Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_002947	3,578,651	C→T	intergenic (+285/‑39)	PP_3158 → / → PP_5589	hypothetical protein/rhs repeat‑associated core domain‑containing protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,578,651	0	C	T	100.0%	96.4 / NA	29	intergenic (+285/‑39)	PP_3158/PP_5589	hypothetical protein/rhs repeat‑associated core domain‑containing protein
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (13/16);  total (13/16)

GAATTCAAGGGAAATGGTGTTCTCTAAGGTCATTAATCGTGAAACGTTCGCAAGCGTACACGCCCTACGGCGCTATTTGGGGTGAT‑‑GGCCATTGCTCCGTGTTGAAGTACAATGGTGATCATTTAGACGATCTCGTTAACGGGTATCATTTAGGGGTAGGTAAACGATTGTATCTGCCAGCTTTGATGCGCTTCGCATCGCCCGATGCCTTGAGCCCGTTTTTGAAAGGTGGTATCAACAGCTATTCTTACTGCGCCGGAGATCCTGTAAATTACTCAGACCCTACAGGGCAG  >  NC_002947/3578505‑3578797                                                                                                                                                     |                                                                                                                                                   gAATTCAAGGGAAATGGTGTTCTCTAAGGTCATTAATCGTGAAACGTTCGCAAGCGTACACGCCCTACGGCGCTATTTGGGGTGAT‑‑GGCCATTGCTCCGTGTTGAAGTACAATGGTGATCATTTAGACGATCTCGTTAACGGGTattatt                                                                                                                                                 <  2:15363/150‑1 (MQ=255)  aaTTCAAGGGAAATGGTGTTCTCTAAGGTCATTAATCGTGAAACGTTCGCAAGCGTACACGCCCTACGGCGCTATTTGGGGTGAT‑‑GGCCATTGCTCCGTGTTGAAGTACAATGGTGATCATTTAGACGATCTCGTTAACGGGTATTAttt                                                                                                                                                >  1:570280/1‑150 (MQ=255)       aaGGGAAATGGTGTTCTCTAAGGTCATTAATCGTGAAACGTTCGCAAGCGTACACGCCCTACGGCGCTATTTGGGGTTAT‑‑GGCCATTGCTCCGTGTTGAAGTACAATGGTGATCATTTAGACGATCTCGTTAACGGGTATTATTTAgggg                                                                                                                                           >  1:266419/1‑150 (MQ=255)         gggAAATGGTGTTCTCTAAGGTCATTAATCGTGAAACGTTCGCAAGCGTACACGCCCTACGGCGCTATTTGGGGTGAT‑‑GGCCATTGCTCCGTGTTGAAGTACAATGGTGATCATTTAGACGATCTCGTTAACGGGTATTATTTAGGggta                                                                                                                                         <  1:42518/150‑1 (MQ=255)          ggAAATGGTGTTCTCTAAGGTCATTAATCGTGAAACGTTCGCAAGCGTACACGCCCTACGGCGCTATTTGGGGTGATGAGGCCGATG‑‑CCGTGTTGAAGTACAATGGTGATCATTTAGACGATCTCGTTAACGGGTATTATTTAGGggtag                                                                                                                                        >  1:224555/1‑150 (MQ=255)            aaaTGGTGTTCTCTAAGGTCATTAATCGTGAAACGTTCGCAAGCGTACACGCCCTACGGCGCTATTTGGGGTGAT‑‑GGCGATTGCTCCGTGTTGAAGTACAATGGTGTTCATTTAGACGATCTCGTTAACGGGTATTATTTAGGggtaggt                                                                                                                                      <  2:158527/150‑1 (MQ=255)                    ttCTCTAAGGTCATTAATCGTGAAACGTTCGCAAGCGTACACGCCCTACGGCGCTATTTGGGGTGAT‑‑GGCCATTGCTCCGTGTTGAAGTACAATGGTGATCATTTAGACGATCTCGTTAACGGGTATTATTTAGGGGTAGGTAGACGAtt                                                                                                                              <  2:385406/150‑1 (MQ=255)                         tAAGGTCATTAATCGTGAAACGTTCGCAAGCGTACACGCCCTACGGCGCTATTTGGGGTGAT‑‑GGCCATTGCTCCGTGTTGAAGTACAATGGTGATCATTTAGACGATCTCGTTAACGGGTATTATTTAGGGGTAGGTAAACGATTGTATc                                                                                                                         <  2:266419/150‑1 (MQ=255)                                    aTCGTGAAACGTTCGCAAGCGTACACGCCCTACGGCTCTATTTGGGGTGAT‑‑GGCCATTGCTCCGTGTTGAAGTACAATGGTGATCATTTAGACGATCTCGTTAACGGGTATTATTTAGGGGTAGGTAAACGATTGTATCTGCCAGCTTTg                                                                                                              <  2:289353/150‑1 (MQ=255)                                     tCGTGAAACGTTCGCAAGCGTACACGCCCTACGGCGCTATTTGGGGTGAT‑‑GGCCATTGCTCCGTGTTGAAGTACAATGGTGATCATTTAGACGATCTCGTTAACGGGTATTATTTAGGGGTAGGTAAACGATTGTATCTGCCAGCTTTGa                                                                                                             <  1:259085/150‑1 (MQ=255)                                      cGTGAAACGTTCGCAAGCGTACACGCCCTACGGCGCTATTTGGGGTGAT‑‑GGCCATTGCTCCGTGTTGAAGTACAATGGTGATCATTTAGACGATCTCGTTAACGGGTATTATTTAGGGGTAGGTAAACGATTGTATCTGCCAGCTTTGAt                                                                                                            <  1:141556/150‑1 (MQ=255)                                           aaCGTTCGCAAGCGTACACGCCCTACGGCGCTATTTGGGGTGAT‑‑GGCCATTGCTCCGTGTTGAAGTACAATGGTGATCATTTAGACGATCTCGTTAACGGGTATTATTTAGGggtag                                                                                                                                        >  1:132105/1‑117 (MQ=255)                                           aaCGTTCGCAAGCGTACACGCCCTACGGCGCTATTTGGGGTGAT‑‑GGCCATTGCTCCGTGTTGAAGTACAATGGTGATCATTTAGACGATCTCGTTAACGGGTATTATTTAGGggtag                                                                                                                                        <  2:132105/117‑1 (MQ=255)                                            aCGTTCGCAAGCGTACACGCCCTACGGCGCTATTTGGGGTGAT‑‑GGCCATTGCTCCGTGTTGAAGTACAATGGTGATCATTTAGACGATCTCGTTAACGGGTATTATTTAGGGGTAGGTAAACGATTGTATCTGCCAGCTTTGATGCGCtt                                                                                                      >  2:394625/1‑150 (MQ=255)                                                  gCAAGCGTACACGCCCTACGGCGCTATTTGGGGTGAT‑‑GGCCATTGCTCCGTGTTGAAGTACAATGGTGATCATTTAGACGATCTCGTTAACGGGTATTATTTAGGGGTAGGTAAACGATTGTATCTGCCAGCTTTGAt                                                                                                            <  1:376031/138‑1 (MQ=255)                                                  gCAAGCGTACACGCCCTACGGCGCTATTTGGGGTGAT‑‑GGCCATTGCTCCGTGTTGAAGTACAATGGTGATCATTTAGACGATCTCGTTAACGGGTATTATTTAGGGGTAGGTAAACGATTGTATCTGCCAGCTTTGAt                                                                                                            >  2:376031/1‑138 (MQ=255)                                                  gCAAGCGTACACGCCCTACGGCGCTATTTGGGGTGAT‑‑GGCCATTGCTCCGTGTTGAAGTACAATGGTGATCATTTAGACGATCTCGTTAACGGGTATTATTTAGGGGTAGGTAAACGATTGTATCTGCCAGCTTTGATGCGCTTCGCATc                                                                                                <  1:640339/150‑1 (MQ=255)                                                            acGCCCTACGGCGCTATTTGGGGTGAT‑‑GGCCATTGCTCCGTGTTGAAGTACAATGGTGATCATTTAGACGATCTCGTTAACGGGTATTATTTAGGGGTAGGTAAACGATTGTATCTGCCAGCTTTGATGCGCTTCGCATCGCCCGATGcc                                                                                      >  2:449595/1‑150 (MQ=255)                                                                                  gTGAT‑‑GGCCATTGCTCCGTGTTGAAGTACAATGGTGATCATTTAGACGATCTCGTTAACGGGTATTATTTAGGGGTAGGTAAACGATTGTATCTGCCAGCTTTGATGCGCTTCGCATCGCCCGATGCCTTGAGCCCGTTTTTGAAAggtg                                                                <  1:449595/150‑1 (MQ=255)                                                                                                 cTCCGTGTTGAAGTACAATGGTGATCATTTAGACGATCTCGTTAACGGGTATTATTTAGGGGTAGGTAAACGATTGTATCTGCCAGCTTTGATGCGCTTCGCATCGCCCGATGCCTTGAGCCCGTTTTTGAAAGGTGGTATCAAc                                                        <  2:634825/145‑1 (MQ=255)                                                                                                 cTCCGTGTTGAAGTACAATGGTGATCATTTAGACGATCTCGTTAACGGGTATTATTTAGGGGTAGGTAAACGATTGTATCTGCCAGCTTTGATGCGCTTCGCATCGCCCGATGCCTTGAGCCCGTTTTTGAAAGGTGGTATCAAc                                                        >  