGGCAGCGCCGGCGGCACGGTCTCGGTCACCATCAGTATCGGc                                                                                                    <  7:19020/149‑1 (MQ=255)                                  gCCGCATGTGGAAGCCGTGCGTGAAGTGATCGCCAATTACGTGATGCACCTGCGCGATCAGCACAACCGCCCGCAGGACGATAC‑CGCCGG‑GC‑GCCAGCGCCGG‑GCTGGCAGCGCCGGCGGCACGGTCTCGGTCACCATCAGTATCGGCg                                                                                                   >  4:52679/1‑149 (MQ=255)                                   ccGCATGTGGAAGCCGTGCGTGAAGTGATCGCCAATTACGTGATGCACCTGCGCGATCAGCACAACCGCCCGCAGGACGATAC‑CGCCGG‑GC‑GCCAGCGCCGG‑CCTGGCAGCGCCCGCGGCACGGTCTCCGTCACCATCAGTAACGGCGt                                                                                                  >  7:300645/1‑149 (MQ=255)                                       aTGTGGAAGCCGTGCGTGAAGTGATCGCCAATTACGTGATGCACCTGCGCGATCAGCACAACCGCCCGCAGGACGATAC‑CGCAGG‑GC‑GCCAGCGCCGG‑GCTGGCAGCGCCGGCGGCACGGTCTCGGTCACCATCAGTATCGGCGTGGcc                                                                                              <  6:235096/149‑1 (MQ=255)                                            gAAGCCGTGCGTGAAGTGATCGCCAATTACGTGATGCACCTGCGCGATCAGCACAACCGCCCGCAGGACGATAC‑CGCCGG‑GC‑GCCAGCGCCGG‑GCTGGCAGCGCCGGCGGCACGGTCTCGGTCACCATCAGTATCGGCGTGGCCGAgcg                                                                                         >  3:78961/1‑149 (MQ=255)                                            gAAGCCGTGCGTGAAGTGATCGCCAATTACGTGATGCACCTGCGCGATCAGCACAACCGCCCGCAGGACGATAC‑CGCCGG‑GC‑GCCAGCGCCGG‑GCTGGCAGCGCCGGCGGCACGGTCTCGGTCACCATCAGTATCGGCGTGGCCGAgcg                                                                                         >  7:107947/1‑149 (MQ=255)                                             aaGCCGTGCGTGAAGTGATCGCCAATTACGTGATGCACCTGCGCGATCAGCACAACCGCCCGCAGGACGATAC‑CGCCGG‑GC‑GCCAGCGCCGG‑GCTGGCAGCGCCGGCGGCACGGTCTCGGTCACCATCAGTATCGGCGTGGCCGAgcgc                                                                                        <  3:52679/149‑1 (MQ=255)                                                      gtgAAGTGATCGCCAATTACGTGATGCACCTGCGCGATCAGCACAACCGCCCGCAGGACGATAC‑CGCCGG‑GC‑GCCAGCGCCGG‑GCTGGCAGCGCCGGCGGCACGGTCTCGGTCACCATCAGTATCGGCGTGGCCGAGCGCCAGGCCGat                                                                               <  3:299896/149‑1 (MQ=255)                                                          aGTGATCGCCAATTACGTGATGCACCTGCGCGATCAGCACAACCGCCCGCAGGACGATAC‑CGCCGG‑GC‑GCCAGCGCCGG‑GCTGGCAGCGCCGGCGGCACGGTCTCGGTCACCATCAGTATCGGCGTGGCCGAGCGCCAGGCCGatcatc                                                                           <  8:185056/149‑1 (MQ=255)                                                                cGCCAATTACGTGATGCACCTGCGCGATCAGCACAACCGCCCGCAGGACGATAC‑CGCCGG‑GC‑GCCAGCGCCGG‑GCTGGCAGCGCCGGCGGCACGGTCTCGGt                                                                                                                    >  8:137004/1‑102 (MQ=255)                                                                cGCCAATTACGTGATGCACCTGCGCGATCAGCACAACCGCCCGCAGGACGATAC‑CGCCGG‑GC‑GCCAGCGCCGG‑GCTGGCAGCGCCGGCGGCACGGTCTCGGt                                                                                                                    <  7:137004/102‑1 (MQ=255)                                                                     