Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,505,308:1	+G	10.2%	coding (377/1074 nt)	PP_3103 ←	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,505,308	1	.	G	10.2%	176.0 / 15.8	49	coding (377/1074 nt)	PP_3103	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base . (23/21);  new base G (2/3);  total (25/24)
Fisher's exact test for biased strand distribution p-value = 6.67e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.29e-01

GATCGGGTAGTGGTCGCAATGGCTCCGGTTGCGCTTGTGCACGAGAGATCGGTGTGGCCTCTTTGGGCTGCAACTCCGGCTGCGCCAACAGTTTCTGCTCATTCTTCGCCAACCAGGCCGCCAGCTGCTTGTTGGAGATCTCGGCCTGCA‑GCCGAGCGCTCCGGGCGGCAATGCTTTCCATGCTGCTCATGACGCCGGCCTTCATCTGCCCCCGAGTAAGGTAGGTGACGATGGCTGTCAGTAACAGCAGCACCAACTGCTCCTGCCCGCGAGCAAGCTGGCGTGCAGCGCG  >  NC_002947/3505159‑3505450                                                                                                                                                       |                                                                                                                                               gATCGGGTAGTGGTCGCAATGGCTCCGGTTGCGCTTGTGCACGAGAGATCGGTGTGGCCTCTTTGGGCTGCAACTCCGGCTGCGCCAACAGTTTCTGCTCATTCTTCGCCAACCAGGCCGCCAGCTGCTTGTTGGAGATCTCGGCCTGCa                                                                                                                                                 >  2:649626/1‑150 (MQ=255)  aTCGGGTAGTGGTCGCAATGGCTCCGGTTGCGCTTGTGCACGAGAGATCGGTGTGGCCTCTTTGGGCTGCAACTCCGGCTGCGCCAACAGTTTCTGCTCATTCTTCGCCAACCAGGCCGCCAGCTGCTTGTTGGAGATCTCGGCCTGCA‑g                                                                                                                                               >  1:707599/1‑150 (MQ=255)   tCGGGTAGTGGTCGCAATGGCTCCGGTTGCGCTTGTGCACGAGAGATCGGTGTGGCCTCTTTGGGCTGCAACTCCGGCTGCGCCAACAGTTTCTGCTCATTCTTCGCCAACCAGGCCGCCAGCTGCTTGTTGGAGATCTCGGCCTGCA‑Gc                                                                                                                                              >  2:1126197/1‑150 (MQ=255)        tAGTGGTCGCAATGGCTCCGGTTGCGCTTGTGCACGAGAGATCGGTGTGGCCTCTTTGGGCTGCAACTCCGGCTGCGCCAACAGTTTCTGCTCATTCTTCGCCAACCAGGCCGCCAGCTGCTTGTTGGAGATCTCGGCCTGCA‑GCCGAgc                                                                                                                                         <  2:1079555/150‑1 (MQ=255)         ggTGGTCGCAATGGCGGCGGGTGCGCTTGTGCACGAGAGATCGGTGTGGCCTCTTTGGGCTGCAACTCCGGCTGCGCCAACAGTTTCTGCTCATTCTTCGCCAACCAGGCCGCCAGCTGCTTGTTGGAGATCTCGG‑CTGCAGGCCGAgat                                                                                                                                        <  2:308218/149‑3 (MQ=255)             gTCGCAATGGCTCCGGTTGCGCTTGTGCACGAGAGATCGGTGTGGCCTCTTTGGGCTGCAACTCCGGCTGCGCCAACAGTTTCTGCTCATTCTTCGCCAACCAGGCCGCCAGCTGCTTGTTGGAGATCTCGGCCTGCA‑GCCGa                                                                                                                                           <  2:64299/143‑1 (MQ=255)             