Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,083,377	G→A	7.7%	Q231* (CAG→TAG)	PP_2692 ←	BCCT family transporter

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,083,377	0	G	A	7.7%	152.7 / 2.3	52	Q231* (CAG→TAG)	PP_2692	BCCT family transporter
Reads supporting (aligned to +/- strand):  ref base G (23/25);  new base A (2/2);  total (25/27)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.40e-01

TTCGCTGACAAAGCGGATGCCTTTGAGGCCCACCAGGCACGATACAGTGTACATCGCGGTGACCAGGACGATGGTCAGCGACTGGGTGACGATAGTGTTGGGCAACTCCCACACGGCGTGCATGGCGCTGCTGATCTGCAG‑GCCAAGGAAACCGATCGGACCGATGGTGCCGGCCACTACCGCGATGATCGAGGCAGCGTCGGCCAAGGTGCCGATCGGGCCCTTGAGCGCTCGCTTGCCGAACAGGGGGTAGAGCAGGGTACGCGGCGCCAGCGGAAGGCCTTT  >  NC_002947/3083240‑3083524                                                                                                                                          |                                                                                                                                                     ttCGCTGACAAAGCGGATGCCTTTGAGGCCCACCAGGCACGATACAGTGTACATCGCGGTGACCAGGACGATGGTCAGCGACTGGGTGACGATAGTGTTGGGCAACTCCCACACGGCGTGCATGGCGCTGCTGATCTGCAG‑GCCAAg                                                                                                                                            >  8:285040/1‑147 (MQ=255) ttCGCTGACAAAGCGGATGCCTTTGAGGCCCACCAGGCACGATACAGTGTACATCGCGGTGACCAGGACGATGGTCAGCGACTGGGTGACGATAGTGTTGGGCAACTCCCACACGGCGTGCATGGCGCTGCTGATCTGCAG‑GCCAAg                                                                                                                                            <  7:285040/147‑1 (MQ=255)  tCGCTGACAAAGCGGATGCCTTTGAGGCCCACCAGGCACGATACAGTGTACATCGCGGTGACCAGGACGATGGTCAGCGACTGGGTGACGATAGTGTTGGGCAACTCCCACACGGCGTGCATGGCGCTGCTGATCTGCAG‑GCCAAGGa                                                                                                                                          <  3:138121/148‑1 (MQ=255)    gCTGACAAAGCGGATGCCTTTGAGGCCCACCAGGCACGATACAGTGTACATCGCGGTGACCAGGACGATGGTCAGCGACTGGGTGACGATAGTGTTGGGCAACTCCCACACGGCGTGCATGGCGCTGCTGATCTGCAG‑GCCAAGGAAAc                                                                                                                                       <  2:261492/149‑1 (MQ=255)         cAAAGCGGATGCCTTTGAGGCCCACCAGGCACGATACAGTGTACATCGCGGTGACCAGGACGATGGTCAGCGACTGGGTGACGATAGTGTTGGGCAACTCCCACACGGCGTGCATGGCGCTGCTGATCTGCAG‑GCCAAGGAAACCGATc                                                                                                                                  <  3:135966/149‑1 (MQ=255)            aGCGGATGCCTTTGAGGCCCACCAGGCACGATACAGTGTACATCGCGGTGACCAGGACGATGGTCAGCGACTGGGTGACGATAGTGTTGGGCAACTCCCACACGGCGTGCATGGCGCTGCTGATCTGCAG‑GCCAAGGAAACCGATCGGa                                                                                                                               <  5:86799/149‑1 (MQ=255)              cGGATGCCTTTGAGGCCCACCAGGCACGATACAGTGTACATCGCGGTGACCAGGACGATGGTCAGCGACTGGGTGACGATAGTGTTGGGCAACTCCCACACGGCGTGCATGGCGCTGCTGATCTGCAG‑GCCAAGGAAACCGATCGGAcc                                                                                                                             >  4:5946/1‑149 (MQ=255)                   gCCTTTGAGGCCCACCAGGCACGATACAGTGTACATCGCGGTGACCAGGACGATGGTCAGCGACTGGGTGACGATAGTGTTGGGCAACTCCCACACGGCGTGCATGGCGCTGCTGATCTGCAG‑GCCAAGGAAACCGATCGGACCGATg                                                                                                                         <  1:150382/148‑1 (MQ=255)                            