Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	1,058,264:1	+T	13.0%	intergenic (‑190/+30)	PP_0914 ← / ← sodB	GGDEF domain‑containing protein/superoxide dismutase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	1,058,264	1	.	T	13.0%	178.6 / 25.1	54	intergenic (‑190/+30)	PP_0914/sodB	GGDEF domain‑containing protein/superoxide dismutase
Reads supporting (aligned to +/- strand):  ref base . (20/27);  new base T (4/3);  total (24/30)
Fisher's exact test for biased strand distribution p-value = 6.87e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.63e-01

GTGTATCGGTTGCCTGACCCCGCAACTTGAATGCGCTGTATCAATCTTCCAGAGGTTTGATGTTAGCGTGGTATGCGGCCTGAGCAAGCAAAACCGTGCCAGCCTGTTTGCGGCAACACAGGCACAAAAAAACCCGGCACATG‑GCCGGGTTTCTCGTTCAAGGCCGAATGACTCAGGCCTTGAAGGTCTTGCCTTCGAACTGCTCGGCAACGAAGGCCCAGTTGACCAGGTTCCAGAACGCCTCGACGTACTTCGGACGCAGGTTGCGGTAGTCGATGTAGTAGGCGTGT  >  NC_002947/1058122‑1058411                                                                                                                                                |                                                                                                                                                    gtgtATCGGTTGCCTGACCCCGCAACTTGAATGCGCTGTATCAATCTTCCAGAGGTTTGATGTTAGCGTGGTATGCGGCCTGAGCAAGCAAAACCGTGCCAGCCTGTTTGCGGCAACACAGGCACAAAAAAACCCGGCACATG‑GCCGGGt                                                                                                                                              <  2:905025/150‑1 (MQ=255) gtgtATCGGTTGCCTGACCCCGCAACTTGAATGCGCTGTATCAATCTTCCAGAGGTTTGATGTTAGCGTGGTATGCGGCCTGAGCAAGCAAAACCGTGCCAGCCTGTTTGCGGCAACACAGGCACAAAAAAACCCGGC‑CATGTGCCGGGt                                                                                                                                              <  1:1166462/150‑1 (MQ=255)    tATCGGTTGCCTGACCCCGCAACTTGAATGCGCTGTATCAATCTTCCAGAGGTTTGATGTTAGCGTGGTATGCGGCCTGAGCAAGCAAAACCGTGCCAGCCTGTTTGCGGCAACACAGGCACAAAAAAACCCGGCACATG‑GCCGGGTTtc                                                                                                                                           >  1:485770/1‑150 (MQ=255)      tCGGTTGCCTGACGCCGCAACTTGAATGCGCTGTATCAATCTTCCAGAGGTTTGATGTTAGCGTGGTATGCGGCCTGAGCAAGCAAAACCGTGCCAGCCTGTTTGCGGCAACACAGGCACGAAAAAACCCGGCACATG‑GCCGGGTTtctc                                                                                                                                         <  1:1113320/150‑1 (MQ=255)         gTTGCCTGACCCCGCAACTTGAATGCGCTGTATCAATCTTCCAGAGGTTTGATGTTAGCGTGGTATGCGGCCTGAGCAAGCAAAACCGTGCCAGCCTGTTTGCGGCAACACAGGCACAAAAAAACCCGGCACATG‑GCCGGGTTTCTCGtt                                                                                                                                      <  2:485770/150‑1 (MQ=255)              cTGACCCCGCAACTTGAATGCGCTGTATCAATCTTCCAGAGGTTTGATGTTAGCGTGGTATGCGGCCTGAGCAAGCAAAACCGTGCCAGCCTGTTTGCGGCAACACAGGCACAAAAAAACCCGGCACATG‑GCCGGGTTTCTCGTTCAAgg                                                                                                                                 >  1:955463/1‑150 (MQ=255)                   cccGCAACTTGAATGCGCTGTATCAATCTTCCAGAGGTTTGATGTTAGCGTCGTATGCGGCCTGAGCAAGCAAAACCGTGCCAGCCTGTTTGCGGCAACACAGGCACAAAAAAACCCGGCACATG‑GCCGGGTTTCTCGTTCAAGGCCGaa                                                                                                                            <  1:512454/150‑1 (MQ=255)                     cGCAACTTGAATGCGCTGTATCAATCTTCCAGCGGTTTGATGTTAGCGTGGTATGCGGCCTGAGCAAGCAAAACCGTGCCAGCCTGTTTGCGGCAACACAGGCACAAAAAAACCCGGCACATG‑GCCGGGTTTCTCGTTCAAGGCCGAATg                                                                                                                          >  2:1398477/1‑150 (MQ=255)                         