gTCGCAATGGCTCCGGTTGCGCTTGTGCACGAGAGATCGGTGTGGCCTCTTTGGGCTGCAACTCCGGCTGCGCCAACAGTTTCTGCTCATTCTTCGCCAACCAGGCCGCCAGCTGCTTGTTGGAGATCTCGGCCTGCA‑GCCGa                                                                                                                                           >  1:64299/1‑143 (MQ=255)             gTCGCAATGGCTCCGGTTGCGCTTGTGCACGAGAGATCGGTGTGGCCTCTTTGGGCTGCAACTCCGGCTGCGCCAACAGTTTCTGCTCATTCTTCGCCAACCAGGCCGCCAGCTGCTTGTTGGAGATCTCGGCCTGCA‑GCCGAGCGCTcc                                                                                                                                    >  1:302594/1‑150 (MQ=255)              tCGCAATGGCTCCGGTTGCGCTTGTGCACGAGAGATCGGTGTGGCCTCTTTGGGCTGCAACTCCGGCTGCGCCAACAGTTTCTGCTCATTCTTCGCCAACCAGGCCGCCAGCTGCTTGTTGGAGATCTCGGCCTGCA‑GCCGAGCGCTCCg                                                                                                                                   >  1:265327/1‑150 (MQ=255)               cGCAATGGCTCCGGTTGCGCTTGTGCACGAGAGATCGGTGTGGCCTCTTTGGGCTGCAACTCCGGCTGCGCCAACAGTTTCTGCTCATTCTTCGCCAACCAGGCCGCCAACTGCTTGTTGGAGATCTCGGCCTGCA‑GCCGAGCGCTCCgg                                                                                                                                  <  1:829062/150‑1 (MQ=255)                  aaTGGCTCCGGTTGCGCTTGTGCACGAGAGATCGGTGTGGCCTCTTTGGGCTGCAACTCCGGCTGCGCCAACAGTTTCTGCTCATTCTTCGCCAACCAGGCCGCCAGCTGCTTGTTGGAGATCTCGGCCTGCA‑GCCGAGCGCTCCGggcg                                                                                                                               <  1:96895/150‑1 (MQ=255)                   aTGGCTCCGGTTGCGCTTGTGCACGAGAGATCGGTGTGGCCTCTTTGGGCTGCAACTCCGGCTGCGCCAACAGTTTCTGCTCATTCTTCGCCAACCAGGCCGCCAGCTGCTTGTTGGAGATCTCGGCCTGCA‑GCCGAGCGCTCCGggcgg                                                                                                                              <  2:300099/150‑1 (MQ=255)                   aTGGCTCCGGTTGCGCTTGTGCACGAGAGATCGGTGTGGCCTCTTTGGGCTGCAACTCCGGCTGCGCCAACAGTTTCTGCTCATTCTTCGCCAACCAGGCCGCCAGCTGCTTGTTGGAGATCTCGGCCTGCA‑GCCGAGCGCTCCGggcgg                                                                                                                              <  2:301439/150‑1 (MQ=255)                       cTCCGGTTGCGCTTGTGCACGAGAGATCGGTGTGGCCTCTTTGGGCTGCAACTCCGGCTGCGCCAACAGTTTCTGCTCATTCTTCGCCAACCAGGCCGCCAGCTGCTTGTTGGAGATCTCGGCCTGCA‑GCCGAGCGCTCCGGGCGGCAAt                                                                                                                          <  2:283156/150‑1 (MQ=255)                            gTTGCGCTTGTGCACGAGAGATCGGTGTGGCCTCTTTGGGCTGCAACTCCGGCTGCGCCAACAGTTTCTGCTCATTCTTCGCCAACCAGGCCGCCAGCTGCTTGTTGGAGATCTCGGCCTGCA‑GCCGAGCGCTCCGGGCGGCAATGCttt                                                                                                                     <  2:265327/150‑1 (MQ=255)                               