Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,534,777	C→A	9.4%	intergenic (+64/‑91)	atoB → / → PP_3124	3‑oxoacid CoA‑transferase subunit B/short chain fatty acid transporter

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,534,777	0	C	A	9.4%	158.1 / 6.9	53	intergenic (+64/‑91)	atoB/PP_3124	3‑oxoacid CoA‑transferase subunit B/short chain fatty acid transporter
Reads supporting (aligned to +/- strand):  ref base C (24/24);  new base A (2/3);  total (26/27)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.94e-01

AGCGTCGAGGAAATCATCGAGAAAACCGCCGGCAAACTGATCGTGCCGGATGATGTGAAGGAAATGACCTTCTAAGGCATGACGTGATCTCACCCTGTAGGCGCGGGTTTACCCGCGAATGCGTCGGTACATTGACCGCCGCATTCGCGGGTAAGCCTGTTCCTACAGGTTTTTTGCGTTGCCTGGCAATACCGCTTCATCCCATAAAACCAATAAAAGGAATTCAACCGTGGCCGCTGAAATTCAAGACAGCCGCTCCGCGCGCTTTGCCTTGC  >  NC_002947/3534639‑3534913                                                                                                                                           |                                                                                                                                         aGCGTCGAGGAAATCATCGAGAAAACCGCCGGCAAACTGATCGTGCCGGATGATGTGAAGGAAATGACCTTCTAAGGCATGACGTGATCTCACCCTGTAGGCGCGGGTTTACCCGCGAATGCGGCGGTCAATGTACCGACGCATTcgc                                                                                                                                 <  1:182223/148‑1 (MQ=38) aGCGTCGAGGAAATCATCGAGAAAACCGCCGGCAAACTGATCGTGCCGGATGATGTGAAGGAAATGACCTTCTAAGGCATGACGTGATCTCACCCTGTAGGCGCGGGCTTACCCGCGAATGCGGCGGTCAATGTACCGACGCATTcgc                                                                                                                                 <  5:129200/148‑1 (MQ=38)  gCGTCGAGGAGATCATCGAGAAAACCGCCGGCAAACTGATCGTGCCGGATGATGTGAAGGAAATGACCTTCTAAGGCATGACGTGATCTCACCCTGTAGGCGCGGGTTTACCCGCGAATGCGTCGGTACATTGACCGCCGCATTCGCgg                                                                                                                               <  2:227625/149‑1 (MQ=255)  gCGTCGAGGAAATCATCGAGAAAACCGCCGGCAAACTGATCGTGCCGGATGATGTGAAGGAAATGACCTTCTAAGGCATGACGTGATCTCACCCTGTAGGCGCGGGTTTACCCGCGAATGCGTCGGTACATTGACCGCCGCATTCGCgg                                                                                                                               <  5:29784/149‑1 (MQ=255)              tcatcGAGAAAACCGCCGGCAAACTGATCGTGCCGGATGATGTGAAGGAAATGACCTTCTAAGGCATGACGTGATCTCACCCTGTAGGCGCGGGTTTACCCGCGAATGCGTCGGTACATTGACCGCCGCATTCGCGGGTAAGCCTGTTc                                                                                                                   >  4:59340/1‑149 (MQ=255)                 tcGAGAAAACCGCCGGCAAACTGATCGTGCCGGATGATGTGAAGGAAATGACCTTCTAAGGCATGACGTGATCTCACCCTGTAGGCGCGGGTTTACCCGCGAGTGCGTCGGTACATTGACCGCCGCATTCGCGGGTAAGc                                                                                                                         >  7:278890/1‑140 (MQ=255)                 tcGAGAAAACCGCCGGCAAACTGATCGTGCCGGATGATGTGAAGGAAATGACCTTCTAAGGCATGACGTGATCTCACCCTGTAGGCGCGGGTTTACCCGCGAGTGCGTCGGTACATTGACCGCCGCATTCGCGGGTAAGc                                                                                                                         <  8:278890/140‑1 (MQ=255)                     gaAAACCGCCGGCAAACTGATCGTGCCGGATGATGTGAAGGAAATGACCTTCTAAGGCATGACGTGATCTCACCCTGTAGGCGCGGGTTTACCCGCGAATGCGTCGGTACATTGACCGCCGCATTCGCGGGTAAGCCTGTTCCTACAgg                                                                                                            >  6:201050/1‑149 (MQ=255)                                  