aCTTGAATGCGCTGTATCAATCTTCCAGAGGTTTGATGTTAGCGTGGTATGCGGCCTGAGCAAGCAAAACCGTGCCAGCCTGTTTGCGGCAACACAGGCACAAAAAAACCCGGCACATG‑GCCGGGTTTCTCGTTCAAGGCCGAATGACTc                                                                                                                      <  1:1309006/150‑1 (MQ=255)                           ttGAATGCGCTGTATCAATCTTCCAGAGGTTTGATGTTAGCGTGGTATGCGGCCTGAGCAAGCAAAACCGTGCCAGCCTGTTTGCGGCAACACAGGCACAAAAAAACCCGGCACATG‑GCCGGGTTTCTCGTTCAAGGCCGAATGACTCAg                                                                                                                    <  1:1185999/150‑1 (MQ=255)                           ttGAATGCGCTGTATCAATCTTCCAGAGGTTTGATGTTAGCGTGGTATGCGGCCTGAGCAAGCAAAACCGTGCCAGCCTGTTTGCGGCAACACAGGCACAAAAAAACCCGGCACATG‑GCCGGGTTTCTCGTTCAAGGCCGAATGACTCAg                                                                                                                    <  2:50803/150‑1 (MQ=255)                                tGCGCTGTATCAATCTTCCAGAGGTTTGATGTTAGCGTGGTATGCGGCCTGAGCAAGCAAAACCGTGCCAGCCTGTTTGCGGCAACACAGGCACAAAAAAACCCGGCACATG‑GCCGGGTTTCTCGTTCAAGGCCGAATGACTCAGGCCtt                                                                                                               <  2:1052511/150‑1 (MQ=255)                                   gcTGTATCAATCTTCCAGAGGTTTGATGTTAGCGTGGTATGCGGCCTGAGCAAGCAAAACCGTGCCAGCCTGTTTGCGGCAACACAGGCACAAAAAAACCCGGCACATG‑GCCGGGTTTCTCGTTCAAGGCCGAATGACTCAGGCCTTGaa                                                                                                            >  1:1174325/1‑150 (MQ=255)                                    cTGTATCAATCTTCCAGAGGTTTGATGTTAGCGTGGTATGCGGCCTGAAGAAGCAAACCCGTCCCAGCCTGTTTGCGGCAACACAGGCACAAAAAAACCCGGCACATC‑GCCGGGTTTCTCGATCAAGGCCGAATGGCTCAGGCCTTTAAg                                                                                                           <  2:524988/150‑1 (MQ=255)                                           aaTCTTCCAGAGGTTTGATGTTAGCGTGGTATGCGGCCTGAGCAAGCAAAACCGTGCCAGCCTGTTTGCGGCAACACAGGCACAAAAAAACCCGGTACATG‑GCCGGGTTTCTCGTTCAAGGCCGAATGACTCAGGCCTTGAAGGTCTTGc                                                                                                    >  2:645612/1‑150 (MQ=255)                                             tCTTCCAGAGGTTTGATGTTAGCGTGGTATGCGGCCTGAGCAAGCAAAACCGTGCCAGCCTGTTTGCGGCAACACAGGCACAAAAAAACCCGGCACATG‑GCCGGGTTTCTCGTTCAAGGCCGAATGACTCAGGCCTTGAAGGTCTTGCCt                                                                                                  >  2:1246475/1‑150 (MQ=255)                                             tCTTCCAGAGGTTTGATGTTAGCGTGGTATGCGGCCTGAGCAAGCAAAACCGTGCCAGCCTGTTTGCGGCAACACAGGCACAAAAAAACCCGGCACATG‑GCCGGGTTTCTCGTTCAAGGCCGAATGACTCAGGCCTTGAAGGTCTTGCCt                                                                                                  >  1:308298/1‑150 (MQ=255)                                              cTTCCAGAGGTTTGATGTTAGCGTGGTATGCGGCCTGAGCAAGCAAAACCGTGCCAGCCTGTTTGCGGCAACACAGGCACAAAAAAACCCGGCACATG‑GCCGGGTTTCTCGTTCAAGGCCGAATGACTCAGGCCTTGAAGGTCTTGCCtt                                                                                                 <  2:1177633/150‑1 (MQ=255)                                                  cAGAGGTTTGATGTTAGCGTGGTATGCGGCCTGAGCAAGCAAAACCGTGCCAGCCTGTTTGCGGCAACACAGGCACAAAAAAACCCGGCACATG‑GCCGGGTTTCTCGTTCAAGGCCGAATGACTCAGGCCTTGAAGGTccggc                                                                                                    <  1:275291/143‑5 (MQ=255)                                                  cAGAGGTTTGATGTTAGCGTGGTATGCGGCCTGAGCAAGCAAAACCGTGCCAGCCTGTTTGCGGCAACACAGGCACAAAAAAACCCGGCACATG‑GCCGGGTTTCTCGTTCAAGGCCGAATGACTCAGGCCTTGAAGGTCTTGc                                                                                                    >  2:275291/1‑143 (MQ=255)                                                   