Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	1,403,590	G→A	13.6%	intergenic (‑56/+25)	PP_1227 ← / ← PP_1228	membrane protein/methyl‑accepting chemotaxis transducer

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	1,403,590	0	G	A	13.6%	105.8 / 6.7	44	intergenic (‑56/+25)	PP_1227/PP_1228	membrane protein/methyl‑accepting chemotaxis transducer
Reads supporting (aligned to +/- strand):  ref base G (18/20);  new base A (2/4);  total (20/24)
Fisher's exact test for biased strand distribution p-value = 6.73e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.55e-01

AACAGGGTGGCGGCGATCGAGGTGCGTAAAAGCCCTTGTTCGCTGGTGATGTCGAAGAAAGTGGATCGGGTTGGATTAGGCATAAGTTGTGCTCAAGAATAACGATGGTGCGGTGCCTGTCAGGGCCTCTTCGCGGGCGTGCCCGCGAAGAGGCCCTGACAGGCTAGACGCGAAACTGCTCCATCAGCGCCTGCTGCT‑‑GGTTGGCCAGCCGGTTCAGGGCTTGGCTGATGCGTGCCGATTCATCGGCCTGCCCAGCCAGTGATTCTGTCACGTCTCGAATGCCG  >  NC_002947/1403452‑1403735                                                                                                                                           |                                                                                                                                                    aaCAGGGTGGCGGCGATCGAGGTGCGTAAAAGCCCTTGTTCGCTGGTGATGTCGAAGAAAGTGGATCGGGTTGGATTAGGCATAAGTTGTGCTCAAGAATAACGATGGTGCGGTGCCTGTCAGGGCCTCTTCGCGGGCACGCCCGCGaa                                                                                                                                           <  3:6736/149‑1 (MQ=255)   cAGGGTGGCGGCGATCGAGGTGCGTAAAAGCCCTTGTTCGCTGGTGATGTCGAAGAAAGTGGATCGGGTTGGATTAGGCATAAGTTGTGCTCAAGAATAACGATGGTGCGGTGCCTGTCAGGGCCTCTTCGCGGGCGTGCCCGCGAaga                                                                                                                                         <  5:165630/149‑1 (MQ=255)   cAGGGTGGCGGCGATCCAGGTGCGTAAAAGCCCTTGTTCGCTGGTGATGTCGAAGAAAGTGGATCGGGTTGGATTAGGCATAAGTTGTGCTCAAGAATAACGATGGTGCGGTGCCTGTCAGGGCCTCTTCGCGGGCGTGCCCGCGAaga                                                                                                                                         <  7:132512/149‑1 (MQ=255)      gttGGCGGCGATCGAGGTGCGTAAAAGCCCTTGTTCGCTGGTGATGTCGAAGAAAGTGGATCGGGTTGGATTAGGCATAAGGAGTGCTCAAGAATAACGATGGTGCGGTGCCTGTCAGGGCCTCTTCGCGGGCACGCCCGCGAAGAGGc                                                                                                                                      <  1:244700/147‑1 (MQ=255)      ggTGGCGGCGATCGAGGTGCGTAAAAGCCCTTGTTCGCTGGTGATGTCGAAGAAAGTGGATCGGGTTGGATTAGGCATAAGTTGTGCTCAAGAATAACGATGGTGCGGTGCCTGTCAGGGCCTCTTCGCGGGCGTGCCCGCGAAGAGGc                                                                                                                                      <  4:308232/149‑1 (MQ=255)       gTGGCGGCGATCGAGGTGCGTAAAAGCCCTTGTTCGCTGGTGATGTCGAAGAAAGTGGATCGGGGTGGATTAGGCATAAGTTGTGCTCAAGAATAACGATGGTGCGGTGCCTGTCAGGGCCTCTTCGCGGGCGTGCCCGCGAAGAGGcc                                                                                                                                     <  6:95325/149‑1 (MQ=255)                