aaaCTGATCGTGCCGTATGATGTGAAGGAAATGACCTTCTAAGGCATGACGTGATCTCACCCTGTAGGCGCGGGTTTACCCGCGAATGCGTCGGTACATTGACCGCCGCATTCGCGGGTAAGCCTATTc                                                                                                                   <  2:219221/129‑1 (MQ=255)                                       gATCGTGCCGGATGATGTGAATGAAATGACCTTCTAAGGCATGACGTGATCTCACCCTGTAGGCGCGGGTTTACCCGCGAATGCGTCGGTACATTGCCCGCCGCAGTCGCGGGTAAGCCTGGTCGTAAAGGTTTTTTGCGTTggatgg                                                                                           >  4:189764/1‑143 (MQ=255)                                        aTCGTGCCGGATGATGTTAAGGAAATGACCTTCTAAGGCATGACGTGATCTCACCCTGTAGGCGCGGGTTTACCCGCGAATGCGTCGGTACATTGACCGCCGCATTCGCGGGTAAGCCTGTTCCTACAGGTTTTTTGCGTTGCCTGGc                                                                                          <  2:204018/148‑1 (MQ=255)                                            tGCCGGTTTATGTGAAGGAAATGTCCTTCTAAGGCATGTCGTGATCTCACCGTGTAGGCGCGGGTTTAGGGGCGAATGCGTCTGTACTTTGAGGGCCGCATTCGCGTGTAAGCGTGTTCCTACAGGTTTTTTGCGTTGCCTGGCAATAc                                                                                     <  2:172047/149‑1 (MQ=255)                                               cGGATGATGTGAAGGAAATGACCTTCTAAGGCATGACGTGATCTCACCCTGTAGGCGCGGGTTTACCCGCGAATGCGTCGGTACATTGACCGCCGCATTCGCGGGTAAGCCTGTTCCTACAGGTTTTTTGCGTTGCCTgg                                                                                           <  7:154915/140‑1 (MQ=255)                                               cGGATGATGTGAAGGAAATGACCTTCTAAGGCATGACGTGATCTCACCCTGTAGGCGCGGGTTTACCCGCGAATGCGTCGGTACATTGACCGCCGCATTCGCGGGTAAGCCTGTTCCTACAGGTTTTTTGCGTTGCCTgg                                                                                           >  8:154915/1‑140 (MQ=255)                                               cGGATGATGTGAAGGAAATGACCTTCTAAGGAATGACGTGATCTCACCCTGTAGGCGCGGGTTTACCCGCGAATGCGTCGGTACATTGACCGCCGCATTCGCGGGTAAGCCTGTTCCTACAGGTTTTTTGCGTTGCATGGCAATACCg                                                                                   >  7:8415/1‑148 (MQ=255)                                                  atgatgTGAAGGAAATGACCTTCTAAGGCATGACGTGATCTCACCCTGTAGGCGCGGGTTTACCCGCGAATGCGTCGGTACATTGACCGCCGCATTCGCGGGTAAGCCTGTTCCTACAGGTTTTTTGCGTTGCCTGGCAATACCGCTTc                                                                               <  5:201050/149‑1 (MQ=255)                                                   ttatttgAAGGAAATGACCTTCTAAGGCATGACTTGATCTCACACTGTTGGCGCGGGTTTACCCGCGAATGCGTCGGTACATTGACCGCGGCATTCGCGGGTAAGCCTGTTCCTACAGGTTTTTTGCGTTGCCTGGCAATACCGCTTc                                                                               <  8:211718/143‑1 (MQ=39)                                                      tgtgAAGGAAATGACCTTCTAAGGCATGACGTGATCTCACCCTGTAGGCGCGGGTTTACCCGCGAATGCGTCGGTACATTGACCGCCGCATTCGCGGGTAAGCCTGTTCCTACAGGTTTTTTGCGTTGCCTGGCAATACCGCTTCATcc                                                                           >  7:326852/1‑149 (MQ=255)                                                      tgtgAAGGAAATGACCTTCTAAGGCATGACGTGATCTCACCCTGTAGGCGCGGGTTTACCCGCGAATGCGTCGGTACATTGACCGCCGCATTCGCGGGTAAGCCTGTTCCTACAGGTTTTTTGCGTTGCCTGGCAATACCGCTTCATc                                                                            <  3:189764/148‑1 (MQ=255)                                                         gAAGGAAATGACCTTCTAAGGCATGACGTGATCTCACCCTGTAGGCGCGGGTTTACCCGCGAATGCGTCGGTACATTGACCGCCGCATTCGCGGGTAAGCCTGTTCCTACAGGTTTTTTGCGTTGCCTGGCAATACCGCTTCATCCCa                                                                         >  7:239410/1‑148 (MQ=255)                                                                 tGACCTTCTAAGGCATGACGTGATCTCACCCTGTAGGCGCGGGTTTACCCGCGAATGCGTCGGTACATTGACCGCCGCATTCGCGGGTAAGCCTGTTCCTACAGGTTTTTTGCGTTGCCTGGCAATACCGCTTCATCCCATAAAACCaa                                                                <  8:326852/149‑1 (MQ=255)                                                                      ttCTAAGGCATGACGTGATCTCACCCTGTAGGCGCGGGTTTACCCGCGAATGCGTCGGTACATTGACCGCCGCATTCGCGGGTAAGCCTGTTCCTACAGGTTTTTTGCGTTGCCTGGCAATACCGCTTCATCCCATAAAACCAATaa                                                             >  7:234554/1‑147 (MQ=255)                                                                       tCTAAGGCATGACGTGATCTCACCCTGTAGGCGCGGGTTTACCCGCGAATGCGTCGGTACATTGACCGCCGCATTCGCGGGTAAGCCTGTTCCTACAGGTTTTTTGCGTTGCCTGGCAATACCGCTTCATCCCATAAAACCAATAAAAg                                                          >  4:238921/1‑149 (MQ=255)                                                                        cTAAGGCATGACGTGATCTCACCCTGTAGGCGCGGGTTTACCCGCGAATGCGTCGGTACATTGACCGCCGCATTCGCGGGTAAGCCTGTTCCTACAGGTTTTTTGCGTTGCCTGGCAATACCGCTTCATCCCATAAAACCAATaaaa                                                           <  1:6000/147‑1 (MQ=255)                                                                           aGGCATGACGTGATCTCACCCTGTAGGCGCGGGTTTACCCGCGAATGCGTCGGTACATTGACCGCCGCATTCGCGGGTAAGCCTGTTCCTACAGGTTTTTTGCGTTGCCTGGCAATACCGCTTCATCCCATAAAACCAATAAAAGGAAt                                                      >  3:298009/1‑149 (MQ=255)                                                                                      gATCTCACCCTGTAGGCGCGGGTTTACCCGCGAATGCGTCGGTACATTGACCGCCGCATTCGCGGGTAAGCCTGTTCCTACAGGTTTTTTGCGTTGCCTGGCAATACCGCTTCATCCCATAAAACCAATAAAAGGaa                                                       >  4:135907/1‑137 (MQ=255)                                                                                      gATCTCACCCTGTAGGCGCGGGTTTACCCGCGAATGCGTCGGTACATTGACCGCCGCATTCGCGGGTAAGCCTGTTCCTACAGGTTTTTTGCGTTGCCTGGCAATACCGCTTCATCCCATAAAACCAATAAAAGGaa                                                       <  3:135907/137‑1 (MQ=255)                                                                                          tcACCCTGTAGGCGCGGGTTTTCCCGCGAATGCGTCGGTACATTGACCGCCGCATTCGCGGGTAAGCCTGTTCCTACAGGTTTTTTGCGTTGCCTGGCAATACCGCTTCATCCCATAAAACCAATAAAAGGAATTCAACCGTGGCCGCt                                       >  4:153014/1‑149 (MQ=255)                                                                                          tcACCCTGTAGGCGCGGGTTTACCCGCGAATGCGTCGGTACATTGACCGCCGCATTCGCGGGTAAGCCTGTTCCTACAGGTTTTTTGCGTTGCCTGGCAATACCGCTTCATCCCATAAAACCAATAAAAGGAATTCAACCGTGGCCGCt                                       >  2:332209/1‑149 (MQ=255)                                                                                           cACCCTGTAGGCGCGGGTTTACCCGCGAATGCGTCGGTACATTGACCGCCGCATTCGCGGGTAAGCCTGTTCCTACAGGTTTTTTGCGTTGCCTGGCAATACCGCTTCATCCCATAAAACCAATaaaa                                                           <  5:105554/128‑1 (MQ=255)                                                                                           cACCCTGTAGGCGCGGGTTTACCCGCGAATGCGTCGGTACATTGACCGCCGCATTCGCGGGTAAGCCTGTTCCTACAGGTTTTTTGCGTTGCCTGGCAATACCGCTTCATCCCATAAAACCAATaaaa                                                           >  6:105554/1‑128 (MQ=255)                                                                                             