agagGTTTGATGTCAGTGTGGTATTCGGCCTCAGCAAGCAAAACCGTGCCAGCCTGTTTGCGGCAACACAGGCACAAAAAAACCCGGCACATG‑GCCGGGTTTCTCGTTCAAGGCCGAATTACTCAGGCCTTGAAGGTCTTGCCTTCGAAc                                                                                            <  2:704050/150‑1 (MQ=255)                                                      ggTTTGATGTTAGCGTGGTATGCGGCCTGAGCAAGCAAAACCGTGCCAGCCTGTTTGCGGCAACACAGGCACAAAAAAACCCGGCACATG‑GCCGGGTTTCTCGTTCAAGGCCGAATGACTCAGGCCTTGAAGGTCTTGCCTTCGAACTGc                                                                                         <  2:1174325/150‑1 (MQ=255)                                                              gTTAGCGTGGTATGCGGCCTGAGCAAGCAAAACCGTGCCAGCCTGTTTGCGGCAACACAGGCACAAAAAAACCCGGCACATG‑GCCGGGTTTCTCGTTCAAGGCCGAATGACGTGGGCCTTGAAGGTCTTGCCTTCGAACTGCTCGGCAAc                                                                                 >  1:373139/1‑150 (MQ=255)                                                                 aGCGTGGTATGCGGCCTGAGCAAGCAAAACCGTGCCAGCCTGTTTGCGGCAACACAGGCACAAAAAAACCCGGTACATG‑GCCGGGTTTCTCGTTCAAGGCCGAATGACTCAGGCCTTGAAGGTCTTGCCTTCGAACTGCTCGGCAACGaa                                                                              <  1:645612/150‑1 (MQ=255)                                                                 aGCGTGGTATGCGGCCTGAGCAAGCAAAACCGTGCCAGCCTGTTTGCGGCAACACAGGCACAAAAAAACCCGGCACATG‑GCCGGGTTTCTCGTTCAAGGCCGAATGACTCAGGCCTTGAAGGTCTTGCCTTCGAACTGCTCGGCAACGaa                                                                              <  1:310183/150‑1 (MQ=255)                                                                       gTATGCGGCCTGAGCAAGCAAAACCGTGCCAGCCTGTTTGCGGCAACACAGGCACAAAAAAACCCGGC‑CATGTGCCGGGttttttt                                                                                                                                        <  2:799261/86‑5 (MQ=37)                                                                          tGCGGCCTGAGCAAGCAAAACCGTGCCAGCCTGTTTGCGGCAACACAGGCACAAAAAAACCCGGCACATG‑GCCGGGTTTCTCGTTCAAGGCCGAATGACTCAGGCCTTGAAGGTCTTGCCTTCGAACTGCTCGGCAACGAAGGCCCAGtt                                                                     >  2:780095/1‑150 (MQ=255)                                                                               ccTGAGCAAGCAAAACCGTGCCAGCCTGTTTGCGGCCACACATGCACAAAAAAACCCGGCACATG‑GCCGGGTTGCTCGTTCAAGGCCGAATGACTCAGGCCTTGAAGGTCTTGCCTTCGAACTGCTCGGCAACGAAGGCCCAGTTGACCa                                                                <  1:93334/150‑1 (MQ=255)                                                                               ccTGAGCAAGAAAAACCGTGCCAGCCTGTTTGCGGCAACACAGGCACAAAAAAACCCGGCACATG‑GCCGGGTTTCTCGTTCAAGGCCGAATGACTCAGGCCTTGAAGGTCTTGCCTTCGAACTGCTCGGCAACGAAGGCCCAGTTGACCa                                                                <  2:308298/150‑1 (MQ=255)                                                                                            aaCCGTGCCAGCCTGTTTGCGGCAACACAGGCACAAAAAAACCCGGCACATG‑GCCGGGTTTCTCGATCAAGGCCGAATGACTCAGGCCTTGAAGGTCTTGCCTTCGAACTGCTCGGCAACGAAGGCCCAGTTGACCAGGTTCCAGAACGc                                                   >  1:184004/1‑150 (MQ=255)                                                                                              ccGTGCCAGCCTGTTTGCGGCAACACAGGCACAAAAAAACCCGGCACATG‑GCCGGGTTTCTCGTTCAAGGCCGAATGACTc                                                                                                                      >  2:964397/1‑81 (MQ=255)                                                                                              ccGTGCCAGCCTGTTTGCGGCAACACAGGCACAAAAAAACCCGGCACATG‑GCCGGGTTTCTCGTTCAAGGCCGAATGACTc                                                                                                                      <  1:964397/81‑1 (MQ=255)                                                                                                     