aTCGAGGTGCGTAAAAGCCCTTGTTCGCTGGTGATGTCGAAGAAAGTGGATCGGGTTGGATTAGGCATAAGTTGTGCTCAAGAATAACGATGGTGCGGTGCCTGTCAGGGCCTCTTCGCGGGCGTGCCCGCGAAGAGGCCCTGACAGGc                                                                                                                            >  1:178151/1‑149 (MQ=255)                aTCGAGGTGCGTAAAAGCCCTTGTTAGCTGGTGATGTCGAAGAAAGTGGATCGGGTTGGATTAGGCATAAGTTGTGCTCAAGAATAACGATGGTGCGGTGCCTGTCAGGGCCTCTTCGCGGGCGTGCACGCGAAGAGTCCCTGACAGGc                                                                                                                            >  5:163718/1‑149 (MQ=255)                      gTGCGTAAAAGCCCTTGTTCGCTGGTGATGTCGAAGAAAGTGGATCGGGTTGGATTAGGCATAAGTTGTGCTCAAGAATAACGATGGTGCGGTGCCTGTCAGGGCCTCTTCGCGGGCGTGCCCGCGAAGAGGCCCTGACAGGCTAGAcg                                                                                                                      >  3:167328/1‑149 (MQ=255)                            aaaaGCCCTTGTTCGCTGGTGATGTCTAAGAAAGTGGATCGGGTTGTATTAGGCATAAGTTGTGCTCAAGAATAACGATGGTGCGGTGCCTGTCAGGGCCTCTTCGCGGGCGTGCCCGCGAAGAGGCCCTGACAGGCTAGACGCGaaa                                                                                                                 <  6:163718/148‑1 (MQ=255)                                  ccTTGTTCGCTGGTGATGTCGAAGAAAGTGGATCGGGTTGGATTAGGCATAAGTTGTGCTCAAGAATAACGATGGTGCGGTGCCTGTCAGGGCCTCTTCGCGGGCGTGCCCGCGAAGAGGCCCTGACAGGCTAGACGCGAAACTGCTc                                                                                                           >  5:118709/1‑148 (MQ=255)                                      gTTCGCTGGTGATGTCGAAGAAAGTGGATCGGGTTGGATTAGGCATAAGTTGTGCTCAAGAATAACGATGGTGCGGTGCCTGTCAGGGCCTCTTCGCGGGCGTGCCCGCGAAGAGGCCCTGACAGGCTAGACGCGAAACTGCTCCATc                                                                                                       <  4:167328/148‑1 (MQ=255)                                                   gTCGAAGAAAGTGGATCGGGTTGGATTAGGCATAAGTTGTGCTCAAGAATAACGATGGTACGGTGCCTGTCAGGGCCTCTTCGCGGGCGTGCCCGCGAAGAGGCCCTGACAGGCTAGACGCGaaa                                                                                                                 >  6:29282/1‑125 (MQ=255)                                                   gTCGAAGAAAGTGGATCGGGTTGGATTAGGCATAAGTTGTGCTCAAGAATAACGATGGTACGGTGCCTGTCAGGGCCTCTTCGCGGGCGTGCCCGCGAAGAGGCCCTGACAGGCTAGACGCGaaa                                                                                                                 <  5:29282/125‑1 (MQ=255)                                                    tCGAAGAAAGTGGATCGGGTTGGATTAGGCATAAGTTGTGCTCAAGAATAACGATGGTGCGGTGCCTGTCAGGGCCTCTTCGCGGGCGTGCCCGCGAAGAGGCCCTGACAGGCTAGACGCGAAACTGCTCCATCAGCGCCTGCTGCT‑‑gg                                                                                      >  6:184529/1‑149 (MQ=255)                                                      gaagaaAGTGGATCGGGTTGGATTAGGCATAAGTTGTGCTCAAGAATAACGATGGTGCGGTGCCTGTCAGGGCCTCTTCGCGGGCGTGCCCGCGAAGAGGCCCTGACAGGCTAGACGCGAAACTGCTCCATCAGCGCCTGCTGCT‑‑GGtt                                                                                    <  2:178151/149‑1 (MQ=255)                                                                