cccTGTAGGCGCGGGTTTACCCGCGAATGCGTCGGTACATTGACCGCCGCATTCGCGGGTAAGCCTGTTCCTACAGGTTTTTTGCGtt                                                                                                 <  4:327878/88‑1 (MQ=255)                                                                                             cccTGTAGGCGCGGGTTTACCCGCGAATGCGTCGGTACATTGACCGCCGCATTCGCGGGTAAGCCTGTTCCTACAGGTTTTTTGCGtt                                                                                                 >  3:327878/1‑88 (MQ=255)                                                                                             cccTGTAGGCGCGGGTTTACCCGCGAATGCGTCGGTACATTGACCGCCGCATTCGCGGGTAAGCCTGTTCCTACAGGTTTTTTGCGTTGCCTGGCAATACCGCTTCATCCCATAAAACCAATAAAAGGAATTCAACCGTGGCCGCTGaa                                    <  4:298009/149‑1 (MQ=255)                                                                                              ccTGTAGGCGCGGGTTTACCCGCGAATGCGTCGGTACATTGACCGCCGCATTCGCGGGTAAGCCTGTTCCTACAGGTTTTTTGCGTTGCCTGGCAATACCGCTTCATCCCATAAAACCAATAAAAGGAATTCAACCGTGGCCGCTGaaa                                   >  1:57721/1‑149 (MQ=255)                                                                                                  tAGGCGCGGGTTTACCCGCGAATGCGTCGGTACATTGACCGCCGCATTCGCGGGTAAGCCTGTTCCTACAGGTTTTTTGCGTTGCCTGGCAATACCGCTTCATCCCATAAAACCAATAAAAGGAATTCAACCGTGGCCGCTGAAATTCa                               <  1:332209/149‑1 (MQ=255)                                                                                                              tACACGCGAATGCGTGGGTAGATTGTCCGCAGCTTTCGGGGGTAAGGCTGTTCCTAGAGGTTTTTTGCGTTGCCTGGCAATTCCGGTTCATCACATAATACCATTAAAAGGAATTCAACCGTGGCCGCTGAAATTCAAGACAGCCgat                    <  8:8415/148‑3 (MQ=255)                                                                                                                 ccGCGAATGCGTCGGTACATTGACCGCCGCATTCGCGGGTAAGCCTGTTCCTACAGGTTTTTTGCGTTGCCTGGCAATACCGCTTCATCCCATAAAACCAATAAAAGGAATTCAACCGTGGCCGCTGAAATTCAAGACAGCCGCTCcgc                >  5:205142/1‑149 (MQ=255)                                                                                                                  cgcgAATGCGGCGGTCAATGTACCGACGCATTCGCGGGTAAGCCTGTTCCTACAGGTTTTTTGCGTTGCCTGGCAATACCGCTTCATCCCATAAAACCAATAAAAGGAATTCAACCGTGGCCGCTGAAATTCAAGACAGCCGCTCcgcg               >  7:276017/1‑149 (MQ=38)                                                                                                                   gcgAATGCGTCGGTACATTGACCGCCGCATTCGCGGGTAAGCCTGTTCCTACAGGTTTTTTGCGTTGCCTGGCAATACCGCTTCATc                                                                            <  7:142798/87‑1 (MQ=255)                                                                                                                   gcgAATGCGTCGGTACATTGACCGCCGCATTCGCGGGTAAGCCTGTTCCTACAGGTTTTTTGCGTTGCCTGGCAATACCGCTTCATCCCATAAAACCAATAAAAGGAATTCAACCGTGGCCGCTGAAATTCAAGACAGCCGCTCcgcgc              >  6:230680/1‑149 (MQ=255)                                                                                                                   gcgAATGCGTCGGTACATTGACCGCCGCATTCGCGGGTAAGCCTGTACCTACAGGTTTTTTGCGTTGCCTGGCAATACCGCTTCATc                                                                            >  8:142798/1‑87 (MQ=255)                                                                                                                    cgAATGCGTCGGTACATTGACCGCCGCATTCGCGGGTAAGCCTGTTCCTACAGGTTTTTTGCGTTGCCTGGCAATACCGCTTCATCCCATAAAACCAATAAAAGGAATTCAACCGTGGCCGCTGAAATTCAAGACAGCCGCTCcgcgcg             >  3:269087/1‑149 (MQ=255)                                                                                                                     