Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	4,896,434	C→T	9.3%	intergenic (+67/‑141)	PP_4304 → / → sbp‑I	VIC family cation transporter/sulfate ABC transporter substrate‑binding protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	4,896,434	0	C	T	9.3%	121.0 / 2.9	43	intergenic (+67/‑141)	PP_4304/sbp‑I	VIC family cation transporter/sulfate ABC transporter substrate‑binding protein
Reads supporting (aligned to +/- strand):  ref base C (20/19);  new base T (2/2);  total (22/21)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.23e-01

GACCTGCCACAAGAAGACCCACGAGCAGGGGGCGGCGTTCTGTTCTCGCTGTGGGAATGGGTTGTTTCCCAAAGCGTGATAGCGCCTGCGCCGGCCTCTTCGCGGGTAAATCCGCTCCTACAGGCGCGGACCG‑TGCGCGGTCC‑‑‑CCCGTAGGA‑GCGGGTTTACCCGCGAAGAGGCCGGCACAGGCAGAAGCATAACCAAAGCATTTTTTGTTCTTTAACCCGTATAAACCCACCCGTTATAGTCGCTGGCAATCTGCCCCAACACCCTTCAAGAACAAGGACGCAACGTGAAAA  >  NC_002947/4896289‑4896581                                                                                                                                                      |                                                                                                                                                     gACCTGCCACAAGAAGACCCACGAGCAGGGGGCGGCGTTCTGTTCTCGCTGTGGGAATGGGTTGTTTCCCAAAGCGTGATAGCGCCTGCGCCGGCCTCTTCGCGGGTAAATCCGCTCCTACAGGCGCGGACCG‑TGCGCGGTCC‑‑‑CCCg                                                                                                                                                     >  7:265313/1‑147 (MQ=255) gACCTGCCACAAGAAGACCCACGAGCAGGGGGCGGCGTTCTGTTCTCGCTGTGGGAATGGGTTGTTTCCCAAAGCGTGATAGCGCCTGCGCCGGCCTCTTCGCGGGTAAATCCGCTCCTACAGGCGCGGACCG‑TGCGCGGTCC‑‑‑CCCg                                                                                                                                                     <  8:265313/147‑1 (MQ=255) gACCTGCCACAAGAAGACCCACGAGCAGGGGGCGGCGTTCTGTTCTCGCTGTGGGAATGGGTTGTTTCCCAAAGCGTGATAGCGCCTGCGCCGGCCTCTTCGCGGGTAAATCCGCTCCTACAGGCGCGGACCG‑TGCGCGGTCC‑‑‑CCCGTa                                                                                                                                                   <  5:59328/149‑1 (MQ=255) gACCTGCCACAAGAAGACCCACGAGCAGGGGGCGGCGTTCTGTTCTCGCTGTGGGAATGGGTTGTTTCCCAAAGCGTGATAGCGCCTGCGCCGGCCTCTTCGCGGGTAAATCCGCTCCTACAGGCGCGGACCG‑TGCGCGGTCC‑‑‑CCCGTa                                                                                                                                                   <  4:215834/149‑1 (MQ=255)        cacaAGAAGACCCACGAGCAGGGGGCGGCGTTCTGTTCTCGCTGTGGGAATGGGTTGTTTCCCAAAGCGTGATAGCGCCTGCGCCGGCCTCTTCGCGGGTAAATCCGCTCCTACAGGCGCGGACCG‑TGCGCGGTCC‑‑‑CCCGTAGGA‑GCgg                                                                                                                                           <  7:121595/149‑1 (MQ=255)        cacaAGAAGACCCACGAGCAGGGGGCGGCGTTCTGTTCTCGCTGTGGGAATGGGTTGTTTCCCAAAGCGTGATAGCGCCTGCGCCGGCCTCTTCGCGGGTAAATCCGCTCCTACAGGCGCGGACCG‑TGCGCGGTCC‑‑‑CCCGTAGGA‑GCgg                                                                                                                                           <  7:42407/149‑1 (MQ=255)        cacaAGAAGACCCACGAGCAGGGGGCGGCGTTCTGTTCTCGCTGTGGGAATGGGTTGTTTCCCAAAGCGTGATAGCGCCTGCGCCGGCCTCTTCGCGGGTAAATCCGCTCCTACAGGCGCGGACCG‑TGCGCGGTCC‑‑‑CCCGTAGGA‑GCgg                                                                                                                                           <  1:261079/149‑1 (MQ=255)            