gATCGGGTTGGATTAGGCATAAGTTGTGCTCAAGAATAACGATGGTGCGGTGCCTGTCAGGGCCTCTTCGCGGGCGTGCCCGCGAAGAGGCCCTGACAGGCTAGACGCGAAACTGCTCCATCAGCGCCTGCTGCT‑‑GGTTGGCCAGCCgg                                                                          >  6:276677/1‑149 (MQ=255)                                                                  tCGGGTTGGATTAGGCATAAGTTGTGCTCAAGAATAACGATGGTGCGGTGCCTGTCAGGGCCTCTTCGCGGGCGTGCCCGCGAAGAGGCCCTGACAGGCTAGACGCGAAACTGCTCCATCAGCGCCTGCTGCT‑‑GGTTGGCCAGCCGGtt                                                                        <  5:276677/149‑1 (MQ=255)                                                                      gTTGGATTAGGCATAAGTTGTGCTCAAGAATAACGATGGTGCGGTGCCTGTCAGGGCCTCTTCGCGGGCGTGCCCGCGAAGAGGCCCTGACAGGCTAGACGCGAAAc                                                                                                                <  3:301811/107‑1 (MQ=255)                                                                      gTTGGATTAGGCATAAGTTGTGCTCAAGAATAACGATGGTGCGGTGCCTGTCAGGGCCTCTTCGCGGGCGTGCCCGCGAAGAGGCCCTGACAGGCTAGACGCGAAAc                                                                                                                >  4:301811/1‑107 (MQ=255)                                                                      gTTGGATTAGGCATAAGTTGTGCTCAAGAATAACGATGGTGCGGTGCCTGTCAGGGCCTCTTCGCGGGCGTGCCCGCGAAGAGGCCCTGACAGGCTAGACGCGAAACTGCTCCATCAGCGCCTGCTGCT‑‑GGTTGGCCAGCCGGTTCAgg                                                                    >  1:256587/1‑149 (MQ=255)                                                                              aGGCATAAGTTGTGCTCAAGAATAACGATGGTGCGGTGCCTGTCAGGGCCGCTTCGCGGGCGTGCCCGCGAAGAGGCCCTGACAGGCTAGACGCGAAACTGCTCCATCAGCGCCTGCTGCT‑‑GGTTGGCCAGCCGGTTCAGGGCTTGGc                                                             <  6:118709/148‑1 (MQ=255)                                                                               ggCATAAGTTGTGCTCAAGAATAACGATGGTGCGGTGCCTGTCAGGGCCTCTTCGCGGGCGTGCCCGCGAAGAGGCCCTGACAGGCTAGACGCGAAACTGCTCCATCAGCGCCTGCTGCT‑‑GGTTGGCCAGCCGGTTCAGGGCTTGGCt                                                            >  4:134895/1‑148 (MQ=255)                                                                                  aTAAGTTGTGCTCAAGAATAACGATGGTGCGGTGCCTGTCAGGGCCTCTTCGCGGGCGTGCCCGCGAAGAGGCCCTGACAGGCTAGACGCGAAACTGCTCCATCAGCGCCTGCTGCT‑‑GGTTGGCCAGCCGGTTCAGGGCTTGGCTGATg                                                        >  4:219379/1‑149 (MQ=255)                                                                                   tAAGTTGTGCTCAAGAATAACGATGGTGCGGTGCCTGTCAGGGCCTCTTCGCGGGCGTGCCCGCGAAGAGGCCCTGACAGGCTAGACGCGAAACTGCTCCATCAGCGCCTGCTGCT‑‑GGTTGGCCAGCCGGTTCAGGGCTTGGCTGATGc                                                       >  6:21340/1‑149 (MQ=255)                                                                                       ttGTGCTCAAGAATAACGATGGTGCGGTGCCTGTCAGGGCCTCTTCGCGGGCGTGCCCGCGAAGAGGCCCTGACAGGCTAGACGCGAAACTGCTCCATCAGCGCCTGCTGCT‑‑GGTTGGCCAGCCGGTTCAGGGCTTGGCTGATGCGTGc                                                   >  2:108447/1‑149 (MQ=255)                                                                                       