gAATGCGTCGGTACATTGACCGCCGCATTCGCGGGTAAGCCTGTTCCTACAGGTTTTTTGCGTTGCCTGGCAATACCGCTTCATCCCATAAAACCAATAAAAGGAATTCAACCGTGGCCGCTGAAATTCAAGACAGCCGCTCCgcgcgc            <  5:230680/149‑1 (MQ=255)                                                                                                                     gAATGCGGCGGTCAATGTACCGACGCATTCGCGGGTAAACCCGCGCCTACAGGTTTTTTGCGTTGCCTGGCAATACCGCTTCATCCCATAAAACCAATAAAAGGAATTCAACCGTGGCCGCTGAAATTCAAGa                            <  8:138475/133‑1 (MQ=21)                                                                                                                     gAATGCGGCGGTCAATGTACCGACGCATTCGCGGGTAAACCCGCGCCTACAGGTTTTTTGCGTTGCCTGGCAATACCGCTTCATCCCATAAAACCAATAAAAGGAATTCAACCGTGGCCGCTGAAATTCAAGa                            >  7:138475/1‑133 (MQ=21)                                                                                                                       aTGCGTCGGTACATTGACCGCCGCATTCGCGGGTAAGCCTGTTCCTACAGGTTTTTTGCGTTGCCTGGCAATACCGCTTCATCCCATAAAACCAATAAAAGGAATTCAACCGTGGCCGCTGAAATTCAAGACAGCCGCTCcgc                >  8:235519/1‑143 (MQ=255)                                                                                                                       aTGCGTCGGTACATTGACCGCCGCATTCGCGGGTAAGCCTGTTCCTACAGGTTTTTTGCGTTGCCTGGCAATACCGCTTCATCCCATAAAACCAATAAAAGGAATTCAACCGTGGCCGCTGAAATTCAAGACAGCCGCTCcgc                <  7:235519/143‑1 (MQ=255)                                                                                                                           gTCGGTACATTGACCGCCGCATTCGCGGGTAAGCCTGTTCCTACAGGTTTTTTGCGTTGCCTGGCAATACCGCTTCATCCCATAAAACCAATAAAAGGAATTCAACCGTGGCCGCTGAAATTCAAGACAGCCGCTCCGCGCGCTTTGcc      <  8:234554/149‑1 (MQ=255)                                                                                                                            tCGGTACATTGACCGCCGCATTCGCGGGTAAGCCTGTTCCTACAGGTTTTTTGCGTTGCCTGGCAATACCGCTTCATCCCATAAAACCAATAAAAGGAATTCAACCGTGGCCGCTGAAATTCAAGACAGCCGCTCCGCGCGCTTTGCCt     <  3:59340/149‑1 (MQ=255)                                                                                                                               gTACATTGACCGCCGCATTCGCGGGTAAGCCTGTTCCTACAGGTTTTTTGCGTTGCCTGGCAATACCGCTTCATCCCATAAAACCAATAAAAGGAATTCAACCGTGGCCGCTGAAATTCAAGACAGCCGCTCCGCGCGCTTTGCCTTgc  >  3:4193/1‑149 (MQ=255)                                                                                                                                   aTTGACCGCCGCATTCGCGGGTAAGCCTGTTCCTACAGGTTTTTTGCGTTGCCTGGCAATACCGCTTCATCCCATAAAACCAATAAAAGGAATTCAACCGTGGCCGCTGAAATTCAAGACAGCCGCTCCgcgcgc            <  6:158861/135‑1 (MQ=255)                                                                                                                                   aTTGACCGCCGCATTCGCGGGTAAGCCTGTTCCTACAGGTTTTTTGCGTTGCCTGGCAATACCGCTTCATCCCATAAAACCAATAAAAGGAATTCAACCGTGGCCGCTGAAATTCAAGACAGCCGCTCCgcgcgc            >  5:158861/1‑135 (MQ=255)                                                                                                                                           |                                                                                                                                         AGCGTCGAGGAAATCATCGAGAAAACCGCCGGCAAACTGATCGTGCCGGATGATGTGAAGGAAATGACCTTCTAAGGCATGACGTGATCTCACCCTGTAGGCGCGGGTTTACCCGCGAATGCGTCGGTACATTGACCGCCGCATTCGCGGGTAAGCCTGTTCCTACAGGTTTTTTGCGTTGCCTGGCAATACCGCTTCATCCCATAAAACCAATAAAAGGAATTCAACCGTGGCCGCTGAAATTCAAGACAGCCGCTCCGCGCGCTTTGCCTTGC  >  NC_002947/3534639‑3534913

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: ‑