agaagaCCCACGAGCAGGGGGCGGCGTTCTGTTCTCGCTGTGGGAATGGGTTGTTTCCCAAAGCGTGATAGCGCCTGCGCCGGCCTCTTCGCGGGTAAATCCGCTCCTACAGGCGCGGACCG‑TGCGCGGTCC‑‑‑CCCGTAGGA‑GCGGGttt                                                                                                                                       <  4:266672/149‑1 (MQ=255)             gaagaCCCACGAGCAGGGGGCGGCGTTCTGTTCTCGCTGTGGGAATGGGTTGTTTCCCAAAGCGTGATAGCGCCTGCGCCGGCCTCTTCGCGGGTAAATCCGCTCCTACAGGCGCGGACCG‑TGCGCGGTCC‑‑‑CCCGTAGGA‑GCGGGTTTa                                                                                                                                      <  1:27519/149‑1 (MQ=255)             gaagaCCCACGAGCAGGGGGCGGCGTTCTGTTCTCGCTGTGGGAATGGGTTGTTTCCCAAAGCGTGATAGCGCCTGCGACGGCCTCTTCGCGGGGAAATCCGCTCCTACATGCGCCGACCG‑TGCGCGGTCC‑‑‑CCCGTAGGA‑GCGGGTTTa                                                                                                                                      >  7:251213/1‑149 (MQ=255)                   ccACGAGCAGGGGGCGGCGTTCTGTTCTCGCTGTGGGAATGGGTTGTTTCCCAAAGCGTGATAGCGCCTGTGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACGGG‑‑‑GGACCG‑CGCACGGTCCGCGCCTGTAGGA‑GCGGATTTAc                                                                                                                                     >  7:224421/1‑144 (MQ=14)                   ccACGAGCAGGGGGCGGCGTTCTGTTCTCGCTGTGGGAATGGGTTGTTTCCCAAAGCGTGATAGCGCCTGTGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACGGG‑‑‑GGACCG‑CGCACGGTCCGCGCCTGTAGGA‑GCGGATTTAc                                                                                                                                     <  8:224421/144‑1 (MQ=14)                   ccACGAGCAGGGGGCGGCGTTCTGTTCTCGCTGTGGGAATGGGTTGTTTCCCAAAGCGTGATAGCGCCTGCGCCGGCCTCTTCGCGGGTAAATCCGCTCCTACAGGCGCGGACCG‑TGCGCGGTCC‑‑‑CCCGTAGGA‑GCgg                                                                                                                                           >  1:338991/1‑138 (MQ=255)                   ccACGAGCAGGGGGCGGCGTTCTGTTCTCGCTGTGGGAATGGGTTGTTTCCCAAAGCGTGATAGCGCCTGCGCCGGCCTCTTCGCGGGTAAATCCGCTCCTACAGGCGCGGACCG‑TGCGCGGTCC‑‑‑CCCGTAGGA‑GCgg                                                                                                                                           <  2:338991/138‑1 (MQ=255)                        aGCAGGGGGCGGCGTTCTGTTCTCGCTGTGGGAATGGGTTGTTTCCCAAAGCGTGATAGCGCCTGCGCCGGCCTCTTCGCGGGTAAACCCGCTCCTACGGG‑‑‑GGACCG‑CGCACGGTCCGCGCCTGTAGGA‑GCGGATTTACCCGCGAagag                                                                                                                           <  2:180019/149‑1 (MQ=14)                                      ttctgttctCGCTGTGGGAATGGGTTGTTTCCCAAAGCGTGATAGCGCCTGCGCCGGCCTCTTCGCGGGTAAATCCGCTCCTACAGGCGCGGACCG‑TGCGCGGTcc‑‑‑ccc                                                                                                                                                      >  1:347996/1‑109 (MQ=255)                                      ttctgttctCGCTGTGGGAATGGGTTGTTTCCCAAAGCGTGATAGCGCCTGCGCCGGCCTCTTCGCGGGTAAATCCGCTCCTACAGGCGCGGACCG‑TGCGCGGTcc‑‑‑ccc                                                                                                                                                      <  2:347996/109‑1 (MQ=255)                                        ctgttctCGCTGTGGGAATGGGTTGTTTCCCAAAGCGTGATAGCGCCTGCGCCGGCCTCTTCGCGGGTAAATCCGCTCCTACAGGCGCGGACCG‑TGCGCGGTCC‑‑‑CCCGTAGGA‑GCGGGTTTACCCGCGAAGAGGCCGGCACAGGCAGa                                                                                                            <  3:127042/148‑1 (MQ=255)                                            