gcgcTTGTGCACGAGAGATCGGTGTGGCCTCTTTGGGCTGCAACTCCGGCTGCGCCAACAGTTTCTGCTCATTCTTCGCCAACCAGGCCGCCAGCTGCTTGTTGGAGATCTCGGCCTGCA‑GCCGAGCGCTCCGGGCGGCAATGCTTTCCa                                                                                                                  <  1:380627/150‑1 (MQ=255)                                 gcTTGTGCACGAGAGATCGGTGTGGCCTCTTTGGGCTGCAACTCCGGCTGCGCCAACAGTTTCTGCTCATTCTTCGCCAACCAGGCCGCCAGCTGCTTGTTGGAGATCTCGGCCTGCA‑GCCGAGCGCTCCGGGCGTCAATGCTTTCCAtg                                                                                                                >  1:98755/1‑150 (MQ=255)                                         aCGAGAGATCGGTGTGGCCTCTTTGGGCTGCAACTCCGGCTGCGCCAACAGTTTCTGCTCATTCTTCGCCAACCAGGCCGCCAGCTGCTTGTTGGAGATCTCGGCCTGCA‑GCCGAGCGCTCCGGGCGGCAATGCTTTCCATGCTGCTCAt                                                                                                        >  2:992634/1‑150 (MQ=255)                                         aCGAGAGATCGGTGTGGCCTCTTTGGGCTGCAACTCCGGCTGCGCCAACAGTTTCTGCTCATTCTTCGCCAACCAGGCCGCCAGCTGCTTGTTGGAGATCTCGG‑CTGCAGGCCGAgat                                                                                                                                        >  2:410537/1‑116 (MQ=255)                                         aCGAGAGATCGGTGTGGCCTCTTTGGGCTGCAACTCCGGCTGCGCCAACAGTTTCTGCTCATTCTTCGCCAACCAGGCCGCCAGCTGCTTGTTGGAGATCTCGG‑CTGCAGGCCGAgat                                                                                                                                        <  1:410537/118‑3 (MQ=255)                                                      gtgGCCTCTTTGGGCTGCAACTCCGGCTGCGCCAACAGTTTCTGCTCATTCTTCGCCAACCAGGCCGCCAGCTGCTTGTTGGAGATCTCGGCCTGCA‑GCCGAGCGCTCCGGGCGGCAATGCTTTCCATGCTGCTCATGACGCCGGCCTTc                                                                                           <  2:940694/150‑1 (MQ=255)                                                       tgGCCTCTTTGGGCTGCAACTCCGGCTGCGCCAACAGTTTCTGCTCATTCTTCGCCAACCAGGCCGCCAGCTGCTTGTTGGAGATCTCGGCCTGCA‑GCCGAGCGCTCCGGGCGGCAATGCTTTCCATGCTGCTCATGACGCCGGCCTTCa                                                                                          >  1:681677/1‑150 (MQ=255)                                                         gCCTCTTTGGGCTGCAACTCCGGCTGCGCCAACAGTTTCTGCTCATTCTTCGCCAACCAGGCCGCCAGCTGCTTGTTGGAGATCTCGGCCTGCA‑GCCGAGCGCTCCGGGCGGCAATGCTTTCCATGCTGCTCATGACGCAGGCCTTCATc                                                                                        >  2:458143/1‑150 (MQ=255)                                                           ctctTTGGGCTGCAACTCCGGCTGCGCCAACAGTTTCTGCTCATTCTTCGCCAACCAGGCCGCCAGCTGCTTGTTGGAGATCTCGGCCTGCA‑GCCGAGCGCTCCGGGCGGCAATGCTTTCCATGCTGCTCATGACGCCGGCCTTCATCTg                                                                                      <  2:849879/150‑1 (MQ=255)                                                           ctctTTGGGCTGCAACTCCGGCTGCGCCAACAGTTTCTGCTCATTCTTCGCCAACCAGGCCGCCAGCTGCTTGTTGGAGATCTCGGCCTGCA‑GCCGAGCGCTCCGGGCGGCAATGCTTTCCATGCTGCTCATGACGCCGGCCTTCATCTg                                                                                      >  1:1034883/1‑150 (MQ=255)                                                           ctctTTGGGCTGCAACTCCGGCTGCGCCAACAGTTTCTGCTCATTCTTCGCCAACCAGGCCGCCAGCTGCTTGTTGGAGATCTCGG‑CTGCAGGCCGAga                                                                                                                                         <  1:1059490/99‑2 (MQ=255)                                                           ctctTTGGGCTGCAACTCCGGCTGCGCCAACAGTTTCTGCTCATTCTTCGCCAACCAGGCCGCCAGCTGCTTGTTGGAGATCTCGG‑CTGCAGGCCGAga                                                                                                                                         >  2:1059490/1‑98 (MQ=255)                                                                  ggCTGCAACTCCGGCTGCGCCAACAGTTTCTGCTCATTCTTCGCCAACCAGGCCGCCAGCTGCTTGTTGGAGATCTCGGCCTGCA‑GCCGAGCGCTCCGGGCGGCAATGCTTTCCATGCTGCTCATGACGCCGGCCTTCATCTGCCCCCGa                                                                               <  2:302594/150‑1 (MQ=255)                                                                   gCTGCAACTCCGGCTGCGCCAACAGTTTCTGCTCATTCTTCGCCAACCAGGCCGCCAGCTGCTTGTTGGAGATCTCGGCCTGCA‑GCCGAGCGCTCCGGGCGGCAATGCTTTCCATGCTGCTCATGACGCCGGCCTTCATCTGCCCCCGAg                                                                              >  2:39879/1‑150 (MQ=255)                                                                     tGCAACTCCGGCTGCGCCAACAGTTTCTGCTCATTCTTGGCCAACCCGGCCGCCAGCTGCTTGTTGGAGATCTCGGCCTGCA‑GCCGAGCGCTCCCGGCGGCAATGCTTCAAATGCTCCATATCACCCCGGCTCCCATCTTTCCCCGATTa                                                                            <  2:799956/150‑1 (MQ=255)                                                                           tCCGGCTGCGCCAACAGTTTCTGCTCATTCTTCGCCAACCAGGCCGCCAGCTGCTTGTTGGAGATCTCGGCCTGCA‑GCCGAGCGCTCCGGGCGGCAATGCTTTCCATGCTGCTCATGACGCCGGCCTTCATCTGCCCCCGAGTAaggtag                                                                      >  1:818826/1‑150 (MQ=255)                                                                             cGGCTGAGCCAACAGTTTCTGCTCATTCTTCGCCACTCTGGCCGCCAGCTGCTTGTTGGAGATCTCGGCCTGCA‑GCCGAGCGCGCCGGGCGGCAATGCTTTCCATGCTGCTCATGACGCCGGCCTTCATCTGCCCCCGAGTAaggtaggg                                                                    <  2:497637/150‑2 (MQ=255)                                                                                      cAACAGTTTCTGCTCATTCTTCGCCAACGAGGCCGCCAGCTGCTTGTTGGAGATCTCGGCCTGCA‑GCCGAGCGCTCCGGGCGGCAATGCTTTCCATGCTGCTCATGACGCCGGCCTTCATCTGCCCCCGAGTAAGGTAGGTGACGATGGc                                                           >  1:271769/1‑150 (MQ=255)                                                                                       aaCAGTTTCTGCTCATTCTTCGCCAACCAGGCCGCCAGCTGCTTGTTGGAGATCTCGGCCTGCA‑GCCGAGCGCTCCGGGCGGCAATGCTTTCCATGCTGCTCATGACGCCGGCCTTCATCTGCCCCCGAGTAAGGTAGGTGACGATGGCt                                                          <  1:992634/150‑1 (MQ=255)                                                                                       