Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,460,273:1	+A	9.1%	coding (132/1446 nt)	PP_3075 ←	transcriptional regulator

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,460,273	1	.	A	9.1%	202.9 / 15.2	55	coding (132/1446 nt)	PP_3075	transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base . (26/24);  new base A (3/2);  total (29/26)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.92e-01

GCCGGGGATCACTGTTTCGCACGGCTGGCCGATGGCACTGGCAGCGTCGGCCAGGCCAAAGCGT‑CGGGCGTAGCGTTCGTT‑CATCCAGACGATGCG‑‑TGCCTGGCGGTCGACGATCACCGTGCCCTCGCTGGACTGTTCGATGATC‑TCGAACAG‑CGAGCGGATCGCCAGTTGCCGTACCTGGGGGTAGTCCTTGAGGCTGTCGCTGTCGTGCATGGGTGAACATCCTGAATCATGTATTGGCACAAGCCCGCGAAAAGGCCAGGCCTGAAAACTCATCGTCGGGGGTCAAAC  >  NC_002947/3460129‑3460419                                                                                                                                                      |                                                                                                                                                    gCCGGGGATCACTGTTTCGCACGGCTGGCCGATGGCACTGGCAGCGTCGGCCAGGCCAAAGCGT‑CGGGCGTAGCGTTCGTT‑CATCCACAAGAGCCGGACGCGCGGCGGT‑G‑CTGTCGCCGTGCCCTCGCTGGACTGTTCGATGATC‑TCGaa                                                                                                                                                <  1:570777/150‑1 (MQ=255)       gATCACTGTTTCGCACGGCTGGCCGATGGCACTGGCAGCGTCGGCCAGGCCAAAGCGT‑CGGGCGTAGCGTTCGTT‑CATCCAGACGATGCG‑‑TGCCTGGCGGTCGACGATCACCGTGCCCTCGCTGGACTGTTCGATGATC‑TCGAACag‑cga                                                                                                                                         >  2:404330/1‑150 (MQ=255)           aCTGTTTCGCACGGCTGGCCGATGGCACTGGCAGCGTCGGCCAGGCCAAAGCGT‑CGGGCGTAGCGTTCGTT‑CATCCAGACGATGCG‑‑TGCCTGGCGGTCGACGATCACCGTGCCCTCGCTGGACTGTTCGATGATC‑TCGAACAG‑CGAGCgg                                                                                                                                     >  2:281965/1‑150 (MQ=255)            cTGTTTCGCACGGCTGGCCGATGGCACTGGCAGCGTCGGCCAGGCCAAAGCGT‑CGGGCGTAGCGTTCGTT‑CATCCAGACGATGCG‑‑TGCCTGGCGGTCGACGATCACCGTGCCCTCGCTGGACTGTTCGATGATC‑TCGAACAG‑CGAGCGGa                                                                                                                                    >  2:1111734/1‑150 (MQ=255)             tGTTTCGCACGGCTGGCCGATGGCACTGGCAGCGTCGGCCAGGCCAAAGCGT‑CGGGCGTAGCGTTCGTT‑CATCCAGACGATGCG‑‑TGCCTGGCGGTCGACGATCACCGTGCCCTCGCTGGACTGTTCGATGATC‑TCGAACAG‑CGAGCGGAt                                                                                                                                   >  1:909447/1‑150 (MQ=255)             tGTTTCGCACGGCTGGCCGATGGCACTGGCAGCGTCGGCCAGGCCAAAGCGT‑CGGGCGTAGCGTTCGTT‑CATCCAGACGATGCG‑‑TGCCTGGCGGTCGACGATCACCGTGCCCTCGCTGGACTGTTCGATGATC‑TCGAACAG‑CGAGCGGAt                                                                                                                                   >  1:671685/1‑150 (MQ=255)              gTTTCGCACGGCTGGCCGATGGCACTGGCAGCGTCGGCCAGGCCAAA‑CGTGCGGGCGTAGCGTTCGTT‑CATCCAGACGATGCG‑‑TGCCTGGCGGTCGACGATCACCGTGCCCTCGCTGGACTGTTCGATGATC‑TCGAACAG‑CGAGCGGATc                                                                                                                                  <  1:397065/150‑1 (MQ=255)               tttCGCACGGCTGGCCGATGGCACTGGCAGCGTCGGCCAGGCCAAAGCGT‑CGGGCGTAGCGTTCGTT‑CATCCAGACGATGCG‑‑TGCCTGGCGGTCGACGATCACCGTGCCCTCGCTGGACTGTTCGATGATC‑TCGAACAG‑CGAGCGGATCg                                                                                                                                 >  2:141582/1‑150 (MQ=255)                     aCGGCTGGCCGATGGCACTGGCAGCGTCGGCCAGGCCAAAGCGT‑CGGGCGTAGCGTTCGTT‑CATCCAGACGATGCG‑‑TGCCTGGCGGTCGACGATCACCGTGCCCTCGCTGGACTGTTCGATGATC‑TCGAACAG‑CGAGCGGATCGCCAGtt                                                                                                                           <  2:347745/150‑1 (MQ=255)                          tGGCCGATGGCACTGGCAGCGTCGGCCAGGCCAAAGCGT‑CGGGCGTAGCGTTCGTT‑CATCCAGACGATGCG‑‑TGCCTGGCGGTCGACGATCACCGTGCCCTCGCTGGACTGTTCGATGGTC‑TCGAGCAG‑CGAGCGGATCGCCAGTTGCCgg                                                                                                                      >  2:559546/1‑149 (MQ=255)                                   gCACTGGCAGCGTCGGCCAGGCCAAAGCGT‑CGGGCGTAGCGTTCGTT‑CATCCAGACGATGCG‑‑TGCCTGGCGGTCGACGATCACCGTGCCCTCGCTGGACTGTTCGATGATC‑TCGAACAG‑CGAGCGGATc                                                                                                                                  >  2:374610/1‑129 (MQ=255)                                   gCACTGGCAGCGTCGGCCAGGCCAAAGCGT‑CGGGCGTAGCGTTCGTT‑CATCCAGACGATGCG‑‑TGCCTGGCGGTCGACGATCACCGTGCCCTCGCTGGACTGTTCGATGATC‑TCGAACAG‑CGAGCGGATc                                                                                                                                  <  1:374610/129‑1 (MQ=255)                                    cACTGGCAGCGTCGGCCAGGCCAAAGCGT‑CGGGCGTAGCGTTCGTT‑CATCCAGACGATGCG‑‑TGCCTGGCGGTCGACGATCACCGTGCCCTCGCTGGACTGTTCGATGATC‑TCGAACAG‑CGAGCGGATCGCCAGTTGCCGTACCTGGGGGt                                                                                                            >  2:384523/1‑150 (MQ=255)                                         gCAGCGTCGGCCAGGCCAAAGCGT‑CGGGCGTAGCGTTCGTT‑CATCCAGACGATGCG‑‑TGCCTGGCGGTCGACGATCACCGTGCCCTCGCTGGACTGTTCGATGATC‑TCGAACAG‑CGAGCGGATCGCCAGTTGCCGTACCTGGGGGTAGTcc                                                                                                       >  1:1087885/1‑150 (MQ=255)                                         gCAGCGTCGGCCAGGCCAAAGCGT‑CGGGCGTAGCGTTCGTT‑CATCCAGACGATGCG‑‑TGCCTGGCGGTCGACGATCACCGTGCCCTCGCTGGACTGTTCGATGATC‑TCGAACAG‑CGAGCGGATCGCCAGTTGCCGTACCCGGGGGTAGTcc                                                                                                       >  2:255927/1‑150 (MQ=255)                                              gTCGGCCAGGCCAAAGCGT‑CGGGCGTAGCGTTCGTT‑CATCCAGACGATGCG‑‑TGCCTGGCGGTCGACGATCACCGTGCCCTCGCTGGACTGTTCGATGATC‑TCGAACAG‑CGAGCGGATCGCCAGTTGCCGTACCTGGGGGTAGTCCTTGAg                                                                                                  <  2:761766/150‑1 (MQ=255)                                              gTCGGCCAGGCCAAAGCGT‑CGGGCGTAGCGATAGTTATATTTTG‑CGATGCG‑‑TGCCTGGCGGTCGACGATCACCGTGCCCTCGCTGGACTGTTCGATGATC‑TCGAACAG‑CGAGCGGATCGCCAGTTGCCGTACCTGGGGGTAGTCCTTGAg                                                                                                  <  2:820821/150‑1 (MQ=255)                                                    caggccaAAGCGT‑CGGGCGTAGCGTTCGTT‑CATCCAGACGATGCG‑‑TGCCTGGCGGTCGACGATCACCGTGCCCTCGCTGGACTGTTCGATGATC‑TCGAACAG‑CGAGCGGATCGCCAGTTGCCGTACCTGGGGGTAGTCCTTGAGgctgtc                                                                                            <  2:671685/150‑1 (MQ=255)                                                       gccaCAGCGT‑CGGGCGTAGCGTACGCT‑CATCCAGACGATGCG‑‑TGCCTGGCGGTCGACGATCACCGTGCCCTCGCTGCACTGTTCGATGATC‑TCGAACAG‑CGAGCGGATCGCCAGTTGCCGTACCTGCGGGTAGTCCTTGAGgctgtcgct                                                                                         <  2:554694/150‑1 (MQ=255)                                                       gccaAAGCGT‑CGGGCGTAGCGTTCGTT‑CATCCAGACGATGCG‑‑TGCCTGGCGGTCGACGATCACCGTGCCCTCGCTGGACTGTTCGATGATC‑TCGAACAG‑CGAGCGGATCGCCAGTTGCCGTACCTGGGGGTAGTCCTTGAGgctgtcgct                                                                                         >  2:169923/1‑150 (MQ=255)                                                         caAAGCGT‑CGGGCGTAGCGTTCGTT‑CATCCAGACGATGCG‑‑TGCCTGGCGGTCGACGATCACCGTGCCCTCGCTGGACTGTTCGATGATC‑TCGAACAG‑CGAGCGGATCGCCAGTTGCCGTACCTGGGGGTAGTCCTTGAGgctgtcgctgt                                                                                       >  1:832396/1‑150 (MQ=255)                                                         caAAGCGT‑CGGGCGTAGCGTTCGTT‑CATCCAGACGATGCG‑‑TGCCTGGCGGTCGACGATCACCGTGCCCTCGCTGGACTGTTCGA‑GATCATCGAACagtcc                                                                                                                                          >  2:527265/1‑97 (MQ=255)                                                         caAAGCGT‑CGGGCGTAGCGTTCGTT‑CATCCAGACGATGCG‑‑TGCCTGGCGGTCGACGATCACCGTGCCCTCGCTGGACTGTTCGA‑GATCATCGAACagtcc                                                                                                                                          <  1:527265/100‑4 (MQ=255)                                                                t‑CGGGCGTAGCGTTCGTT‑CATCCAGACGATGCG‑‑TGCCTGGCGGTCGACGATCACCGTGCCCTCGCTGGACTGTTCGATGATC‑TCGaa                                                                                                                                                <  2:377584/87‑1 (MQ=255)                                                                t‑CGGGCGTAGCGTTCGTT‑CATCCAGACGATGCG‑‑TGCCTGGCGGTCGACGATCACCGTGCCCTCGCTGGACTGTTCGATGATC‑TCGaa                                                                                                                                                >  1:377584/1‑87 (MQ=255)                                                                   gggCGTAGCGTTCGTT‑CATCCAGACGATGCG‑‑TGCCTGGCGGTCGACGATCACCGTGCCCTCGCTGGACTGTTCGATGATC‑TCGAACAG‑CGAGCGGATCGCCAGTTGCCGTACCTGGGGGTAGTCCTTGAGGCTGTCGCTGTCGTGCATgg                                                                              <  2:353359/150‑1 (MQ=255)                                                                            gttcgtt‑cATCCAGACGATGCG‑‑TGCCTGGCGGTCGACGATCACCGTGCCCTCGCTGGACTGTTCGATGATC‑TCGAACAG‑CGAGCGGATCGCCAGTTGCCGTACCTGGGGGTAGTCCTTGAGGCTGTCGCTGTCGTGCATGGGTGAACATc                                                                     <  