tctcGCTGTGGGAATGGGTTGTTTCCCAAAGCGTGATAGCGCCTGCGCCGGCCTCTTCGCGGGTAAATCCGCTCCTACAGGCGCGGACCG‑TGAGCGGTCC‑‑‑CCCGTAGGA‑GCGGGTTTACCCGCGAAGAGGCCGGCACAGGCAGAAGCa                                                                                                        >  5:382631/1‑148 (MQ=255)                                              tcGCTGTGGGAATGGGTTGTTTCCCAAAGCGTGATAGCGCCTGCGCCGGCCTCTTCGCGGGTAAATCCGCTCCTACAGGCGCGGACCG‑TGCGCGGTCC‑‑‑CCCGGAGGA‑GCCGGTTTACCCGCGAAGAGGCCGGCACAGGCAGAAGCATaa                                                                                                     >  5:173636/1‑149 (MQ=255)                                                                 tttCCCAAAGCGTGATAGCGCCTGCGCCGGCCTCTTAGCCGGTAAATACGCTCCTAAAGGCGCGGAACG‑TGCGCGGTCC‑‑‑CCCGTAGGA‑GCCGGTTTACCCGCCAAGAGGCCGGCACAAGCAGAACCATAACCAAAGCAAttttttttat                                                                                  >  4:298714/1‑147 (MQ=255)                                                                     ccAAAGCGTGATAGCGCCTGCGCCGGCCTCTTCGCGGGTAAATCCGCTCCTACAGGCGCGGACCG‑TGCGCGGTCC‑‑‑CCCGTAGGA‑GCGGGTTTACCCGCGAAGAGGCCGGCACAGGCAGAAGCATAACCAAAGCATTTTTTGTTCTTTaa                                                                              >  6:108749/1‑149 (MQ=255)                                                                                tAGCGCCTGCGCCGGCCTATTCGCTGGTAAATCCGATCCTACTGGCGCGGACCG‑TGCGCGTTCC‑‑‑CCCGTAGGA‑GCGGGTTTACCCGCGAAGAGGCCGGCACAGGCAGAAGCATAACCAAAGCATTTTTTGTTCTTTAACCCGTATaaa                                                                    <  8:251213/148‑1 (MQ=39)                                                                                  gcgcCTGCGCCGGCCTCTTCGCGGTTAAATCCGCTCCTACAGGCGCGGACCG‑TGCGCGGTCC‑‑‑CCCGTTGTA‑GGGGTTTTACCCGCTAAGAGGCCGGCACAGGCAGAAGCATAACCAAAGCATTTTTTGTTCTTTAACCCGTATAAacc                                                                  <  1:378486/148‑1 (MQ=255)                                                                                          gcCGGCCTCTTCGCGGGTAAATCGGCGCCTACAGGCGCGGACCG‑TGTGCGGTCC‑‑‑CCCGTAGGA‑GCGGGTTTACCCGCGAAGAGGCCGGCACAGGCAGAAGCATAACCAAAGCATTTTTTGTTCTTTAACCCGTATAAACCCACCCGTta                                                         <  6:382631/149‑1 (MQ=255)                                                                                            cGGCCTCTTCGCGGGTAAATCCGCTCCTACAGGCGCGGACCG‑TGCGCGGTCC‑‑‑CCCGTAGGA‑GCGGGTTTACCCGCGAAGAGGCCGGCACAGGCAGAAGCATAACCAAAGCATTTTTTGTTCTTTAACCCGTATAAACCCACCCGTtata                                                       >  6:218569/1‑149 (MQ=255)                                                                                                 tctTCGCGGGTAAATCCGCTCCTACAGGCGCGGACCG‑TGCGCGGTCC‑‑‑CCCGTAGGA‑GCGGGTTTACCCGCGAAGAGGCCGGCACAGGCAGAAGCATAACCAAAGCATTTTTTGTTCTTTAACCCGTATAAACCCACCCGTTATAGTCGc                                                  >  7:124656/1‑149 (MQ=255)                                                                                                  ctTCGCGGGTAAACCCGCTCCTACGGG‑‑‑GGACCG‑CGCACGGTCCGCGCCTGTAGGA‑GCGGATTTACCCGCGAAGAGGCCGGCACAGGCAGAAGCATAACCAAAGCATTTTTTGTTCTTTAACCCGTATAAACCCACCCGTTATAGTCGCt                                                 >  8:226570/1‑149 (MQ=14)                                                                                                     cgcgGGTAAATCCGCTCCTACAGGCGCGGACCG‑TGCGCGGTCC‑‑‑CCCGTAGGA‑GCGGGTTTACCCGCGAAGAGGCCGGCACAGGCAGAAGCATAACCAAAGCATTTTTTGTTCTTTAACCCGTATAAACCCACCCGTTATAGTCGCTgg                                               >  7:149664/1‑148 (MQ=255)                                                                                                             aaTCCGCTCCTACAGGCGCGGACCG‑TGCGCGGTCC‑‑‑CCCGTAGGA‑GCGGGTTTACCCGCGAAGAGGCCGGCACAGGCAGAAGCATAACCAAAGCATTTTTTGTTCTTTAACCCGTATAAACCCACCCGTTATAGTCGCTGGCAATCTGc                                       <  5:108749/148‑1 (MQ=255)                                                                                                             aaTCCGCTCCTACAGGCGCGGACCG‑TGCGCGGTCC‑‑‑CACGTAGGA‑GCGGGTTTACCCGCGAAGAGGCCGGCACAGGCAGAAGCATAACCAAAGCATTTTTTGTTCTTTAACCCGTATAAACCCACCCGTTATAGTCGCTGGCAATCTGc                                       <  3:298714/148‑1 (MQ=255)                                                                                                              aTCCGCTCCTACAGGCGCGGACCGTTGCGCGGTCC‑‑‑CCCGTAGGA‑GCGGGTTTACCCGCGAAGAGGCCGGCACAGGCAGAAGCATAACCAAAGCATTTTTTGTTCTTTAACCCGTATAAACCCACCCGTTATAGTCGCTGGCAATCTGcc                                      >  7:56886/1‑149 (MQ=255)                                                                                                                  gCTCCTACAGGCGCGGACCG‑TGCGCGGTCC‑‑‑CCCGTAGGA‑GCGGGTTTACCCGCGAAGAGGCCGGCACAGGCAGAAGCATAACCAAAGCATTTTTTGTTCTTTAACCCGt                                                                         <  7:71173/109‑1 (MQ=255)                                                                                                                  gCTCCTACAGGCGCGGACCG‑TGCGCGGTCC‑‑‑CCCGTAGGA‑GCGGGTTTACCCGCGAAGAGGCCGGCACAGGCAGAAGCATAACCAAAGCATTTTTTGTTCTTTAACCCGt                                                                         >  8:71173/1‑109 (MQ=255)                                                                                                                      cTACAGGCGCGGACCG‑TGGGCGGTCC‑‑‑CCCGTAGTA‑GCGGGTTTACCCGCGAAGAGGCCGGCACAGGCAGAAGCATAACCAAAGCATTTTTTGTTCTTTAACCCGTATAAACCCACCCGTTATAGTCGCTGGCAATCTGCCCCAACAccc                             <  6:173636/149‑1 (MQ=255)                                                                                                                      cTACAGGCGCGGACCG‑TGCGCGGTCC‑‑‑CCCGTAGGA‑GCGGGTTTACCCGCGAAGAGGCCGGCACAGGCAGAAGCATAACCAAAGCATTTTTTGTTCTTTAACCCGTATAAACCCACCCGTTATAGTCGCTGGCAATCTGCCCCAACAccc                             >  1:110740/1‑149 (MQ=255)                                                                                                                          aGGCGCGGACCG‑TGCGCGGTCC‑‑‑CCCGTAGGA‑GCGGGTTTACCCGCGAAGAGGCCGGCACAGGCAGAAGCATAACCAAAGCATTTTTTGTTCTTTAACCCGTATAAACCCACCCGTTATAGTCGCTg                                                <  2:328208/126‑1 (MQ=255)                                                                                                                            gcgcGGACCG‑TGCGCGGTCC‑‑‑CCCGTAGGAGGCGGGTTTACCCGCGAAGAGGCCGGCACAGGCAGAAGCATAACCAAAGCATTTTTTGTTCTTTAACCCGTATAAACCCACCCGTTATAGTCGCTGGCAATCTGCCCCAACACCCTTc                          >  1:29840/1‑147 (MQ=255)                                                                                                                                  aCCG‑TGCGCGGTCC‑‑‑CCCGTAGGA‑GCGGGTTTACCCGCGAAGAGGCCGGCACAGGCAGAAGCATAACCAAAGCATTTTTTGTTCTTTAACCCGTATAAACCCACCCGTTATAGTCGCTGGCAATCTGCCCCAACACCCTTCAAGAACAAg                 >  1:28181/1‑149 (MQ=255)                                                                                                                                    cG‑TGCGCGGTCC‑‑‑CCCGTAGGA‑GCGGGTTTACCCGCGAAGAGGCCGGCACAGGCAGAAGCATAACCAAAGCATTTTTTGTTCTTTAACCCGTATAAACCCACCCGTTATAGTCGCTGGCAATCTGCCCCAACACCCTTCAAGAACAAGGa               >  4:4093/1‑149 (MQ=255)                                                                                                                                       tGCGCGGTCC‑‑‑CCCGTAGGA‑GCGGGTTTACCCGCGAAGAGGCCGGCCCAGGCAGAAGCATAACCAAAGCATTTTTTGTTCTTTAACCCGTATAAACCCACCCGTTATAGTCGCTGGCAATCTGCCCCAACACCCTTCAAGAACAAGGACg             >  1:87342/1‑149 (MQ=255)                                                                                                                                            ggTCC‑‑‑CCCGTAGGA‑GCGGGTTTACCCGCGAAGAGGCCGGCACAGGCAGAAGCATAACCAAAGCATTTTTTGTTCTTTAACCCGTATAAACCCACCCGTTATAGTCGCTGGCAATCTGCCCCAACACCCTTCAAGAACAAGGACGCAACg        >  6:341262/1‑149 (MQ=255)                                                                                                                                             gTCC‑‑‑CCCGTAGGA‑GCGGGTTTACCCGCGAAGAGGCCGGCACAGGCAGAAGCATAACCAAAGCATTTTTTGTTCTTTAACCCGTATAAACCCACCCGTTATAGTCGCTGGCAATCTGCCACAACACCATTCAAGAACAAGGACGAAACGt       >  2:375976/1‑149 (MQ=255)                                                                                                                                             gTCC‑‑‑CCCGTAGGA‑GCGGGTTTACACGCGAAGAGGCCGGCACAGGCAGAAGCATAACCAAAGCATTTTTTGTTCTTTAACCCGTATAAACCCACCCGTTATAGTCGCTGGCAATCTGCCCCAACACCCTTCAAGAACAAGCACGCAACGt       >  4:350987/1‑149 (MQ=255)                                                                                                                                              tCC‑‑‑CCCGTAGGA‑GCGGGTTTACCCGCGAAGAGGCCGGCACAGGCAGAAGCATAACCAAAGCATTTTTTGTTCTTTAACCCGTATAAACCCACCCGTTATAGTCGCTGGCAATCTGCCCCAACACCCTTCAAGAACAAGGACGCAACGTg      <  2:29840/149‑1 (MQ=255)                                                                                                                                                     ccGTAGGA‑GCGGGTTTACCCGCGAAGAGGCCGGCACAGGCAGAAGCATAACCAAAGCATTTTTTGTTCTTTAACCCGTATAAACCCACCCGTTATAGTCGCTGGCAATCTGCCCCAACAccc                             <  1:100131/122‑1 (MQ=255)                                                                                                                                                     ccGTAGGA‑GCGGGTTTACCCGCGAAGAGGCCGGCACAGGCAGAAGCATAACCAAAGCATTTTTTGTTCTTTAACCCGTATAAACCCACCCGTTATAGTCGCTGGCAATCTGCCCCAACACCCTTCAAGAACAAGGACGCAACGTGaaa   >  8:328912/1‑148 (MQ=255)                                                                                                                                                     ccGTAGGA‑GCGGGTTTACACGCGAAGAGGCCGGCACAGGCAGAAGCATAACCAAAGCATTTTTTGTTCTTTAACCCGTATAAACCCACCCGTTATAGTCGCTGGCAATCTGCCCCAACAccc                             >  2:100131/1‑122 (MQ=255)                                                                                                                                                      cGTAGGA‑GCGGGTTTACCCGCGAAGAGGCCGGCACAGGCAGAAGCATAACCAAAGCATTTTTTGTTCTTTAACCCGTATAAACCCACCCGTTATAGTCGCTGGCAATCTGCCCCAACACCCTTCAAGAACAAGGACGCAACGTGaaaa  >  1:7395/1‑148 (MQ=255)                                                                                                                                                      |                                                                                                                                                     GACCTGCCACAAGAAGACCCACGAGCAGGGGGCGGCGTTCTGTTCTCGCTGTGGGAATGGGTTGTTTCCCAAAGCGTGATAGCGCCTGCGCCGGCCTCTTCGCGGGTAAATCCGCTCCTACAGGCGCGGACCG‑TGCGCGGTCC‑‑‑CCCGTAGGA‑GCGGGTTTACCCGCGAAGAGGCCGGCACAGGCAGAAGCATAACCAAAGCATTTTTTGTTCTTTAACCCGTATAAACCCACCCGTTATAGTCGCTGGCAATCTGCCCCAACACCCTTCAAGAACAAGGACGCAACGTGAAAA  >  NC_002947/4896289‑4896581

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: ‑