1:634825/1‑145 (MQ=255)                                                                                                   ccGTGTTGAAGTACAATGGTGATCATTTAGACGATCTCGTTAACGGGTATTATTTAGGGGTAGGTAAACGATTGTATCTGCCAGCTTTGATGCGCTTCGCATCGCCCGATGCCTTGAGCCCGTTTTTGAAAGGTGGTATCAACAGCTAtt                                                 >  1:344050/1‑150 (MQ=255)                                                                                                         tGAAGTACAATGGTGATCATTTAGACGATCTCGTTAACGGGTATTATTTAGGGGTAGGTAAACGATTGTATCTGCCAGCTTTGATGCGCTTCGCATCGCCCGATGCCTTGAGCCCGTTTTTGAAAGGTGGTATCAACAGCTATTCTTACt                                           <  2:344050/150‑1 (MQ=255)                                                                                                                       gATCATTTAGACGATCTCGTTAACGGGTATTATTTAGGGGTAGGTAAACGATTGTATCTGCCAGCTTTGATGCGCTTCGCATCGCCCGATGCCTTGAGCCCGTTTTTGAAAGGTGGTATCAACAGCTATTCTTACTGCGCCGGAGATCCt                             <  1:394625/150‑1 (MQ=255)                                                                                                                            tttAGACGATCTCGTTAACGGGTATTATTTAGGGGTAGGTAAACGATTGTATCTGCCAGCTTTGATGCGCTTCGCATCGCCCGATGCCTTGAGCCCGTTTTTGAAAGGTGGTATCAACAGCTATTCTTACTGCGCCGGAGATCCTGTa                          >  1:403722/1‑148 (MQ=255)                                                                                                                            tttAGACGATCTCGTTAACGGGTATTATTTAGGGGTAGGTAAACGATTGTATCTGCCAGCTTTGATGCGCTTCGCATCGCCCGATGCCTTGAGCCCGTTTTTGAAAGGTGGTATCAACAGCTATTCTTACTGCGCCGGAGATCCTGTa                          <  2:403722/148‑1 (MQ=255)                                                                                                                                   gATCTCGTTAACGGGTATTATTTAGGGGTAGGTAAACGATTGTATCTGCCAGCTTTGATGCGCTTCGCATCGCCCGATGCCTTGAGCCCGTTTTTGAAAGGTGGTATCAACAGCTATTCTTACTGCGCCGGAGATCCTGTAAATTa                     <  1:522999/146‑1 (MQ=255)                                                                                                                                   gATCTCGTTAACGGGTATTATTTAGGGGTAGGTAAACGATTGTATCTGCCAGCTTTGATGCGCTTCGCATCGCCCGATGCCTTGAGCCCGTTTTTGAAAGGTGGTATCAACAGCTATTCTTACTGCGCCGGAGATCCTGTAAATTa                     >  2:522999/1‑146 (MQ=255)                                                                                                                                   gATCTCGTTAACGGGTATTATTTAGGGGTAGGTAAACGATTGTATCTGCCAGCTTTGATGCGCTTCGCATCGCCCGATGCCTTGAGCCCGTTTTTGAAAGGTGGTATCAACAGCTATTCTTACTGCGCCGGAGATCCTGTAAATTACTCa                 >  1:176204/1‑150 (MQ=255)                                                                                                                                         gTTAACGGGTATTATTTAGGGGTAGGTAAACGATTGTATCTGCCAGCTTTGATGCGCTTCGCATCGCCCGATGCCTTGAGCCCGTTTTTGAAAGGTGGTATCAACAGCTATTCTTACTGCGCCGGAGATCCTGTAAATTACTCAGACCCt           >  2:539837/1‑150 (MQ=255)                                                                                                                                                  tattatTTAGGGGTAGGTAAACGATTGTATCTGCCAGCTTTGATGCGCTTCGCATCGCCCGATGCCTTGAGCCCGTTTTTGAAAGGTGGTATCAACAGCTATTCTTACTGCGCCGGAGATCCTGTAAATTACTCAGACCCTACAGGGCAg  <  1:539837/150‑1 (MQ=255)                                                                                                                                                     |                                                                                                                                                   GAATTCAAGGGAAATGGTGTTCTCTAAGGTCATTAATCGTGAAACGTTCGCAAGCGTACACGCCCTACGGCGCTATTTGGGGTGAT‑‑GGCCATTGCTCCGTGTTGAAGTACAATGGTGATCATTTAGACGATCTCGTTAACGGGTATCATTTAGGGGTAGGTAAACGATTGTATCTGCCAGCTTTGATGCGCTTCGCATCGCCCGATGCCTTGAGCCCGTTTTTGAAAGGTGGTATCAACAGCTATTCTTACTGCGCCGGAGATCCTGTAAATTACTCAGACCCTACAGGGCAG  >  NC_002947/3578505‑3578797

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