Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	5,490,732	G→C	7.1%	S17R (AGC→AGG)	PP_5714 ←	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	5,490,732	0	G	C	7.1%	169.7 / 2.5	54	S17R (AGC→AGG)	PP_5714	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (27/23);  new base C (2/2);  total (29/25)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CAGTAGTTCCTGAACCAGTCCGGCTCCAGGCCTTCGTTGAAGTCCCCCCAGGCAACTTGCTGGGCAAACGCATTGGCCAACAGGATGTCGTCACGGGCTTCGCGACTAACACCTGGCAAGAATGACAGCAGGCTGCTGTGGACGAGTTTGCCACTGGCG‑GCACCTTGATTGAACTCACTCATTTTCGACTCCTGAGGTAGTGGCAAGTTTGACCTGGCTGCGGTACTGCAATTGCTTGACCTTGATAGCGTCATGCAAGCCCGGACTTATCGAACTG  >  NC_002947/5490601‑5490877                                                                                                                                    |                                                                                                                                                   cAGTAGTTCCTGAACCAGTCCGGCTCCAGGCCTTCGTTGAAGTCCCCCCAGGCAACTTGCTGGGCAAACGCATTGGCCAACAGGATGTCGTCACGGGCTTCGCGACTAACACCTGGCAAGAATGACAGCAGGCTGCTGTGGACGAGttt                                                                                                                                   >  8:247145/1‑149 (MQ=255)      gtTCCTGAACCAGTCCGGCTCCAGGCCTTCGTTGAAGTCCCCCCAGGCAACTTGCTGAGCAAACGCATTGGCCAACAGGATGTCGTCACGGGCTTCGCGACTAACACCTGGCAAGAATGACAGCAGGCTGCTGTGGACGAGTTTGCCAc                                                                                                                              >  1:83357/1‑149 (MQ=255)       ttCCTGAACCAGTCCGGCTCCAGGCCTTCGTTGAAGTCCCCCCAGGCAACTTGCTGGGCAAACGCATTGGCCAACAGGATGTCGTCACGGGCTTCGCGACTAACACCTGGCAAGAATGACAGCAGGCTGCTGTGGACGAGttt                                                                                                                                   >  7:52206/1‑143 (MQ=255)       ttCCTGAACCAGTCCGGCTCCAGGCCTTCGTTGAAGTCCCCCCAGGCAACTTGCTGGGCAAACGCATTGGCCAACAGGATGTCGTCACGGGCTTCGCGACTAACACCTGGCAAGAATGACAGCAGGCTGCTGTGGACGAGttt                                                                                                                                   <  8:52206/143‑1 (MQ=255)       ttCCTGAACCAGTCCGGCTCCAGGCCTTCGTTGAAGTCCCCCCAGGCAACTTGCTGGGCAAACGCATTGGCCAACAGGATGTCGTCACGGGCTTCGCGACTAACACCTGGCAAGAATGACAGCAGGCTGCTGTGGACGAGTTTGcacct                                                                                                                             >  6:56881/1‑145 (MQ=255)             aaCCAGTCCGGCTCCAGGCCTTCGTTGAAGTCCCCCCAGGCAACTTGCTGGGCAAACGCATTGGCCAACAGGATGTCGTCACGGGCTTCGCGACTAACACCTGGCAAGAATGACAGCAGGCTGCTGTGGACGAGTTTGCCACTggcg‑g                                                                                                                       <  4:229469/148‑1 (MQ=255)                  gTCCGGCTCCAGGCCTTCGTTGAAGTCCCCCCAGGCAACTTGCTGGGCAAACGCATTGGCCAACAGGATGTCGTCACGGGCTTCGCGACTAACACCTGGCAAGAATGACAGCAGGCTGCTGTGGACGAGTTTGCCACTGGCG‑GCACCtt                                                                                                                 <  2:24529/149‑1 (MQ=255)                          ccAGGCCTTCGTTGAAGTCCCCCCAGGCAACTTGCTGGGCAAACGCATTGGCCAACAGGATGTCGTCACGGGCTTCGCGACTAACACCTGGCAAGAATGACAGCAGGCTGCTGTGGACGAGTTTGCCACTGGCG‑GCACCTTGATTGAac                                                                                                         >  3:301002/1‑149 (MQ=255)                           cAGGCCTTCGTTGAAGTCCCCCCAGGCAACTTGCTGGGCAAACGCATTGGCCAACAGGATGTCGTCACGGGCTTCGCGACTAACACCTGGCAAGAATGACAGCAGGCTGCTGTGGACGAGTTTGCCACTGGCG‑GCACCTTGATTGAac                                                                                                         <  1:255473/148‑1 (MQ=255)                            