gCCCACCAGGCACGATACAGTGTACATCGCGGTGACCAGGACGATGGTCAGCGACTGGGTGACGATAGTGTTGGGCAACTCCCACACGGCGTGCATGGCGCTGCTGATCTGCAG‑GCCAAGGAAACCGATCGGACCGATGGTGCCGGcc                                                                                                                >  6:188335/1‑148 (MQ=255)                            gCCCACCAGGCACGATACAGTGTACATCGCGGTGACCAGGACGATGGTCAGCGACTGGGTGACGATAGTGTTGGGCAACTCCCACACGGCGTGCATGGCGCTGCTGATCTGCAG‑GCCAAGGAAACCGATCGGACCGATGGTGCCGGcc                                                                                                                <  5:188335/148‑1 (MQ=255)                               caccaGGCACGATACAGTGTACATCGCGGTGACCAGGACGATGGTCAGCGACTGGGTGACGATAGTGTTGGGCAACTCCCACACGGCGTGCATGGCGCTGCTGATCTGCAG‑GCCAAGGAAACCGATCGGACCGATGGTGCCGGCCACTa                                                                                                            >  6:20921/1‑149 (MQ=255)                                    ggCACGATACAGTGTACATCGCGGTGACCAGGACGATGGTCAGCGACTGGGTGACGATAGTGTTGGGCAACTCCCACACGGCGTGCATGGCGCTGCTGATCTACAG‑GCCAAGGaaa                                                                                                                                        <  7:11812/116‑1 (MQ=255)                                    ggCACGATACAGTGTACATCGCGGTGACCAGGACGATGGTCAGCGACTGGGTGACGATAGTGTTGGGCAACTCCCACACGGCGTGCATGGCGCTGCTGATCTACAG‑GCCAAGGaaa                                                                                                                                        <  7:16578/116‑1 (MQ=255)                                    ggCACGATACAGTGTACATCGCGGTGACCAGGACGATGGTCAGCGACTGGGTGACGATAGTGTTGGGCAACTCCCACACGGCGTGCATGGCGCTGCTGATCTACAG‑GCCAAGGaaa                                                                                                                                        >  8:11812/1‑116 (MQ=255)                                    ggCACGATACAGTGTACATCGCGGTGACCAGGACGATGGTCAGCGACTGGGTGACGATAGTGTTGGGCAACTCCCACACGGCGTGCATGGCGCTGCTGATCTACAG‑GCCAAGGaaa                                                                                                                                        >  8:16578/1‑116 (MQ=255)                                       aCGATACAGTGTACATCGCGGTGACCAGGACGATGGTCAGCGACTGGGTGACGATAGTGTTGGGCAACTCCCACACGGCGTGCATGGCGCTGCTGATCGGCAG‑GCCAAGGAAACCGATCGGACCGATGGTGCCGGCCACTACCGCgat                                                                                                     >  6:27907/1‑148 (MQ=255)                                          aTACAGTGTACATCGCGGTGACCAGGACGATGGTCAGCGACTGGGTGACGATAGTGTTGGGCAACTCCCACACGGCGTGCATGGCGCTGCTGATCTGCAG‑GCCAAGGAAACCGATCGGACCGATGGTGCCGGCCACTACCGCGATGATc                                                                                                 >  3:17852/1‑149 (MQ=255)                                              aGTGTACATCGCGGTGACCAGGACGATGGTCAGCGACTGGGTGACGATAGTGTTGGGCAACTCCCACACGGCGTGCATGGCGCTGCTGATCTGCAG‑GCCAAGGAAACCGATCGGACCGATGGTGCCGGCCACTACCGCGATGATCGAgg                                                                                             >  2:259183/1‑149 (MQ=255)                                                      tCGCGGTGACCAGGACGATGGTCAGCGACTGGGTGACGATAGTGTTGGGCAACTCCCACACGGCGTGCATGGCGCTGCTGATCTGCAG‑GCCAAGGAAACCGATCGGACCGATGGTGCCGGCCACTACCGCGATGATCGAGGCa                                                                                           >  6:195497/1‑143 (MQ=255)                                                      tCGCGGTGACCAGGACGATGGTCAGCGACTGGGTGACGATAGTGTTGGGCAACTCCCACACGGCGTGCATGGCGCTGCTGATCTGCAG‑GCCAAGGAAACCGATCGGACCGATGGTGCCGGCCACTACCGCGATGATCGAGGCa                                                                                           <  5:195497/143‑1 (MQ=255)                                                         