aTTACGTGATGCACCTGCGCGATCAGCACAACCGCCCGCAGGACGATAC‑CGCCGG‑GC‑GCCAGCGCCGG‑GCTGGCAGCGCCGGCGGCACGGTCTCGGTCACCATCAGTATCGGCGTGGCCGAGCGCCAGGCCGATCATCGCAACCCCGAg                                                                <  6:119402/149‑1 (MQ=255)                                                                      ttACGTGATGCACCTGCGCGATCAGCACAACCGCCCGCAGGACGATAC‑CGCCGG‑GC‑GCCAGCGCCGG‑GCTGGCAGCGCcggcg                                                                                                                                 <  7:5254/83‑1 (MQ=255)                                                                      ttACGTGATGCACCTGCGCGATCAGCACAACCGCCCGCAGGACGATAC‑CGCCGG‑GC‑GCCAGCGCCGG‑GCTGGCAGCGCcggcg                                                                                                                                 >  8:5254/1‑83 (MQ=255)                                                                          gTGATGCACCTGCGCGATCAGCACAACCGCCCGCAGGACGATAC‑CGCCGG‑GC‑GCCAGCGCCGG‑GCTGGCAGCGCCGGCGGCACGGTCTCGGTCACCATCAGTATCGGCGTGGCCGAGCGCCAGGCCGATCATCGCAACCCCGCGGCGGt                                                           >  5:199367/1‑149 (MQ=255)                                                                                    tGCGCGATCAGCACAACCGCCCGCAGGACGATAC‑CGCCGG‑GC‑GCCAGCGCCGG‑GCTGGCAGCGCCGGCGGCACGGTCTCGGTCACCATCAGTATCGGCGTGGCCGAGCGCCAGGCCGATCATCGCAACCCCGAGGCGGTGCTGAAATcc                                                 >  1:300703/1‑149 (MQ=255)                                                                                      cgcgATCAGCACAACCGCCCGCAGGACGATAC‑CGCCGG‑GC‑GCCAGCGCCGG‑GCTGGCAGCGCCGGCGGCACGGTCTCGGTCACCATCAGTATCGGCGTGGCCGAGCGCCAGGCCGATCATCGCAACCCCGAGGCGGTGCTGAAATccgc                                               >  8:161731/1‑149 (MQ=255)                                                                                            cAGCACAACCGCCCGCAGGACGATACGCGCCGG‑GC‑GCCAGCGCCGG‑GCTGGCAGCGCCGGCGGCACGGTCTCGGTCACCATCAGTATCGGCGTGGCCGAGCGCCAGGCCGATCATCGCAACCCCGAGGCGGTGCTGAAATCCGCCGAc                                           >  1:2981/1‑148 (MQ=255)                                                                                              gCACAACCGCCCGCAGGACGATAC‑CGCCGG‑GC‑GCCAGCGCCGG‑GCTGGCAGCGCCGGCGGCACGGTCTCGGTCACCATCAGTATCGGCGTGGCCGAGCGCCAGGCCGATCATCGCAACCCCGAGGCCGGGCTGTAATCCGCCGGCCAgg                                       >  8:225367/1‑149 (MQ=255)                                                                                                 tgatggtgaccgagaccgTGC‑CGCCGGCGCTGCCAGCCCGGC‑GCTGGC‑GC‑CCGGCGGTACGGTCTCGGTCACCATCAGTATCGGCGTGGCCGAGCGCCAGGCCGATCATCGCAACCCCGAGGCGGTGCTGAAATCCGCCGACCAGgcgc                                    <  6:96009‑M1/131‑1 (MQ=255)                                                                                                  aaCCGCCCGCAGGACGATAC‑CGCCGG‑GC‑GCCAGCGCCGG‑GCTGGCAGCGCCGGCGGCACGGTCTCGGTCACCATCAGTATCGGCGTGGCCGAGCGCCAGGCCGATCATCGCAACCCCGAGGCGGTGCTGAAATCCGCCGACCAGGCGCt                                   >  4:277963/1‑149 (MQ=255)                                                                                                         cgcAGGACGATAC‑CGCCGG‑GC‑GCCAGCGCCGG‑GCTGGCAGCGCCGGCGGCACGGTCTCGGTCACCATCAGTATCGGCGTGGCCGAGCGCCAGGCCGATCATCGCAACCCCGAGGCGGTGCTGAAATCCGCCGACCAGGCGCTTTa                                <  3:252656/145‑1 (MQ=255)                                                                                                         cgcAGGACGATAC‑CGCCGG‑GC‑GCCAGCGCCGG‑GCTGGCAGCGCCGGCGGCACGGTCTCGGTCACCATCAGTATCGGCGTGGCCGAGCGCCAGGCCGATCATCGCAACCCCGAGGCGGTGCTGAAATCCGCCGACCAGGCGCTTTa                                >  4:252656/1‑145 (MQ=255)                                                                                                          gcAGGACGATAC‑CGCCGG‑GC‑GCCAGCGCCGG‑GCTGGCAGCGCCGGCGGCACGGTCTCGGTCACCATCAGTATCGGCGTGGCCGAgcgc                                                                                        <  6:232223/88‑1 (MQ=255)                                                                                                          gcAGGACGATAC‑CGCCGG‑GC‑GCCAGCGCCGG‑GCTGGCAGCGCCGGCGGCACGGTCTCGGTCACCATCAGTATCGGCGTGGCCGAgcgc                                                                                        >  5:232223/1‑88 (MQ=255)                                                                                                           cgagaccgTGC‑CGCCGGCGCTGCCAGCCCGGC‑GCTGGC‑GC‑CCGGCGGTACGGTCTCGGTCACCATCAGTATCGGCGTGGCCGAGCGCCAGGCCGATCATCGCAACCCCGAGGCGGTGCTGAAATCCGCCGACCAGGCGCTTTAc                               >  4:71038‑M1/9‑144 (MQ=255)                                                                                                           cgagaccgTGC‑CGCCGGCGCTGCCAGCCCGGC‑GCTGGC‑GC‑CCGGCGGTACGGTCTCGGTCACCATCAGTATCGGCGTGGCCGAGCGCCAGGCCGATCATCGCAACCCCGAGGCGGTGCTGAAATCCGCCGACCAGGCGCTTTAc                               <  3:71038‑M1/136‑1 (MQ=255)                                                                                                              gACGATAC‑CGCCGG‑GC‑GCCAGCGCCGG‑GCTGGCGGCGCCGGCGGCACGGTCTCGGTCACCATAAGTATCGGCGTGGCCGAGCGCCAGGCCGATCATCGCAACCCCCCGGCGGTGCTGAAATACGCCGCCCAGGCGCGTTACAGTGCCa                        >  8:198637/1‑148 (MQ=255)                                                                                                              gACGATAC‑CGCCGG‑GC‑GCCAGCGCCGG‑GCTGGCAGCGCCGGCGGCACGGTCTCGGTCACCATCAGTATCGGCGTGGCCGAGCGCCAGGCCGatcatc                                                                           >  5:214270/1‑97 (MQ=255)                                                                                                              gACGATAC‑CGCCGG‑GC‑GCCAGCGCCGG‑GCTGGCAGCGCCGGCGGCACGGTCTCGGTCACCATCAGTATCGGCGTGGCCGAGCGCCAGGCCGatcatc                                                                           <  6:214270/97‑1 (MQ=255)                                                                                                                   TAC‑CGCCGG‑GC‑GCCAGCGCCGG‑GCTGGCAGCGCCGGCGGCACGGTCTCGGTCACCATCAGTATCGGCGTGGCCGAGCGCCAGGCCGATCATCGCAACCCCGAGGCGGTGCTGAAATCCGCCGACCAGGCGCTTTACAGTGCCAAGGgcg                  >  7:161731‑M1/1‑149 (MQ=255)                                                                                                                   TAC‑CGCCGG‑GC‑GCCAGCGCCGG‑GCTGGCAGCGCCGGCGGCACGGTCTCGGTCACCATCAGTATCGGCGTGGCCGAGCGCCAGGCCGATCATCGCAACCCCGAGGCGGTGCTGAAATCCGCCGACCAGGCGCTTTACAGTGCCAAAGgcg                  <  5:98795‑M1/149‑1 (MQ=255)                                                                                                                     