aGGCCTTCGTTGAAGTCCCCCCAGGCAACTTGCTGGGCAAACGCATTGGCCAACAGGATGTCGTCACGGGCTTCGCGACTAACACCTGGCAAGAATGACAGCAGGCTGCTGTGGACGAGTTTGCCACTGGCG‑GCACCTTGATTGAact                                                                                                        >  5:252706/1‑148 (MQ=255)                                       gAAGTCCCCCCAGGCAACTTGCTGGGCAAACGCATTGGCCAACAGGATGTCGTCACGGGCTTCGCGACTAACACCTGGCAAGAATGACAGCAGGCTGCTGTGGACGAGTTTGCCACTGGCG‑GCACCTTGATTGAACTCACTCATTTTc                                                                                             <  4:301002/148‑1 (MQ=255)                                             cccccAGGCAACTTGCTGGGCAAACGCATTGGCCAACAGGATGTCGTCACGGGCTTCGCGACTAACACCTGGCAAGAATGACAGCAGGCTGCTGTGGACGAGTTTGCCACTGGCG‑GCACCTTGATTGAACTCACTCATTTTCGACTCCt                                                                                      <  4:25203/149‑1 (MQ=255)                                               cccAGGCAACTTGCTGGGCAAACGCATTGGCCAACATGATGTCGTCACGGGCTTCGCGACTTACACCTGGCAACAATGACATCAGGCTGCTGTGGACGTGTTTGCCACTGGCG‑GCACCTTGATTGAACTCACTCATTTTCGACTCCTGa                                                                                    <  5:56881/149‑1 (MQ=255)                                               cccAGGCAACTTGCTGGGCAAACGCATTGGCCAACAGGATGTCGTCACGGGCTTCGCGACTAACACCTGGCAAGAATGACAGCAGGCTGCTGTGGACGAGTTTGCCACTGGCG‑GCACCTTGATTGAACTCACTCATTTTCGACTCCTGa                                                                                    <  7:247145/149‑1 (MQ=255)                                                     cAACTTGCTGGGCAAACGCATTGGCCAACAGGATGTCGTCACGGGCTTCGCGACTAACACCTGGCAAGAATGACAGCAGGCTGCTGTGGACGAGTTTGCCACTGGCG‑GCACCTTGATTGAACTCACTCATTTTCGACTCCTGAGGTAGt                                                                              >  6:299080/1‑149 (MQ=255)                                                      aaCTTGCTGGGCAAACGCATTGGCCAACAGGATGTCGTCACGGGCTTCGCGACTAACACCTGGCAAGAATGACAGCAGGCTGCTGTGGACGAGTTTGCCACTGGCG‑GCACCTTGATTGAACTCACTCATTTTCGACTc                                                                                        >  5:166122/1‑138 (MQ=255)                                                      aaCTTGCTGGGCAAACGCATTGGCCAACAGGATGTCGTCACGGGCTTCGCGACTAACACCTGGCAAGAATGACAGCAGGCTGCTGTGGACGAGTTTGCCACTGGCG‑GCACCTTGATTGAACTCACTCATTTTCGACTc                                                                                        <  6:166122/138‑1 (MQ=255)                                                              gggCAAACGCATTGGCCAACAGGATGTCGTCACGGGCTTCGCGACTAACACCTGGCAAGAATGACAGCAGGCTGCTGTGGACGAGTTTGCCACTGGCG‑GCACCTTGATTGAACTCACTCATTTTCGACTCCTGAGGTAGTGGCAAGttt                                                                     >  2:111631/1‑149 (MQ=255)                                                                gCAAACGCATTGGCCAACAGGATGTCGTCACGGGCTTCGCGACTAACACCTGGCAAGAATGACAGCAGGCTGCTGTGGAAGAGTTTGCCACTGGCG‑GCACCTTGATTGAACTAACTCATTTTCGACTCCTGACGTAGTGGCAACTTTg                                                                    >  3:78392/1‑148 (MQ=255)                                                                     cGCATTGGCCAACAGGATGTCGTCACGGGCTTCGCGACTAACACCTGGCAAGAATGACAGCAGGCTGCTGTGGACGAGTTTGCCACTGGCG‑GCACCTTGATTGAACTCACTCATTTTCGACTCCTGAGGTAGTGGCAAGTTTGACCTgg                                                              <  6:252706/149‑1 (MQ=255)                                                                       cATTGGCCAACAGGATGTCGTCACGGGCTTCGCGACTAACACCTGGCAAGAATGACAGCAGGCTGCTGTGGACGAGTTTGCCACTGGCG‑GCACCTTGATTGAACTCACTCATTTTCGACTCCTGAGGTAGTGGCAAGt                                                                       <  2:83005/138‑1 (MQ=255)                                                                       