cgGTGACCAGGACGATGGTCAGCGACTGGGTGACGATAGTGTTGGGCAACTCCCACACGGCGTGCATGGCGCTGCTGATCTGCAG‑GCCAAGGAAACCGATCGGACCGATGGTGCCGGCCACTACCGCGATGATCGAGGCAGCGTCGGc                                                                                   >  2:181135/1‑148 (MQ=255)                                                                cAGGACGATGGTCAGCGACTGGGTGACGATAGTGTTGGGCAACTCCCACACGGCGTGCATGGCGCTGCTGATCTGCAG‑GCCAAGGAAACCGATCGGACCGATGGTGCCGGCCACTACCGCGATGATCGAGGCAGCGTCGGCCAAGGTGc                                                                           >  1:56447/1‑149 (MQ=255)                                                                cAGGACGATGGTCAGCGACTGGGTGACGATAGTGTTGGGCAACTCCCACACGGCGTGCATGGCGCTGCTGATCTGCAG‑GCCAAGGAAACCGATCGGACCGATGGTGCCGGCCACTACCGCGATGATCGAGGCAGCGTCGGCCAAGGTGc                                                                           >  8:173593/1‑149 (MQ=255)                                                                cAGGACGATGGTCAGCGACTGGGTGACGATAGTGTTGGGCAACTCCCACACGGCGTGCATGGCGCTGCTGATCTGCAG‑GCCAAGGAAACCGATCGGACCGATGGTGCCGGCCACTACCGCGATGATCGAGGCAGCGTCGGCCAAGGTGc                                                                           <  1:40842/149‑1 (MQ=255)                                                                     cGATGGTCAGCGACTGGGTGACGATAGTGTTGGGCAACTCCCACACGGCGTGCATGGCGCTGCTGATCTGCAG‑GCCAAGGAAACCGATCGGACCGATGGTGCCGGCCACTACCGCGATGATCGAGGCAGCGTCGGCCAAGGTGCCGATc                                                                      >  1:185654/1‑149 (MQ=255)                                                                       aTGGTCAGCGACTGGGTGACGATAGTGTTGGGCAACTCCCACACGGCGTGCATGGCGCTGCTGATCTGCAG‑GCCAAGGAAACCGATCGGACCGATGGTGCCGGCCACTACCGCGATGATCGAGGCAGCGTCGGCCAAGGTGCCGATCgg                                                                    <  3:5946/149‑1 (MQ=255)                                                                       aTGGTCAGCGACTGGGTGACGATAGTGTTGGGCAACTCCCACACGGCGTGCATGGCGCTGCTGATCTGCAG‑GCCAAGGAAACCGATCGGACCGATGGTGCCGGCCACTACCGCGATGATCCAGGCAGCGTCGGCCAAGGTGCCGATCgg                                                                    <  1:181135/149‑1 (MQ=255)                                                                        tGGTCAGCGACTGGGTGACGATAGTGTTGGGCAACTCCCACACGGCGTGCATGGCGCTGCTGATCTGCAG‑GCCAAGGAAACCGATCGGACCGATGGTGCCGGCCACTACCGCGATGATCGAGGCAGCGTCGGCCAAGGTGCCGATCggg                                                                   <  7:273871/149‑1 (MQ=255)                                                                          gTCAGCGACTGGGTGACGATAGTGTTGGGCAACTCCCACACGGCGTGCATGGCGCTGCTGATCTGCAG‑GCCAAGGAAACCGATCGGACCGATGGTGCCGGCCACTACCGCGATGATCGAGGCAGCGTCGGCCAAGGTGCCGATCGGGcc                                                                 <  1:259183/149‑1 (MQ=255)                                                                             aGCGACTGGGTGACGATAGTGTTGGGCAACTCCCACACGGCGTGCATGGCGCTGCTGATCTGCAG‑GCCAAGGAAACCGATCGGACCGATGGTGCCGGCCACTACCGCGATGATCGAGGCAGCGTCGGCCAAGGTGCCGATCGGGCCCtt                                                              <  2:56447/149‑1 (MQ=255)                                                                                     ggTGACGATAGTGTTGGGCAACTCCCACACGGCGTGCATGGCGCTGCTGATCTGCAG‑GCCAAGGAAACCGATCGGACCGATGGTGCCGGCCACTACCGCGATGATCGAGGCAGCGTCGGCCAAGGTGCCGATCGGGCCCTTGAGcgctc                                                      <  5:55036/149‑1 (MQ=255)                                                                                        gACGATAGTGTTGGGCAACTCCCACACGGCGTGCATGGCGCTGCTGATCTGAAG‑GCCAAGGAAACCGATCGGACCGATGGTGCCGGCCACTACCGCGATGATCGAGGCAGCGTCGGCCAAGGTGCCGATCGGGCCCTTGAGcgctcgct                                                   >  5:282001/1‑149 (MQ=255)                                                                                           gATAGTGTTGGGCAACTCCCACACGGCGTGCATGGCGCTGCTGATCTGCAG‑GCCAAGGAAACCGATCGGACCGATGGTGCCGGc                                                                                                                 <  8:150995/84‑1 (MQ=255)                                                                                           gATAGTGTTGGGCAACTCCCACACGGCGTGCATGGCGCTGCTGATCTGCAG‑GCCAAGGAAACCGATCGGACCGATGGTGCCGGc                                                                                                                 >  7:150995/1‑84 (MQ=255)                                                                                                tgtTGGGCAACTCCCACACGGCGTGCATGGCGCTGCTGATCTGCAG‑GCCAAGGAAACCGATCGGACCGATGGTGCCGGCCACTACCGCGATGATCGAGGCAGCGTCGGCCAAGGTGCCGATCGGGCCCTTGAGCGCTCGCTTGCCGAAc                                           <  7:173593/149‑1 (MQ=255)                                                                                                   tGGGCAACTCCCACACGGCGTGCATGGCGCTGCTGATCTGCAG‑GCCAAGGAAACCGATCGGACCGATGGTGCCGGCCACTACCGCGATGATCGAGGCAGCGTCGGCCAAGGTGCCGATCGGGCCCTTGAGCGCTCGCTTGCCGAACAgg                                        >  5:318635/1‑149 (MQ=255)                                                                                                         aCTCCCACACGGCGTGCATGGCGCTGCTGATCTGCAG‑GCCAAGGAAACCGATCGGACCGATGGTGCCGGCCACTACCGCGATGATCGAGGCAGCGTCGGCCAAGGTGCCGATCGGGCCCTTGAGCGCTCGCTTGCCGAACAGGGGGTag                                  >  7:42899/1‑149 (MQ=255)                                                                                                         aCTCCCACACGGCGTGCATGGCGCTGCTGATCTGCAG‑GCCAAGGAAACCGATCGGACCGATGGTGCCGGCCACTACCGCGATGATCGAGGCAGCGTCGGCCAAGGTGCCGATCGGGCCCTTGAGCGCTCGCTTGCCGAACAGGGGGTag                                  <  5:20921/149‑1 (MQ=255)                                                                                                             ccACACGGCGTGCATGGCGCTGCTGATCTGCAG‑GCCAAGGAAACCGATCGGACCGATGGTGCCGGCCACTACCGCGATGATCGAGGCAGCGTCGGCCAAGGTGCCGATCGGGCCCTTGAGCGCTCGCTTGCCGAACAGGGGGTagag                                >  6:82342/1‑147 (MQ=255)                                                                                                             ccACACGGCGTGCATGGCGCTGCTGATCTGCAG‑GCCAAGGAAACCGATCGGACCGATGGTGCCGGCCACTACCGCGATGATCGAGGCAGCGTCGGCCAAGGTGCCGATCGGGCCCTTGAGCGCTCGCTTGCCGAACAGGGGGTagag                                >  1:6843/1‑147 (MQ=255)                                                                                                             ccACACGGCGTGCATGGCGCTGCTGATCTGCAG‑GCCAAGGAAACCGATCGGACCGATGGTGCCGGCCACTACCGCGATGATCGAGGCAGCGTCGGCCAAGGTGCCGATCGGGCCCTTGAGCGCTCGCTTGCCGAACAGGGGGTAGAGCa                              <  6:318635/149‑1 (MQ=255)                                                                                                                        gCATGGCGCTGCTGATCTGCAG‑GCCAAGGAAACCGATCGGACCGATGGTGCCGGCCACTACCGCGATGATCGAGGCAGCGTCGGCCAAGGTGCCGATCGGGCCCTTGAGCGCTCGCTTGcc                                               >  4:280692/1‑121 (MQ=255)                                                                                                                        gCATGGCGCTGCTGATCTGCAG‑GCCAAGGAAACCGATCGGACCGATGGTGCCGGCCACTACCGCGATGATCGAGGCAGCGTCGGCCAAGGTGCCGATCGGGCCCTTGAGCGCTCGCTTGcc                                               <  3:280692/121‑1 (MQ=255)                                                                                                                         