c‑cgccgG‑GC‑GCCAGCGCCGG‑GCTGGCAGCGCCGGCGGCACGGTCTCGGTCACCATCAGTATCGGCGTGGCCGAGCGCCAGGCCGATCATCGCAACCCCGAGGCGGTGCTGAAATCCGCCGACCAGGCGCTTTACAGTGCCAAAGGcgcg                >  4:31678/1‑149 (MQ=255)                                                                                                                        gccgG‑GT‑GCCCGCGCCTG‑TCTGGCCTCGCCGGCGGCACTGTCTCGGTCACCATCCTTATCGGCGTGGCCGAGCGCCAGGCCGATCATCTCAACCCCCAGGCGGTGCTGAAATCCGCCGACCAGGCGCTTTACAGTGCCAAAGGCGCggg              <  8:45476/149‑1 (MQ=255)                                                                                                                                 gcCAGCGCCGG‑GCTGGCAGCGCCGGCGGCACGGTCTCGGTCACCATCAGTATCGGCGTGGCCGAGCGCCAGGCCGATCATCGCAACCCCGAGGCGGTGCTGAAATCCGCCGACCAGGCGCTTTACAGTGCCAAAGGCGCGGGGCGCAAt       <  3:31678/149‑1 (MQ=255)                                                                                                                                   cAGCGCCGG‑GCTGGCAGCGCCGGCGGCACGGTCTCGGTCACCATCAGTATCGGCGTGGCCGAGCGCCAGGCCGATCATCGCAACCCCGAGGCGGTGCTGAAATCCGCCGACCAGGCGCTTTACAGTGCCAAAGGCGCGGGGCGCAATtg     <  4:78961/149‑1 (MQ=255)                                                                                                                                   cAGCGCCGG‑GCTGGCAGCGCCGGCGGCACGGTCTCGGTCACCATCAGTATCGGCGTGGCCGAGCGCCAGGCCGATCATCGCAACCCCGAGGCGGTGCTGAAATCCGCCGACCAGGCGCTTTACAGTGCCAAAGGCGCGGGGCGCAATtg     >  6:93504/1‑149 (MQ=255)                                                                                                                                    aGCGCCGG‑GCTGGCAGCGCCGGCGGCACGGTCTCGGTCACCATCAGTATCGGCGTGGCCGAGCGCCAGGCCGATCATCGCAACCCCGAGGCGGTGCTGAAATCCGCCGACCAGGCGCTTTACAGTGCCAACGGCGCGGGGCGCAATtgt    <  7:13462/149‑1 (MQ=255)                                                                                                                                      cgcCGGCGCTGCCAGC‑CCGGCGGCACGGTCTCGGTCACCATCAGTATCGGCGTGGCCGAGCGCCAGGCCGATCATCGCAACCCCGAGGCGGTGCTGAAATCCGCCGACCAGGCGCTTTACAGTGCCAAAGGCGCGGGGCGCAATTgtgt  >  6:137112/1‑149 (MQ=255)                                                                                                                                        ccGG‑GCTGGCAGCGCCGGCGGCACGGTCTCGGTCACCATCAGTATCGGCGTGGCCGAGCGCCAGGCCGATCATCGCAACCCCGAGGCGGTGCTg                                                       >  4:191697/1‑94 (MQ=255)                                                                                                                                        ccGG‑GCTGGCAGCGCCGGCGGCACGGTCTCGGTCACCATCAGTATCGGCGTGGCCGAGCGCCAGGCCGATCATCGCAACCCCGAGGCGGTGCTg                                                       >  4:187757/1‑94 (MQ=255)                                                                                                                                                      |                                                                                                                                      GGTGTTCGCCGGCAAGACCGCCGCGGAATGCGTGCCGCATGTGGAAGCCGTGCGTGAAGTGATCGCCAATTACGTGATGCACCTGCGCGATCAGCACAACCGCCCGCAGGACGATAC‑CGCCGG‑GC‑GCCAGCGCCGG‑GCTGGCAGCGCCGGCGGCACGGTCTCGGTCACCATCAGTATCGGCGTGGCCGAGCGCCAGGCCGATCATCGCAACCCCGAGGCGGTGCTGAAATCCGCCGACCAGGCGCTTTACAGTGCCAAAGGCGCGGGGCGCAATTGTGT  >  NC_002947/448378‑448656

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: ‑