aGCCTGTTTGCGGCAACACAGGCACAAAAAAACCCGGCACATG‑GCCGGGTTTCTCGTTCAAGGCCGaa                                                                                                                            <  2:367718/68‑1 (MQ=255)                                                                                                     aGCCTGTTTGCGGCAACACAGGCACAAAAAAACCCGGCACATG‑GCCGGGTTTCTCGTTCAAGGCCGaa                                                                                                                            >  1:367718/1‑68 (MQ=255)                                                                                                           tttGCGGCAACACAGGCACAAAAAAACCCGGCACATG‑GCCGGGTTTCTCGTTCAAGGCCGAATGACTCAGGCCTTGAAGGTCTTGCCTTCGAACTGCTCGGCAACGAAGGCCCAGTTGACCAGGTTCCAGAACGCCTCGACGTACTTCgg                                    >  1:339757/1‑150 (MQ=255)                                                                                                                 gCAACACAGGCACAAAAAAACCCGGCACATG‑GCCGGGTTTCTCGTTCAAGGCCGaa                                                                                                                            <  2:1355589/56‑1 (MQ=255)                                                                                                                 gCAACACAGGCACAAAAAAACCCGGCACATG‑GCCGGGTTTCTCGTTCAAGGCCGaa                                                                                                                            >  1:1355589/1‑56 (MQ=255)                                                                                                                      acaGGCACAAAAAAACCCGGCACATG‑GCCGGGTTTCTCGTTCAAGGCCGAATGACTCAGGCCTTGAAGGTCTTGCCTTCGAACTGCTCGGCAACGAAGGCCCAGTTGACCAGGTTCCAGAACGCCTCGACGTACTTCGGACGCAGGTTGc                         >  2:771044/1‑150 (MQ=255)                                                                                                                       caGGCACAAAAAAACCCGGCACATG‑GCCGGGTTTCTCGTTCAAGGCCGAATGACTCAGGCCTTGAAGGTCTTGCCTTCGAACTGCTCGGCAACGAAGGCCCAGTTGACCAGGTTCCAGAGCGCCTCGACGTACTTCGGACGCAGGTTGCg                        <  1:1398477/150‑1 (MQ=255)                                                                                                                               gagaaaCCCGGC‑CATGTGCCGGGTTTTTCGTTCAAGGCCGAATGACTCAGGCCTTGAAGGTCTTGCCTTCGAACTGCTCg                                                                                      >  1:695356/4‑80 (MQ=25)                                                                                                                               gagaaaCCCGGC‑CATGTGCCGGGTTTTTCGTTCAAGGCCGAATGACTCAGGCCTTGAAGGTCTTGCCTTCGAACTGCTCg                                                                                      <  2:695356/77‑1 (MQ=25)                                                                                                                               aaaaaaCCCGGCACATG‑GCCGGGTTTCTCGTTCAAGGCCGAATGACTCAGGc                                                                                                                  <  2:120995/52‑1 (MQ=255)                                                                                                                               aaaaaaCCCGGCACATG‑GCCGGGTTTCTCGTTCAAGGCCGAATGACTCAGGc                                                                                                                  >  1:120995/1‑52 (MQ=255)                                                                                                                               aaaaaaCCCGGCACATG‑GCCGGGTTCCTCGTTCAAGGCCGAATGACTCAGGCCTTGAAGGTCTTGCCTTCGAACTGCTCGGCAACGAAGGCCCAGTTGACCAGGTTCCAGAACGCCTCGACGTACTTCGGACGCAGGTTGCGGTAGTCGa                <  1:68356/150‑1 (MQ=255)                                                                                                                                aaaaaCCCGGCACATG‑GCCGGGTTTCTCGTTCAAGGCCGAATGACTCAGGCCTTGAAGGTCTTGCCTTCGAACTGCTCGGCAACGAAGGCCCAGTTGACCAGGTTCCAGAACGCCTCGACGTACTTCGGACGCAGGTTGCGGTAGTCGAt               <  1:780095/150‑1 (MQ=255)                                                                                                                                aaaaaCCCGGCACATG‑GCCGGGTTTCTCGTTCAAGGCCGAATGACTCAGGCCTTGAAGGTCTTGCCTTCGAACTGCTCGGCAACGAAGGCCCAGTTGACCAGGTTCCAGAACGCCTCGACGTACTTCGGACGCAGGTTGCGGTAGTCGAt               <  2:339757/150‑1 (MQ=255)                                                                                                                                 aaaaCCCGCCACATG‑GCCGGGTTTCTCGTTCAAGGCCGAATGACTCAGGCCTTGAAGGTCTTGCCTTCGAACTGCTCGGCAACGAAGGCCCAGTTGACCAGGTTCCAGAACGCCTCGACGTACTTCGGACGCAGGTTGCGGTAGTCGATg              <  1:771044/150‑1 (MQ=255)                                                                                                                                  aaaCCCGGCACATG‑GCCGGGTTTCTCGTTCAAGGCCGAATGACTCAGGCCTTGAAGGTCTTGCCTTCGAACTGCTCGGCAACGAAGGCCCAGTTGACCAGGTTCCAGAACGCCTCGACGTACTTCGGACGCAGGTTGCGGTAGTCGATgt             >  1:982003/1‑150 (MQ=255)                                                                                                                                   aaCCCGGCACATG‑GCCGGGTTTCTCGTTCAAGGCCGAATGACTCAGGCCTTGAAGGTCTTGCCTTCGAACTGCTCGGCAACGAAGGCCCAGTTGACCAGGTTCCAGAACGCCTCGACGTACTTCGGACGCAGGTTGCGGTAGTCGATgta            <  1:1246475/150‑1 (MQ=255)                                                                                                                                   aaCCCGGC‑CATGTGCCGGGTTTCTCGTTCAAGGCCGAATGACTCAGGCCTTGAAGGTCTTGCCTTCGAACTGCTCGGCAACGAAGGCCCAGTTGACCAGGTTCCAGAACGCCTCGACGTACTTCGGACGCAGGTTGCGGTAGTCGATgta            >  1:208132/1‑150 (MQ=255)                                                                                                                                   aaCCCGGC‑CATGTGCCGGGTTTCTCGTTCAAGGCCGAATGACTCAGGCCTTGAAGGTCTTGCCTTCGAACTGCTCGGCAACGAAGGCCCAGTTGACCAGGTTCCAGAACGCCTCGACGTACTTCGGACGCAGGTTGCGGTAGTCGATgta            >  2:501343/1‑150 (MQ=255)                                                                                                                                   aaCCCGGC‑CATGTGCCGGGTTTCTCGTTCAAGGCCGAATGACTCAGGCCTTGAAGGTCTTGCCTTCGAACTGCTCGGCAACGAAGGCCCAGTTGACCAGGTTCCAGAACGCCTCGACGTACTTCGGACGCAGGTTGCGGTAGTCGATgta            >  2:985591/1‑150 (MQ=255)                                                                                                                                        ggCACATG‑GCCGGGTTTCTCGTTCAAGGCCGAATGACTCAGGCCTTGAAGGTCTTGCCTTCGAACTGCTCGGCAACGAAGGCCCAGTTGACCAGGTTCCAGAACGCCTCGACGTACTTCGGACGCAGGTTGCGGTAGTCGATGTAGTAgg       >  1:816950/1‑150 (MQ=255)                                                                                                                                             aTG‑GCCGGGTTTCTCGTTCAAGGCCGAATGACTCAGGCCTTGAAGGTCTTGCCTTCGAACTGCTCGGCAACGAAGGCCCAGTTGACCAGGTTCCAGAACGCCTCGACGTACTTCGGACGCAGGTTGCGGTAGTCGATGTAGTAGGCgtgt  >  2:988720/1‑150 (MQ=255)                                                                                                                                                |                                                                                                                                                    GTGTATCGGTTGCCTGACCCCGCAACTTGAATGCGCTGTATCAATCTTCCAGAGGTTTGATGTTAGCGTGGTATGCGGCCTGAGCAAGCAAAACCGTGCCAGCCTGTTTGCGGCAACACAGGCACAAAAAAACCCGGCACATG‑GCCGGGTTTCTCGTTCAAGGCCGAATGACTCAGGCCTTGAAGGTCTTGCCTTCGAACTGCTCGGCAACGAAGGCCCAGTTGACCAGGTTCCAGAACGCCTCGACGTACTTCGGACGCAGGTTGCGGTAGTCGATGTAGTAGGCGTGT  >  NC_002947/1058122‑1058411

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