aaCAGTTTCTGCTCATTCTTCGCCAACCAGGCCGCCAGCTGCTTGTTGGAGATCTCGGCCTGCA‑GCCGAGCGCTCCGGGCGGCAATGCTTTCCATGCTGCTCATGACGCCGGCCTTCATCTGCCCCCGAGTAAGGTAGGTGACGATGGCt                                                          <  2:818826/150‑1 (MQ=255)                                                                                               cTGCTCATTCTTCGCCAACCAGGCCGCCAGCTGCTTGTTGGAGATCTCGGCCTGCA‑GCCGAGCGCTCCGGGCGGCAATGCTTTCCATGCTGCTCATGACGCCGGCCTTCATCTGCCCCCGAGGAAGGCAGGTGACGATGGCTGTCAGTaa                                                  <  1:1004117/150‑1 (MQ=255)                                                                                                  cTCATTCTTCGCCAACCAGGCCGCCAGCTGCTTGTTGGAGATCTCGGCCTGCA‑GCCGAGCGCTCCGGGCGGCAATGCTTTCCATGCTGCTCATGACGCCGGCCTTCATCTGCCCCCGAGTAAGGTAGGTGACGATGGCTGTCAGTAAcag                                               >  2:283154/1‑150 (MQ=255)                                                                                                      ttcttcGCCAACCAGGCCGCCAGCTGCTTGTTGGAGATCTCGGCCTGCA‑GCCGAGCGCTCCGGGCGGCAATGCTTTCCATGCTGCTCATGACGCCGGCCTTCATCTGCCCCCGAGTAAGGTAGGTGACGATGGCTGTCAGTAACagcagc                                           <  2:681677/150‑1 (MQ=255)                                                                                                         ttcGCCAACCAGGCCGCCAGCTGCTTGTTGGAGATCTCGGCCTGCA‑GCCGAGCGCTCCGGGCGGCAATGCTTTCCATGCTGCTCATGACGCCGGCCTTCATCTGCCCCCGAGTAAGGTAGGTGACGATGGCTGt                                                        >  1:919039/1‑134 (MQ=255)                                                                                                         ttcGCCAACCAGGCCGCCAGCTGCTTGTTGGAGATCTCGGCCTGCA‑GCCGAGCGCTCCGGGCGGCAATGCTTTCCATGCTGCTCATGACGCCGGCCTTCATCTGCCCCCGAGTAAGGTAGGTGACGATGGCTGt                                                        <  2:919039/134‑1 (MQ=255)                                                                                                           cGCCAACCAGGCCGCCAGCTGCTTGTTGGAGATCTCGGCCTGCA‑GCCGAGCGCTCCGGGCGGCAATGCTTTCCATGCTGCTCATGACGCCGGCCTTCATCTGCCCCCGAGTAAGGTAGGTGACGATGGCTGTCAGTAACAGCAGCACCaa                                      >  2:383414/1‑150 (MQ=255)                                                                                                                  cAGGCCGCCAGCTGCTTGTTGGAGATCTCGGCCTGCA‑GCCGAGCGCTCCGGGCGGCAATGCTTTCCATGCTGCTCATGACGCCGGCCTTCATCTGCCCCCGAGTAAGGTAGGTGACGATGGCTGTCAGTAACAGCAGCACCAACTGCTcc                               >  1:564007/1‑150 (MQ=255)                                                                                                                  cAGGCCGCCAGCTGCTTGTTGGAGATCTCGGCCTGCA‑GCCGAGCGCTCCGGGCGGCAATGCTTTCCATGCTGCTCATGACGCCGGCCTTCATCTGCCCCCGAGTAAGGTAGGTGACGATGGCTGTCAGTAACAGCAGCACCAACTGCTcc                               >  2:746534/1‑150 (MQ=255)                                                                                                                   aGGCCGCCAGCTGCTTGTTGGAGATCTCGGCCTGCA‑GCCGAGCGCTCCGGGCGGCAATGCTTTCCATGCTGCTCATGACGCCGGCCTTCATCTGCCCCCGAGTAAGGTAGGTGACGATGGCTGTCAGTAACAGCAGCACCAACTGCTCCt                              >  2:322641/1‑150 (MQ=255)                                                                                                                          cAGCTGCTTGTTGGAGATCTCGGCCTGCA‑GCCGAGCGCTCCGGGCGGCAATGCTTTCCATGCTGCTCATGACGCCGGCCTTCATCTGCCCCCGAGTAAGGTAGGTGACGATGGCTGTCAGTAACAGCAGCACCAACTGCTCCTGCCcgcg                       >  1:567507/1‑150 (MQ=255)                                                                                                                                       gagaTCTCGGCCTGCA‑GCCGAGCGCTCCGGGCGGCAATGCTTTCCATGCTGCTCATGACGCCGGCCTTCATCTGCCCCCGAGTAAGGTAGGTGACGATGGCTGTCAGTAACAGCAGCACCAACTGCTCCTGCCCGCGAGCAAGCTGGCGt          >  2:206527/1‑150 (MQ=255)                                                                                                                                        agaTCTCGGCCTGCA‑GCCGAGCGCTCCGGGCGGCAATGCTTTCCATGCTGCTCATGACGCCGGCCTTCATCTGCCCCCGAGTAAGGTAGGTGACGATGGCTGTCAGTAACAGCAGCACCAACTGCTCCTGCCCGCGAGCAAGCTGGCGTg         >  2:333694/1‑150 (MQ=255)                                                                                                                                        agaTCTCGGCCTGCA‑GCCGAGCGCTCCGGGCGGCAATGCTTTCCATGCTGCTCATGACGCCGGCCTTCATCTGCCCCCGAGTAAGGTAGGTGACGATGGCTGTCAGTAACAGCAGCACCAACTGCTCCTGCCCGCGAGCAAGCTGGCGTg         >  2:333677/1‑150 (MQ=255)                                                                                                                                          aTCTCGGCCTGCA‑GCCGAGCGCTCCGGGCGGCAATGCTTTCCATGCTGCTCATGACGCCGGCCTTCATCTGCCCCCGAGTAAGGTAGGTGACGATGGCTGTCAGTAACAGCAGCACCAACTGCTCCTGCGTGGTAGTTAGGTGGCGTGCa       <  2:271769/150‑1 (MQ=255)                                                                                                                                            ctcGGCCTGCA‑GCCGAGCGCTCCGGGCGGCAATGCTTTCCATGCTGCTCATGACGCCGGCCTTCATCTGCCCCCGAGTAAGGTAGGTGACGATGGCTGTCAGTAACAGCAGCACCAACTGCTCCTGCCCGCGAGCAAGCTGGCGTGCAgc     <  2:567507/150‑1 (MQ=255)                                                                                                                                               ggCCTGCA‑GCCGAGCGCTCCGGGCGGCAATGCTTTCCATGCTGCTCATGACGCCGGCCTTCATCTGCCCCCGAGTAAGGTAGGTGACGATGGCTGTCAGTAACAGCAGCACCAACTGCTCCTGCCCGCGAGCAAGCTGGCGTGCAgcgcg  >  1:648591/1‑150 (MQ=255)                                                                                                                                                       |                                                                                                                                               GATCGGGTAGTGGTCGCAATGGCTCCGGTTGCGCTTGTGCACGAGAGATCGGTGTGGCCTCTTTGGGCTGCAACTCCGGCTGCGCCAACAGTTTCTGCTCATTCTTCGCCAACCAGGCCGCCAGCTGCTTGTTGGAGATCTCGGCCTGCA‑GCCGAGCGCTCCGGGCGGCAATGCTTTCCATGCTGCTCATGACGCCGGCCTTCATCTGCCCCCGAGTAAGGTAGGTGACGATGGCTGTCAGTAACAGCAGCACCAACTGCTCCTGCCCGCGAGCAAGCTGGCGTGCAGCGCG  >  NC_002947/3505159‑3505450

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