cATTGGCCAACAGGATGTCGTCACGGGCTTCGCGACTAACACCTGGCAAGAATGACAGCAGGCTGCTGTGGACGAGTTTGCCACTGGCG‑GCACCTTGATTGAACTCACTCATTTTCGACTCCTGAGGTAGTGGCAAGt                                                                       >  1:83005/1‑138 (MQ=255)                                                                            gCCAACAGGATGTCGTCACGGGCTTCGCGACTAACACCTGGCAAGAATGACAGCAGGCTGCTGTGGACGAGTTTGCCACTGGCG‑GCACCTTGATTGAACTCACTCATTTTCGACTCCTGAGGTAGTGGCAAGTTTGACCTGGCTGCgg                                                        >  8:172702/1‑148 (MQ=255)                                                                             ccAACAGGATGTCGTCACGGGCTTCGCGACTAACACCTGGCAAGAATGACAGCAGGCTGCTGTGGCCGAGTTTGCCCCTCGCG‑GCACCTTGATTGAACTCACTCATTTTCGACTCGTGAGGTAGTGGCAAGTTTGACCTGGCTGCGGTa                                                      >  7:213662/1‑149 (MQ=255)                                                                                 cAGGATGTCGTCACGGGCTTCGCGACTAACACCTGGCAAGAATGACAGCAGGCTGCTGTGGACGAGTTTGCCACTGGCG‑GCACCTTGATTGAACTCACTCATTTTCGACTCCTGACGTAGTGGCAAGTTTGACCTGGCTGCGGTACTg                                                   >  4:7580/1‑148 (MQ=255)                                                                                        tcgtcACGGGCTTCGCGACTAACACCTGGCAAGAATGACAGCAGGCTGCTGTGGACGAGTTTGCCACTGGCG‑GCACCTTGATTGAACTCACTCATTTTCGACTCCTGAGGTAGTGGCAAGTTTGACCTGGCTGCGGTACTGCAATTGc                                            <  2:83357/148‑1 (MQ=255)                                                                                        tcgtcACGGGCTTCGCGACTAACACCTGGCAAGAATGACAGCAGGCTGCTGTGGACGAGTTTGCCACTGGCG‑GCACCTTGATTGAACTCACTCATTTTCGACTCCTGAGGTAGTGGCAAGTTTGACCTGGCTGCGGTACTGCAATTGc                                            <  7:172702/148‑1 (MQ=255)                                                                                               gggCTTCGCGACTAACACCTGGCAAGAATGACAGCAGGCTGCTGTGGACGAGTTTGCCACTGGCG‑GCACCttg                                                                                                                <  6:47516/73‑1 (MQ=255)                                                                                               gggCTTCGCGACTAACACCTGGCAAGAATGACAGCAGGCTGCTGTGGACGAGTTTGCCACTGGCG‑GCACCttg                                                                                                                >  5:47516/1‑73 (MQ=255)                                                                                                 gCTTCGCGACTAACACCTGGCAAGAATGACAGCAGGCTGCTGTGGACGAGTTTGCCACTGGCG‑GCACCTTGATTGAACTCACTCATTTTCGACTCCTGAgg                                                                                  >  7:265229/1‑101 (MQ=255)                                                                                                 gCTTCGCGACTAACACCTGGCAAGAATGACAGCAGGCTGCTGTGGACGAGTTTGCCACTGGCG‑GCACCTTGATTGAACTCACTCATTTTCGACTCCTGAgg                                                                                  <  8:265229/101‑1 (MQ=255)                                                                                                  cTTCGCGACTAACACCTGGCAAGAATGACAGCAGGCTGCTGTGGACGAGTTTGCCACTGGCG‑GCACCTTGATTGAACTCACTCATTTTCGACTCCTGAGGTAGTGGCAAGTTTGACCTGGCTGCGGTACTGCAATTGCTTGACCTTGa                                  >  2:262835/1‑148 (MQ=255)                                                                                                      gcgACTAACACCTGGCAAGAATGACAGCAGGCTGCTGTGGACGAGTTTGCCACTGGCG‑GCACCTTGATTGAACTCACTCATTTTCGACTCCTGAGGTAGTGGCAAGTTTGACCTGGCTGCGGTACTGCAATTGCTTGACCTTGATAGc                              <  1:111631/148‑1 (MQ=255)                                                                                                         