ttGTGCTCAAGAATAACGATGGTGCGGTGCCTGTCAGGGCCTCTTCGCGGGCGTGCCCGCGAAGAGGCCCTGACAGGCTAGACGCGAAACTGCTCCATCAGCGCCTGCTGCT‑‑GGTTGGCCAGCCGGTTCAGGGCTTGGCTGATGCGTGc                                                   <  3:134895/149‑1 (MQ=255)                                                                                        tgtgCTCAAGAATAACGATGGTGCGGTGCCTGTCAGGGCCTCTTCGCGGGCGTGCCCGCGAAGAGGCCCTGACAGGCTAGACGCGAAACTGCTCCATCAGCGCCTGCTGCT‑‑GGTTGGCCAGCCGGTTCAGGGCTTGGCTGATGCGTGc                                                   <  5:184529/148‑1 (MQ=255)                                                                                                        gATGGTGCGGTGCCTGTCAGGGCCTCTTCGCGGGCGTGCCCGCGAAGAGGCCCTGACAGGCTAGACGCGAAACTGCTCCATCAGCGCCTGCTGCT‑‑GGTTGGCCAGCCGGTTCAGGGCTTGGCTGATGCGTGCCGATTCATc                                          >  4:239710/1‑141 (MQ=255)                                                                                                        gATGGTGCGGTGCCTGTCAGGGCCTCTTCGCGGGCGTGCCCGCGAAGAGGCCCTGACAGGCTAGACGCGAAACTGCTCCATCAGCGCCTGCTGCT‑‑GGTTGGCCAGCCGGTTCAGGGCTTGGCTGATGCGTGCCGATTCATc                                          <  3:239710/141‑1 (MQ=255)                                                                                                         aTGGTGCGGTGCCCGTCAGGGCCTCTTCGCGGGCGTGCCCGCGAAGAGGCCCTGACAGGCTAGACGCGAAACTGCTCCATCAGCGCCTGCTGCT‑‑GGTTGGCCAGCCGGTTCAGGGCTTg                                                               >  4:344673/1‑119 (MQ=255)                                                                                                         aTGGTGCGGTGCCCGTCAGGGCCTCTTCGCGGGCGTGCCCGCGAAGAGGCCCTGACAGGCTAGACGCGAAACTGCTCCATCAGCGCCTGCTGCT‑‑GGTTGGCCAGCCGGTTCAGGGCTTg                                                               <  3:344673/119‑1 (MQ=255)                                                                                                                       gTCAGGGCCTCTTCGCGGGCGTGCCCGCGAAGAGGCCCTGACAGGCTAGACGCGAAACTGCTCCATCAGCGCCTGCTGCT‑‑GGTTgg                                                                                  <  4:277705/86‑1 (MQ=255)                                                                                                                       gTCAGGGCCTCTTCGCGGGCGTGCCCGCGAAGAGGCCCTGACAGGCTAGACGCGAAACTGCTCCATCAGCGCCTGCTGCT‑‑GGTTgg                                                                                  >  3:277705/1‑86 (MQ=255)                                                                                                                        tCAGGGCCTCTTCGCGGGCGTGCCCGCGAATTGGCCCTGACAGGCTAGACGCGAAACTGCTCCATCAGCGCCTGCTGCTTCCGTTGGCCAGCCGGTTCAGGGCTTGGCTGATGCGTGCCGATTCATCGGCCTGCCCAGCCAGTGATTCt                    <  1:108447/149‑1 (MQ=255)                                                                                                                                tctTCGCGGTCGTGCCCTCGAAGAGGCCCTGACAGGCTAGACGCGAAACTGCTCCTTCAGCGCCTGCTGCT‑‑GGTTGGGGAGGCGGTTGAGGGCTTGGCGGATGCGTGCGGATTCATCGGCCTGCCCAGCCAGTgt                        <  2:253407/135‑2 (MQ=255)                                                                                                                                tctTCGCGGGCGTGCCCGCGAAGAGGCCCTGCCAGGGTGGACGCGAAAGTGCTCCCTCAGCGCCTGCTGCT‑‑GGTTGGCCAGCCGGTTCAGGGCTTGGCTGATGCGTGCCGATTCATCGGCCTGCCCAGCCAGTGa                        >  1:253407/1‑135 (MQ=255)                                                                                                                                tctTCGCGGGCACGCCCGCGAAGAGGCCCTGACAGGCTAGACGCGAAACTGCTCCATCAGCGCCTGCTGCT‑‑GGTTGGCCAGCCGGTTCAGGGCTTGGCTGATGCGTGCCGATTCATCGGCCTGCCCAGCCAGTGATTCt                    >  5:35967/1‑139 (MQ=255)                                                                                                                                tctTCGCGGGCACGCCCGCGAAGAGGCCCTGACAGGCTAGACGCGAAACTGCTCCATCAGCGCCTGCTGCT‑‑GGTTGGCCAGCCGGTTCAGGGCTTGGCTGATGCGTGCCGATTCATCGGCCTGCCCAGCCAGTGATTCt                    <  6:35967/139‑1 (MQ=255)                                                                                                                                  ttCGCGGGCGTGCCCGCGAAGAGGCCCTGACAGGCTAGACGCGAAACTGCTCCATCAGCGCCTGCTGCT‑‑GGTTGGCCAGCCGGTTCAGGGCTTGGCTGATGCGTGCCGATTCATCGGCCTGCCCAGCCAGTGATTCTGTCACGTCTCg         >  5:183583/1‑148 (MQ=255)                                                                                                                                     gcgGGCACGCCCGCGAAGAGGCCCTGACAGGCTAGACGCGAAACTGCTCCATCAGCGCCTGCTGCT‑‑GGTTGGCCAGCCGGTTCAGGGCTTGGCTGATGCGTGCCGATTCATCGGCCTGCCCAGCCAGTGATTCTGTCACGTCTCGaa       <  1:237738/147‑1 (MQ=255)                                                                                                                                     gcgGGCACGCCCGCGAAGAGGCCCTGACAGGCTAGACGCGAAACTGCTCCATCAGCGCCTGCTGCT‑‑GGTTGGCCAGCCGGTTCAGGGCTTGGCTGATGCGTGCCGATTCATCGGCCTGCCCAGCCAGTGATTCTGTCACGTCTCGaa       >  2:237738/1‑147 (MQ=255)                                                                                                                                        ggCGTGCCCGCGAAGAGGCCCTGACAGGCTAGACGCGAAACTGCTCCATCAGCGCCTGCTGCT‑‑GGTTGGCCAGCCGGTTCAGGGCTTGGCTGATGCGTGCCGATTCATCGGCCTGCCCAGCCAGTGATTCTGTCACGTCTCGAATGCCg  <  5:21340/149‑1 (MQ=255)                                                                                                                                        ggCGTGCCCGCGAAGAGGCCCTGACAGGCTAGACGCGAAACTGCTCCATCAGCGCCTGCTGCT‑‑GGTTGGCCAGCCGGTTCAGGGCTTGGCTGATGCGTGCCGATTCATCGGCCTGCCCAGCCAGTGATTCTGTCACGTCTCGAATGCCg  <  2:256587/149‑1 (MQ=255)                                                                                                                                           |                                                                                                                                                    AACAGGGTGGCGGCGATCGAGGTGCGTAAAAGCCCTTGTTCGCTGGTGATGTCGAAGAAAGTGGATCGGGTTGGATTAGGCATAAGTTGTGCTCAAGAATAACGATGGTGCGGTGCCTGTCAGGGCCTCTTCGCGGGCGTGCCCGCGAAGAGGCCCTGACAGGCTAGACGCGAAACTGCTCCATCAGCGCCTGCTGCT‑‑GGTTGGCCAGCCGGTTCAGGGCTTGGCTGATGCGTGCCGATTCATCGGCCTGCCCAGCCAGTGATTCTGTCACGTCTCGAATGCCG  >  NC_002947/1403452‑1403735

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