1:4113/150‑1 (MQ=255)                                                                            gttcgtt‑cATCCAGACGATGCG‑‑TGCCTGGCGGTCGACGATCACCGTGCCCTCGCTGGACTGTTCGATGATC‑TCGAACAG‑CGAGCGGATCGCCAGTTGCCGTACCTGGGGGTAGTCCTTGAGGCTGTCGCTGTCGTGCATGGGTGAACATc                                                                     <  1:141582/150‑1 (MQ=255)                                                                              tcgtt‑cCTCGAGTCGCTGCG‑‑GGCCTGGCGGGCGACGATCACCGTGCCCTCGCTGGACTGTTCGATGATC‑TCGAACAG‑CGAGCGGATCGCCAGTTGCCGTACCTGGGGGTAGTCCTTGAGGCTGTCGCTGTCGTGCATGGGTGAACATCCt                                                                   <  2:1087885/150‑1 (MQ=255)                                                                                       ccAGACGATGCG‑‑TGCCTGGCGGTCGACGATCATCGATCCCTCGCTGGACTGTTCGATGATC‑TCGAACAG‑CGAGCGGATCGCCAGTTGCCGTACCTGGGGGTAGTCCTTGAGGCTGTCGCTGTCGTGCATGGGTGAACATCCTGAATCATg                                                           >  1:366758/1‑150 (MQ=255)                                                                                         aGACGATGCG‑‑TGCCTGGCGGTCGACGATCACCGTGCCCTCGCTGGACTGTTCGATGATC‑TCGAACAG‑CGAGCGGATCGCCAGTCGCCGTACCTGGGGGTAGTCCTTGAGGCTGTCGCTGTCGTGCATGGGTGAACATCCTGAATCATGTa                                                         >  2:875433/1‑150 (MQ=255)                                                                                         aGACGATGCG‑‑TGCCTGGCGGTCGACGATCACCGAGCCCTCGCTGGACTGTTCGATGATC‑TCGAACAG‑CGAGCGGATCGCCAGCCGGAGTACCGGGGGGTAGTCCTTGAGGCTGTCGCTGTCGTGCATGGGTGAACATCCTGAATCATGTa                                                         >  2:875092/1‑150 (MQ=255)                                                                                          gACGATGCG‑‑TGCCTGGCGGTCGACGATCACCGTGCCCTCGCTGGACTGTTCGATGATC‑TCGAACAG‑CGAGCGGATCGCCAGTTGCCGTACCTGGGGGTAGTCCTTGAGGCTGTCGCTGTCGTGCATGGGTGAACATCCTGAATCATGTAt                                                        <  2:545328/150‑1 (MQ=255)                                                                                                     tGCCTGGCGGTCGACGATCACCGTGCCCTCGCTGGACTGTTCGATGATC‑TCGAACAG‑CGAGCGGATCGCCAGTTGCCGTACCTGGGGGTAGTCCTTGAGGCTGTCGCTGTCGTGCATGGGTGAACATCCTGAATCATGTATTGGCACAAg                                               >  1:939949/1‑150 (MQ=255)                                                                                                         tGGCGGTCGACGATCACCGTGCCCTCGCTGGACTGTTCGATGATC‑TCGAACAG‑CGAGCGGATCGCCAGTTGCCGTACCTGGGGGTAGTCCTTGAGGCTGTCGCTGTCGTGCATGGGTGAACATCCTGAATCATGTATTGGCACAAGCCcg                                           <  2:939949/150‑1 (MQ=255)                                                                                                              gTCGACGATCACCGTGCCCTCGCTGGACTGTTCGATGATC‑TCGAACAG‑CGAGCGGATCGCCAGTTGCCGTACCTGGGGGTAGTCCTTGAGGCTGTCGCTGTCGTGCATGGGTGAACATCCTGAATCATGTATTGGCACAAGCCCGCGaaa                                      >  1:546843/1‑150 (MQ=255)                                                                                                                cgacgaTCACCGTGCCCTCGCTGGACTGTTCGATGATC‑TCGAACAG‑CGAGCGGATCGCCAGTTGCCGTACCTGGGGGTAGTCCTTGAGGCTGTCGCTGTCGTGCATGGGTGAACATCCTGAATCATGTATTGGCACAAGCCCGCGAAAag                                    <  1:1120891/150‑1 (MQ=255)                                                                                                                    gaacACCGTGCCCGCGCGCGACGGTCCGAGGATC‑TCGAACAG‑CCAGCGGATCGCCAGTTGCCGTACCTGGGGGTAGTCCTTGAGGCGGTCGCTGTCGTGCATGGGTGAACATCCTGAATCATGTATTGGCATAAGCCCGCGAAAtggcca                                <  2:72908/147‑1 (MQ=255)                                                                                                                    gaTCACCGTGCCCTCGCTGGACTGTTCGATGATC‑TCGAACAG‑CGAGCGGATCGCCAGTTGCCGTACCTGGGGGTAGTCCTTGAGGCTGTCGCTGTCGTGCATGGGTGAACATCCTGAATCATGTATTGGCACAAGCCCGCGAAAaggcca                                <  2:961408/150‑1 (MQ=255)                                                                                                                       cACCGTGCCCTCGCTGGACTGTTCGATGATC‑TCGAACAG‑CGAGCGGATCGCCAGTTGCCGTACCTGGGGGTAGTCCTTGAGGCTGTCGCTGTCGTGCATGGGTGAACATCCTGAATCATGTATTGGCACAAGCCCGCGAAAaggccaggc                             <  1:559546/150‑1 (MQ=255)                                                                                                                           gTGCCCTCGCTGGACTGTTCGATGATC‑TCGAACAG‑CGAGCGGATCGCCAGTTGCCGTACCTGGGGGTAGTCCTTGAGGCTGTCGCTGTCGTGCATGGGTGAACATCCTGAATCATGTATTGGCACAAGCCCGCGAAAAGGCCAGGCCTGa                         >  2:79821/1‑150 (MQ=255)                                                                                                                                cTCGCTGGACTGTTCGATGATC‑TCGAACAG‑CGAGCGGATCGCCAGTTGCCGTACCTGGGGGTAGTCCTTGAGGCTGTCGCTGTCGTGCATGGGTGa                                                                          <  2:658380/96‑1 (MQ=255)                                                                                                                                cTCGCTGGACTGTTCGATGATC‑TCGAACAG‑CGAGCGGATCGCCAGTTGCCGTACCTGGGGGTAGTCCTTGAGGCTGTCGCTGTCGTGCATGGGTGa                                                                          >  1:658380/1‑96 (MQ=255)                                                                                                                                cTCGCTGGACTGTTCGATGATC‑TCGAACAG‑CGAGCGGATCGCCAGTTGCCGTACCTGGGGGTAGTCCTTGAGGCTGTCGCTGTCGTGCATGGGTGAACATCCTGAATCATGTATTGGCACAAGCCCGCGAAAAGGCCAGGCCTGAAAACt                    >  1:18031/1‑150 (MQ=255)                                                                                                                                    gctcgcTGTTCGA‑GATCATCGAACAG‑TGAGCGGATCGCCAGTTGCCGTACCTGGGGGTAGTCCTTGAGGCTGTCGCTGTCGTGCATGGGTGAACATCCTGAATCATGTATTGGCACAAGCCCGCGAAAAGGCCAGGCCTGAAAACTCAtc                >  1:553797/6‑150 (MQ=255)                                                                                                                                       gagtGTTCGATGATC‑TCGAACAG‑CGAGCGGATCGCCAGTTGCCGTACCTGGGGGTAGTCCTTGAGGCTGTCGCTGTCGTGCATGGGTGAACATCCTGAATCATGTATTGGCACAAGCCCGCGAAAAGGCCAGGCCTGAAAACTCAtcgtc             >  2:835217/4‑150 (MQ=255)                                                                                                                                       gACTGTTCGATGATC‑TCGAACAG‑CGAGCGGATCGCCAGTTGCCGTACCTGGGGGTAGTCCTTGAGGCTGTCGCTGTCGTGCATgg                                                                              <  2:765873/85‑1 (MQ=255)                                                                                                                                       gACTGTTCGATGATC‑TCGAACAG‑CGAGCGGATCGCCAGTTGCCGTACCTGGGGGTAGTCCTTGAGGCTGTCGCTGTCGTGCATgg                                                                              >  1:765873/1‑85 (MQ=255)                                                                                                                                       gACTGTTCGATGATC‑TCGAACAG‑CGAGCGGATCGCCAGTTGCCGTACCTGGGGGTAGTCCTTGAGGCTGTCGCTGTCGTGCATGGGTGAACATCCTGAATCATGTATTGCCGCAAGCCCGCGAAAAGGCCAGGCCTGAAAACTCAtcgtc             >  1:560649/1‑150 (MQ=255)                                                                                                                                        gcTGTTCGA‑GATCATCGAACAGTCCAGCGGATCGCCAGTTGCCGTACCTGGGGGTAGTCCTTGAGGCTGTCGCTGTCGTGCATGGGTGAACATCCTGAATCATGTATTGGCACAAGccc                                            >  1:1079410/2‑119 (MQ=38)                                                                                                                                        gcTGTTCGA‑GATCATCGAACAGTCCAGCGGATCGCCAGTTGCCGTACCTGGGGGTAGTCCTTGAGGCTGTCGCTGTCGTGCATGGGTGAACATCCTGAATCATGTATTGGCACAAGccc                                            <  2:1079410/118‑1 (MQ=38)                                                                                                                                        aCTGTTCGATGATC‑TCGAACAG‑CGAGCGGATCGCCAGTTGCCGTACCTGGGGGTAGTCCTTGAGGCTGTCGCTGTCGTGCATGGGTGAACATCCTGAATCATGTATTGGCACAAGCCCGCGAAAAGGCCAGGCCTGAAAACTCAtcgtcg            <  1:169923/150‑1 (MQ=255)                                                                                                                                           gTTCGATGATC‑TCGAACAG‑CGAGCGGATCGCCAGTTGCCGTACCTGGGGGTAGTCCTTGAGGCTGTCGCTGTCGTGCATGGGTGAACATCCTGAATCATGTATTGGCACAAGCCCGCGAAAAGGCCAGGCCTGAAAACTCATCGTCgggg         <  1:281965/150‑1 (MQ=255)                                                                                                                                           gTTCGATGATC‑TCGAACAG‑CGAGCGGATCGCCAGTTGCCGTACCTGGGGGTAGTCCTTGAGGCTGTCGCTGTCGTGCATGGGTGAACATCCTGAATCATGTATTGGCACAAGCCCGCGAAAAGGCCAGGCCTGAAAACTCATCGTCgggg         <  2:909447/150‑1 (MQ=255)                                                                                                                                                  gatC‑TCGAACAG‑CGAGCGGATCGCCAGTTGCCGTACCTGGGGGTAGTCCTTGAGGCTGTCGCTGTCGTGCATGGGTGAACATCCTGAATCATGTATTGGCACAAGCCCGCGAAAAGGCCAGGCCTGAAAACTCATCGTCGGGGGTCAAAc  >  2:712066/1‑150 (MQ=255)                                                                                                                                                      |                                                                                                                                                    GCCGGGGATCACTGTTTCGCACGGCTGGCCGATGGCACTGGCAGCGTCGGCCAGGCCAAAGCGT‑CGGGCGTAGCGTTCGTT‑CATCCAGACGATGCG‑‑TGCCTGGCGGTCGACGATCACCGTGCCCTCGCTGGACTGTTCGATGATC‑TCGAACAG‑CGAGCGGATCGCCAGTTGCCGTACCTGGGGGTAGTCCTTGAGGCTGTCGCTGTCGTGCATGGGTGAACATCCTGAATCATGTATTGGCACAAGCCCGCGAAAAGGCCAGGCCTGAAAACTCATCGTCGGGGGTCAAAC  >  NC_002947/3460129‑3460419

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: ‑