Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,505,303	Δ1 bp	9.4%	coding (382/1074 nt)	PP_3103 ←	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,505,303	0	C	.	9.4%	157.3 / 11.8	53	coding (382/1074 nt)	PP_3103	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (25/23);  new base . (2/3);  total (27/26)
Fisher's exact test for biased strand distribution p-value = 6.69e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.39e-01

GTCGATCGGGTAGTGGTCGCAATGGCTCCGGTTGCGCTTGTGCACGAGAGATCGGTGTGGCCTCTTTGGGCTGCAACTCCGGCTGCGCCAACAGTTTCTGCTCATTCTTCGCCAACCAGGCCGCCAGCTGCTTGTTGGAGATCTCGGCCTGCA‑GCCGAGCGCTCCGGGCGGCAATGCTTTCCATGCTGCTCATGACGCCGGCCTTCATCTGCCCCCGAGTAAGGTAGGTGACGATGGCTGTCAGTAACAGCAGCACCAACTGCTCCTGCCCGCGAGCAAGCTGGCGTGCAGCGCG  >  NC_002947/3505156‑3505450                                                                                                                                                    |                                                                                                                                                     gtCGATCGGGTAGTGGTCGCAATGGCTCCGGTTGCGCTTGTGCACGAGAGATCGGTGTGGCCTCTTTGGGCTGCAACTCCGGCTGCGCCAACAGTTTCTGCTCATTCTTCGCCAACCAGGCCGCCAGCTGCTTGTTGGAGATCTCGGCCt                                                                                                                                                    <  2:723839/150‑1 (MQ=255) gtCGATCGGGTAGTGGTCGCAATGGCTCCGGTTGCGCTTGTGCACGAGAGATCGGTGTGGCCTCTTTGGGCTGCAACTCCGGCTGCGCCAACAGTTTCTGCTCATTCTTCGCCAACCAGGCCGCCAGCTGCTTGTTGGAGATCTCGGCCt                                                                                                                                                    <  1:939303/150‑1 (MQ=255)    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                                                                                                                                           >  1:64299/1‑143 (MQ=255)                gTCGCAATGGCTCCGGTTGCGCTTGTGCACGAGAGATCGGTGTGGCCTCTTTGGGCTGCAACTCCGGCTGCGCCAACAGTTTCTGCTCATTCTTCGCCAACCAGGCCGCCAGCTGCTTGTTGGAGATCTCGGCCTGCA‑GCCGa                                                                                                                                           <  2:64299/143‑1 (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)                                                                                                                                                    |                                                                                                                                                     GTCGATCGGGTAGTGGTCGCAATGGCTCCGGTTGCGCTTGTGCACGAGAGATCGGTGTGGCCTCTTTGGGCTGCAACTCCGGCTGCGCCAACAGTTTCTGCTCATTCTTCGCCAACCAGGCCGCCAGCTGCTTGTTGGAGATCTCGGCCTGCA‑GCCGAGCGCTCCGGGCGGCAATGCTTTCCATGCTGCTCATGACGCCGGCCTTCATCTGCCCCCGAGTAAGGTAGGTGACGATGGCTGTCAGTAACAGCAGCACCAACTGCTCCTGCCCGCGAGCAAGCTGGCGTGCAGCGCG  >  NC_002947/3505156‑3505450

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: ‑