cATGGCGCTGCTGATCTGCAG‑GCCAAGGAAACCGATCGGACCGATGGTGCCGGCCACTACCGCGATGATCGAGGCa                                                                                           >  5:148422/1‑76 (MQ=255)                                                                                                                         cATGGCGCTGCTGATCTGCAG‑GCCAAGGAAACCGATCGGACCGATGGTGCCGGCCACTACCGCGATGATCGAGGCa                                                                                           <  6:148422/76‑1 (MQ=255)                                                                                                                          cttggcctgcagATCAGCAGCGCCAAGGAAACCGATCGGACCGATGGTGCCGGCCACTACCGCGATGATCGAGGCAGCGTCGGCCAAGGTGCCGATCGGGCCCTTGAGCGCTCGCTTGCCGAACAGGGGGTAGAGCAGGGTACgcggcg                  >  3:175524/7‑149 (MQ=255)                                                                                                                             ggcctgcagATCAGCAGCGCCAAGGAAACCGATCGGACCGATGGTGCCGGCCACTACCGCGATGATCGAGGCAGCGTCGGCCAAGGTGCCGATCGGGCCCTTGAGCGCTCGCTTGCCGAACAGGGGGTAGAGCAGGGTACGCGgcgc                 <  3:66294/144‑1 (MQ=255)                                                                                                                             ggcctgcagATCAGCAGCGCCAAGGAAACCGATCGGACCGATGGTGCCGGCCACTACCGCGATGATCGAGGCAGCGTCGGCCAAGGTGCCGATCGGGCCCTTGAGCGCTCGCTTGCCGAACAGGGGGTAGAGCAGGGTACGCGgcgc                 >  4:66294/4‑147 (MQ=255)                                                                                                                               gctgctGATCTGCAG‑GCCAAGGAAACCGATCGGACCGATGGTGCCGGCCACTACCGCGATGATCGAGGCAGCGTCGGCCAAGGTGCCGATCg                                                                     <  3:302509/92‑1 (MQ=255)                                                                                                                               gctgctGATCTGCAG‑GCCAAGGAAACCGATCGGACCGATGGTGCCGGCCACTACCGCGATGATCGAGGCAGCGTCGGCCAAGGTGCCGATCg                                                                     >  4:302509/1‑92 (MQ=255)                                                                                                                                ctgctgATCTGCAG‑GCCAAGGAAACCGATCGGACCGATGGTGCCGGCCACTACCGCGATGATCGAGGCAGCGTCGGCCAAGGTGCCGATCGGGCCCTTGAGCGCTCGCTTGCCGAACAGGGGGTAGAGCAGGGTACGCGGCGCCAGCgg           <  4:17852/149‑1 (MQ=255)                                                                                                                                      aTCTGCAG‑GCCAAGGAAACCGATCGGACCGATGGTGCCGGCCACTACCGCGATGATCGAGGCAGCGTCGGCCAAGGTGCCGATCGGGCCCTTGAGCGCTCGCTTGCCGAACAGGGGGTAGAGCAGGGTACGCGGCGCCAGCGGAAgg       <  5:82342/147‑1 (MQ=255)                                                                                                                                         cgCAG‑GCCAAGGAAACCGATCGGACCGATGGTGCCGGCCACTACCGCGATGATCGAGGCAGCGTCGGCCAAGGTGCCGATCGGGCCCTTGAGCGCTCGCTTGCCGAACAGGGGGTAGAGCAGGGTACGCGGCGCCAGCGGAAGGCCttt  <  5:27907/148‑1 (MQ=255)                                                                                                                                          |                                                                                                                                                     TTCGCTGACAAAGCGGATGCCTTTGAGGCCCACCAGGCACGATACAGTGTACATCGCGGTGACCAGGACGATGGTCAGCGACTGGGTGACGATAGTGTTGGGCAACTCCCACACGGCGTGCATGGCGCTGCTGATCTGCAG‑GCCAAGGAAACCGATCGGACCGATGGTGCCGGCCACTACCGCGATGATCGAGGCAGCGTCGGCCAAGGTGCCGATCGGGCCCTTGAGCGCTCGCTTGCCGAACAGGGGGTAGAGCAGGGTACGCGGCGCCAGCGGAAGGCCTTT  >  NC_002947/3083240‑3083524

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: ‑