aCTAACACCTGGCAAGAATGACAGCAGGCTGCTGTGGACGAGTTTGCCACTGGCG‑GCACCTTGATTGAACTCACTCATTTTCGACTCCTGAGGTAGTGGCAAGTTTGACCTGGCTGCGGTACTGCAATTGCTTGACCTTGATAGCGTCa                          >  3:256004/1‑149 (MQ=255)                                                                                                             acacCTGGCAAGAATGACAGCAGGCTGCTGTGGACGAGTTTGCCACTGGCG‑GCACCTTGATTGAACTCACTCATTTTCGACTCCTGAGGTAGTGGCAAGTTTGACCTGGCTGCGGTACTGCAATTGCTTGACCTTGATAGCGTCATGc                       <  5:299080/148‑1 (MQ=255)                                                                                                             acacCTGGAAAGAATGACAGCAGGCTCTTGTGGACGAGTTTACCACTGGCG‑GAACCTTGATTGAACTCACTCATTTTCGACTCCTGAGGTAGATGCAAGTTTGAACTGGCTGCGGTACTTCAATTGATTGACCTTGATAGCGTCATGc                       >  7:257246/1‑148 (MQ=255)                                                                                                              cacCTGGCAAGAATGACAGCAGGCTGCTGTGGACGAGTTTGCCACTGGCG‑GCACCTTGATTGAACTCACTCATTTTCGACTCCTGAGGTAGTGGCAAGTTTGACCTGGCTGCGGTACTGCAATTGCTTGACCTTGATAGCGTCATGc                       >  5:45060/1‑147 (MQ=255)                                                                                                               acCTGGCAAGAATGACAGCAGGCTGCTGTGGACGAGTTTGCCACTGGCG‑GCACCTTGATTGAACTCACTCATTTTCGACTCCTGAGGTAGTGGCAAGTTTGACCTGGCTGCGGTACTGCAATTGCTTGACCTTGATAGCGTCATGCaat                    >  8:100502/1‑148 (MQ=255)                                                                                                               acCTGGCAAGAATGACAGCAGGCTGCTGTGGACGAGTTTGCCACTGGCG‑GCACCTTGATTGAACTCACTCATTTTCGACTCCTGAGGTAGTGGCAAGTTTGACCTGGCTGCGGTACTGCAATTGCTTGACCTTGATAGCGTCATGCAAg                    >  8:215107/1‑149 (MQ=255)                                                                                                                ccTGGCAAGAATGACAGCAGGCTGCTGTGGACGAGTTTGCCACTGGCG‑GCACCTTGATAGAACTCACTCATTTTCGACTCCTGAGGTAGTGGCAAGTTTGACCTGGCTGCGGTACTGCAATTGCTTGACCTTGATAGCGTCATGCAAGc                   <  3:7580/149‑1 (MQ=255)                                                                                                                 cTGGCAAGAATGACAGCAGGCTGCTGTGGACGAGTTTGCCACTGGCG‑GCACCTTGATTGAACTCACTCATTTTCGACTCCTGAgg                                                                                  <  8:111272/85‑1 (MQ=255)                                                                                                                 cTGGCAAGAATGACAGCAGGCTGCTGTGGACGAGTTTGCCACTGGCG‑GCACCTTGATTGAACTCACTCATTTTCGACTCCTGAgg                                                                                  >  7:111272/1‑85 (MQ=255)                                                                                                                  ttgCAAGAATGACAGCAGGCTGCTGTGGACGAGTTTGCCACTGGCGCGCACCTTGATTGAACTCACTCATTTTc                                                                                             <  1:165868/72‑1 (MQ=255)                                                                                                                  tGGCAAGAATGACAGCAGGCTGCTGTGGACGAGTTTGCCACTGGCG‑GCACCTTGATTGAACTCACTCATTTTc                                                                                             >  2:165868/1‑73 (MQ=255)                                                                                                                    gCAAGAATGACAGCAGGCTGCTGTGGACGAGTTTGCCACTGGCG‑GCACCTTGATTGAACTCACTCATTTTCGACTCCTGAGGTAGTGGCAAGTTTGACCTGGCTGCGGTACTGCAATTGCTTGACCTTGATAGCGTCATGCAAGCCCg                >  3:48463/1‑148 (MQ=255)                                                                                                                         gtccaCAGCAGCCTGCTGTGGACGAGTTTGCCACTGGCG‑GCACCTTGATTGAACTCACTCATTTTCGACTCCTGAGGTAGTGGCAAGTTTGACCTGGCTGCGGTACTGCAATTGCTTGACCTTGATAGc                              <  4:62905/125‑1 (MQ=255)                                                                                                                         gtccaCAGCAGCCTGCTGTGGACGAGTTTGCCACTGGCG‑GCACCTTGATTGAACTCACTCATTTTCGACTCCTGAGGTAGTGGCAAGTTTGACCTGGCTGCGGTACTGCAATTGCTTGACCTTGATAGc                              <  4:58787/125‑1 (MQ=255)                                                                                                                         gtccaCAGCAGCCTGCTGTGGACGAGTTTGCCACTGGCG‑GCACCTTGATTGAACTCACTCATTTTCGACTCCTGAGGTAGTGGCAAGTTTGACCTGGCTGCGGTACTGCAATTGCTTGACCTTGATAGc                              >  3:62905/5‑129 (MQ=255)                                                                                                                         gtccaCAGCAGCCTGCTGTGGACGAGTTTGCCACTGGCG‑GCACCTTGATTGAACTCACTCATTTTCGACTCCTGAGGTAGTGGCAAGTTTGACCTGGCTGCGGTACTGCAATTGCTTGACCTTGATAGc                              >  3:58787/5‑129 (MQ=255)                                                                                                                          aTGACAGCAGGCTGCTGTGGACGAGTTTGCCACTGGCG‑GCACCTTGATTGAACTCACTCATTTTCGACTCCTGAGGTAGTGGCAAGTTTGACCTGGCTGCGGTACTGCAATTGCTTGACCTTGATAGCGTCATGCAAGCCCGGACTTAt         <  7:215107/149‑1 (MQ=255)                                                                                                                             aCAGCATGCTGCTGTGGAAGAGTTTGCCACTGGAG‑GCACATTTATTGAACTCACTCATTTTCGACTCCTTATGTAGTGGCAATTTTGACCTGGCTGCTGTACTGCAATTGCTTGACCTTGATAGCGTCATGCAATCCCGGACTTATCg       <  4:78392/148‑1 (MQ=255)                                                                                                                               agcagGCTGCTGTGGACGAGTTTGCCACTGGCG‑GCACCTTGATTGAACTCACTCATTTTCGACTCCTGAGGTAGTGGCAAGTTTGACCTGGCTGCGGTACTGCAATTGCTTGACCTTGATAGCGTCATGCAAGCCCGGACTTATCGAAc    >  5:302339/1‑149 (MQ=255)                                                                                                                                 cagGCTGCTGTGGACGAGTTTGCCACTGGCG‑GCACCTTGATTGAACTCACTCATTTTCGACTCCTGAGGTAGTGGCAAGTTTGACCTGGCTGCGGTACTGCAATTGCTTGACCTTGATAGCGTCATGCAAGCCCGGACTTATCGAACt   >  2:20196/1‑148 (MQ=255)                                                                                                                                 cagGCTGCTGTGGACGAGTTTGCCACTGGCG‑GCACCTTGATTGAACTCACTCATTTTCGACTCCTGAGGTAGTGGCAAGTTTGACCTGGCTGCGGTACTGCAATTGCTTGACCTTGATAGCGTCATGCAAGCCCGGACTTATCGAACTg  <  4:48463/149‑1 (MQ=255)                                                                                                                                    gctgctGTGGACGAGTTTGCCACTGGCG‑GCACCTTGATTGAACTCACTCATTTTCGACTCCTGAGGTAGTGGCAAGTTTGACCTGGCTGCGGTACTGCAATTGCTTGACCTTGATAGCGTCATGCAAGCCCGGACTTATc        <  4:246204/140‑1 (MQ=255)                                                                                                                                    gctgctGTGGACGAGTTTGCCACTGGCG‑GCACCTTGATTGAACTCACTCATTTTCGACTCCTGAGGTAGTGGCAAGTTTGACCTGGCTGCGGTACTGCAATTGCTTGACCTTGATAGCGTCATGCAAGCCCGGACTTATc        >  3:246204/1‑140 (MQ=255)                                                                                                                                    |                                                                                                                                                   CAGTAGTTCCTGAACCAGTCCGGCTCCAGGCCTTCGTTGAAGTCCCCCCAGGCAACTTGCTGGGCAAACGCATTGGCCAACAGGATGTCGTCACGGGCTTCGCGACTAACACCTGGCAAGAATGACAGCAGGCTGCTGTGGACGAGTTTGCCACTGGCG‑GCACCTTGATTGAACTCACTCATTTTCGACTCCTGAGGTAGTGGCAAGTTTGACCTGGCTGCGGTACTGCAATTGCTTGACCTTGATAGCGTCATGCAAGCCCGGACTTATCGAACTG  >  NC_002947/5490601‑5490877

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