Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,559,123	A→G	8.5%	*474W (TGA→TGG)	PP_3142 →	sugar transferase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,559,123	0	A	G	8.5%	127.0 / 2.2	47	*474W (TGA→TGG)	PP_3142	sugar transferase
Reads supporting (aligned to +/- strand):  ref base A (23/20);  new base G (2/2);  total (25/22)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.84e-01

TTCAGGGGGGAGACCAAGGATATCGAGCAAATGATCCAGCGAGTCGACTCGGACATCGAGTACATCAACAACTGGTCGTTGTGGCTGGACTTCGTGATCCTGGTGCGCACGCTTAATGCCTTCACCGGTAAGCAGGCTTATTGAGCGAAGCGCTCCTGCTTCAAGCGCGCCCAGCTGGTTATTCCTTGTTCAACGGATGCAACACCCTGAACCCCCGCGCTTCTTCCACCAGCCAGTCATGCACCGCCCGCGCACCTGGCTGGTTCAAGCCGCCTGGCGGGTAATGCACCA  >  NC_002947/3558980‑3559270                                                                                                                                                |                                                                                                                                                    ttCAGGGGGGAGACCAAGGATATCGAGCAAATGATCCAGCGAGTCGACTCGGACATCGAGTACATCAACAACTGGTCGTTGTGGCTGGACTTCGTGATCCTGGTGCGCACGCTTAATGCCTTCACCGGTAAGCAGGCTTATTGAGCg                                                                                                                                                  >  5:120076/1‑147 (MQ=255)        gggAGACCAAGGATATCGAGCAAATGATCCAGCGAGTCGACTCGGACATCGAGTACATCAACAACTGGTCGTTGTGGCTGGACTTCGTGATCCTGGTGCGCACGCTTAATGCCTTCACCGGTAAGCAGGCTTATTGAGCGAAGCGCt                                                                                                                                           >  8:261013/1‑147 (MQ=255)        gggAGACCAAGGATATCGAGCAAATGATCCAGCGAGTCGACTCGGACATCGAGTACATCAACAACTGGTCGTTGTGGCTGGACTTCGTGATCCTGGTGCGCACGCTTAATGCCTTCACCGGTAAGCAGGCTTATTGAGCGAAGCGCt                                                                                                                                           <  7:261013/147‑1 (MQ=255)                  ggATATCGAGCAAATGATCCAGCGAGTCGACTCGGACATCGAGTACATCAACAACTGGTCGTTGTGGCTGGACTTCGTGATCCTGGTGCGCACGCTTAATGCCTTCACCGGTAAGCAGGCTTATTGAGCGAAGCGCTCCTGCTTCAAgc                                                                                                                               <  1:204764/149‑1 (MQ=255)                     tatCGAGCAAATGATCCAGCGAGTCGACTCGGACATCGAGTACATCAACAACTGGTCGTTGTGGCTGGACTTCGTGATCCTGGTGCGCACGCTTAATGCCTTCACCGGTAAGCAGGCTTATTGAGCGAAGCGCTCCTGCTTCAAgcgcg                                                                                                                            >  4:216440/1‑149 (MQ=255)                        cGAGCAAATGATCCAGCGAGTCGACTCGGACATCGAGTACATCAACAACTGGTCGTTGTGGCTGGACTTCGTGATCCTGGTGCGCACGCTTAATGCCTTCACCGGTAAGCAGGCTTATTGAGCGAAg                                                                                                                                               <  1:258550/127‑1 (MQ=255)                        cGAGCAAATGATCCAGCGAGTCGACTCGGACATCGAGTACATCAACAACTGGTCGTTGTGGCTGGACTTCGTGATCCTGGTGCGCACGCTTAATGCCTTCACCGGTAAGCAGGCTTATTGAGCGAAg                                                                                                                                               >  2:258550/1‑127 (MQ=255)                             aaaTGATCCAGCGAGTCGACTCGGACATCGAGTACATCAACAACTGGTCGTTGTGGCTGGACTTCGTGATCCTGGTGCGCACGCTTAATGCCTTCACCGGTAAGCAGGCTTATTGAGCGAAGCGCTCCTGCTTCAAGCGCGCCCAGCTg                                                                                                                    <  6:120076/149‑1 (MQ=255)                               aTGATCCAGCGAGTCGACTCGGACATCGAGTACATCAACAACTGGTCGTTGTGGCTGGACTTCGTGATCCTGGTGCGCACGCTTAATGCCTTCACCGGTAAGCAGGCTTATTGAGCGAAGCGCGCCTGCTTCAAGCGCGCCCAGCTGGt                                                                                                                  >  5:3147/1‑149 (MQ=255)                                 gATCCAGCGAGTCGACTCGGACATCGAGTACATCAACAACTGGTCGTTGTGGCTGGACTTCGTGATCCTGGTGCGCACGCTTAATGCCTTCACCGGTAAGCAGGCTTATTGAGCGAAGCGCTCCt                                                                                                                                        >  5:129640/1‑125 (MQ=255)                                 gATCCAGCGAGTCGACTCGGACATCGAGTACATCAACAACTGGTCGTTGTGGCTGGACTTCGTGATCCTGGTGCGCACGCTTAATGCCTTCACCGGTAAGCAGGCTTATTGAGCGAAGCGCTCCt                                                                                                                                        <  6:129640/125‑1 (MQ=255)                                   tCCAGCGAGTCGACTCGGACATCGAGTACATCAACAACTGGTCGTTGTGGCTGGACTTCGTGATCCTGGTGCGCACGCTTAATGCCTTCACCGGTAAGCAGGCTTATTGAGCGAAGCGCTc                                                                                                                                          >  4:42676/1‑121 (MQ=255)                                   tCCAGCGAGTCGACTCGGACATCGAGTACATCAACAACTGGTCGTTGTGGCTGGACTTCGTGATCCTGGTGCGCACGCTTAATGCCTTCACCGGTAAGCAGGCTTATTGAGCGAAGCGCTc                                                                                                                                          <  3:42676/121‑1 (MQ=255)                                      aGCGAGTCGACTCGGACATCGAGTACATCAACAACTGGTCGTTGTGGCTGGACTTCGTGATCCTGGTGCGCACGCTTAATGCCTTCACCGGTAAGCAGGCTTATTGAGCGAAGCGCTCCTGCTTCAAGCGCGCCCAGCTGGTTATTCCt                                                                                                           >  7:135969/1‑149 (MQ=255)                                       gCGAGTCGACTCGGACATCGAGTACATCAACAACTGGTCGTTGTGGCTGGACTTCGTGATCCTGGTGCGCACGCTTAATGCCTTCACCGGTAAGCAGGCTTATTGAGCGAAGCGCTCCTGCTTCAAGCGCGCCCAGCTGGTTATTCCtg                                                                                                          >  4:217032/1‑148 (MQ=255)                                              gACTCGGACATCGAGTACATCAACAACTGGTCGTTGTGGCTGGACTTCGTGATCCTGGTGCGCACGCTTAATGCCTTCACCGGTAAGCAGGCTTATTGAGCGAAGCGCTCCTGCTTCAAGCGCGCCCAGCTGGTTATTCCTTGTTCAAc                                                                                                   >  5:18636/1‑149 (MQ=255)                                                   ggACATCGAGTACATCAACAACTGGTCGTTGTGGCTGGACTTCGTGATCCTGGTGCGCACGCTTAATGCCTTCACCGGTAAGCAGGCTTATTGGGCGAAGCGCTCCTGCTTCAAGCGCGCCCAGCTGGTTATTCCTTGTTCAACGGATg                                                                                              >  1:260991/1‑149 (MQ=255)                                                   ggACATCGAGTACATCAACAACTGGTCGTTGTGGCTGGACTTCGTGATCCTGGTGCGCACGCTTAATGCCTTCACCGGTAAGCAGGCTTATTGAGCGAAGCGCTCCTGCTTCAAGCGCGCCCAGCTGGTTATTCCTTGTTCAACGGAt                                                                                               <  8:135969/148‑1 (MQ=255)                                                   ggACATCGAGTACATCAACAACTGGTCGTTGTGGCTGGACTTCGTGATCCTGGTGCGCACGCTTAATGCCTTCACCGGTAAGCAGGCTTATTGAGCGAAGCGCTCCTGCTTCAAGCGCGCCCAGCTGGTTATTCCTTGTTCAACGGAt                                                                                               <  3:216440/148‑1 (MQ=255)                                                      cATCGAGTACATCAACAACTGGTCGTTGTGGCTGGACTTCGTGATCCTGGTGCGCACGCTTAATGCCTTCACCGGTAAGCAGGCTTATTGAGCGAAGCGCTCCTGCTTCAAGCGCGCCCAGCTGGTTATTCCTTGTTCAACGGATGCaa                                                                                           >  3:54601/1‑149 (MQ=255)                                                      cATCGAGTACATCAACAACTGGTCGTTGTGGCTGGACTTCGTGATCCTGGTGCGCACGCTTAATGCCTTCACCGGTAAGCAGGCTTATTGAGCGAAGCGCTCCTGCTTCAAGCGCGCCCAGCTGGTTATTCCTTGTTCAACGGATGCaa                                                                                           <  6:18636/149‑1 (MQ=255)                                                          gAGTACATCAACAACTGGTCGTTGTGGCTGGACTTCGTGATCCTGGTGCGCACGCTTAATGCCTTCACCGGTAAGCAGGCTTATTGAGCGAAGCGCTc                                                                                                                                          >  2:91213/1‑98 (MQ=255)                                                          gAGTACATCAACAACTGGTCGTTGTGGCTGGACTTCGTGATCCTGGTGCGCACGCTTAATGCCTTCACCGGTAAGCAGGCTTATTGAGCGAAGCGCTc                                                                                                                                          <  1:91213/98‑1 (MQ=255)                                                            gTACATCAACAACTGGTCGTTGTGGCTGGACTTCGTGATCCTGGTGCGCACGCTTAATGCCTTCACCGGTAAGCAGGCTTATTGAGCGAAGCGCTCCTGCTTCAAgcgcgc                                                                                                                           <  7:205401/111‑1 (MQ=255)                                                            gTACATCAACAACTGGTCGTTGTGGCTGGACTTCGTGATCCTGGTGCGCACGCTTAATGCCTTCACCGGTAAGCAGGCTTATTGAGCGAAGCGCTCCTGCTTCAAgcgcgc                                                                                                                           >  8:205401/1‑111 (MQ=255)                                                                  caacaaCTGGTCGTTGTGGCTGGACTTCGTGATCCTGGTGCGCACGCTTAATGCCTTCACCGGTAAGCAGGCTTATTGGGCGAAGCGCTCCTGc                                                                                                                                      >  7:161179/1‑94 (MQ=255)                                                                  caacaaCTGGTCGTTGTGGCTGGACTTCGTGATCCTGGTGCGCACGCTTAATGCCTTCACCGGTAAGCAGGCTTATTGGGCGAAGCGCTCCTGc                                                                                                                                      <  8:161179/94‑1 (MQ=255)                                                                           gTCGTTGTGGCTGGACTTCGTGATCCTGGTGCGCACGCTTAATGCCTTCACCGGTAAGCAGGCTTATTGAGCGAAGCGCTCCTGCTTCAAGCGCGCCCAGCTGGTTATTCCTTGTTCAACGGATGCAACACCCTGAACCCCCGCGcttc                                                                      >  6:253302/1‑149 (MQ=255)                                                                           gTCGTTGTGGCTGGACTTCGTGATCCTGGTGCGCACGCTTAATGCCTTCACCGGTAAGCAGGCTTATTGAGCGAAGCGCTCCTGCTTCAAGCGCGCCCAGCTGGTTATTCCTTGTTCAACGGATGCAACACCCTGAACCCCCGCGcttc                                                                      >  2:173105/1‑149 (MQ=255)                                                                              gTTGTGGCTGGACTTCGTGATCCTGGTGCGCACGCTTAATGCCTTCACCGGTAAGCAGGCTTATTGAGCGAAGCGCTCCTGCTTCAAGCGCGCCCAGCTGGTTATTCCTTGTTCAACGGATGCAACACCCTGAACCCCCGCGCttcttc                                                                   <  6:3147/149‑1 (MQ=255)                                                                                           ttCGTGATCCTGGTGCGCACGCTTAATGCCTTCACCGGTAAGCAGGCTTATTGAGCGAAGCGCTCCTGCTTCAAGCGCGCCCAGCTGGTTATTCCTTGTTCAACGGATGCAACACCCTGAACCCCCGCGCTTCTTCCACCAGCCAGTCa                                                      >  7:227524/1‑149 (MQ=255)                                                                                                  tCCTGGTGCGCACGCTTAATGCCTTCACCGGTAAGCAGGCTTATTGAGCGAAGCGCTCCTGCTTCAAGCGCGCCCAGCTGGTTATTCCTTGTTCAACGGATGCAACACCCTGAACCCCCGCGCTTCTTCCACCAGCCAGTCATGCAccg                                               <  1:173105/149‑1 (MQ=255)                                                                                                       gTGCGCACGCTTAATGCCTTCACCGGTAAGCAGGCTTATTGAGCGAAGCGCTCCTGCTTCAAGCGCGCCCAGCTGGTTATTCCTTGTTCAACGGATGCAACACCCTGAACCCCCGCGCTTCTTCCACCAGCCAGTCATGCAccgcccgc                                          <  4:54601/149‑1 (MQ=255)                                                                                                           gcACGCTTAATGCCTTCACCGGTAAGCAGGCTTATTGAGCGAAGCGCTCCTGCTTCAAGCGCGCCCAGCTGGTTATTCCTTGTTCAACGGATGCAACACCCTGAACCCCCGCGCTTCTTCCACCAGCCAGTCATGCACCGCCCGCGCAc                                      >  1:164230/1‑149 (MQ=255)                                                                                                               gCTTAATGCCTTCACCGGTAAGCAGGCTTATTGAGCGAAGCGCTCCTGCTTCAAGCGCGCCCAGCTGGTTATTCCTTGTTCAACGGATGCAACACCCTGAACCCCCGCGCTTCTTCCACCAGCCAGTCATGCACCGCCCGCGCACctgg                                  >  1:153470/1‑149 (MQ=255)                                                                                                               gCTTAATGCCTTCACCGGTAAGCAGGCTTATTGAGCGAAGCGCTCCTGCTTCAAGCGCGCCCAGCTGGTTATTCCTTGTTCAACGGATGCAACACCCTGAACCCCCGCGCTTCTTCCACCAGCCAGTCATGCACCGCCCGCGCACctgg                                  >  1:322975/1‑149 (MQ=255)                                                                                                                    aTGCCTTCACCGGTAAGCAGGCTTATTGAGCGAAGCGCTCCTGCTTCAAGCGCGCCCAGCTGGTTATTCCTTGTTCAACGGATGCAACACCCTGAACCCCCGCGCTTCTTCCACCAGCCAGTCATGCACCGCCCGCGCACctggctgg                              <  8:227524/148‑1 (MQ=255)                                                                                                                     tGCCTTCACCGGTAAGCAGGCTTATTGAGCGAAGCGCTCCTGCTTCAAGCGCGCCCAGCTGGTTATTCCTTGTTCAACGGATGCAACACCCTGAACCCCCGCGCTTCTTCCACCAGCCAGTCATGCACCGCCCGCGCACCTGGCTGGtt                            <  2:153470/149‑1 (MQ=255)                                                                                                                         ttCACCGGTAAGCAGGCTTATTGAGCGAAGCGCTCCTGCTTCAAGCGCGCCCAGCTGGTTATTCCTTGTTCAACGGATGCAACACCCTGAACCCCCGCGCTTCTTCCACCAGCCAGTCATGCACCGCCCGCGCACCTGGCTGGTTCAAg                        >  5:14142/1‑149 (MQ=255)                                                                                                                               ggTAAGCAGGCTTATTGAGCGAAGCGCTCCTGCTTCAAGCGCGCCCAGCTGGTTATTCCTTGTTCAACGGATGCAACACCCTGAACCCCCGCGCTTCTTCCAccagc                                                            <  1:17875/107‑1 (MQ=255)                                                                                                                               ggTAAGCAGGCTTATTGAGCGAAGCGCTCCTGCTTCAAGCGCGCCCAGCTGGTTATTCCTTGTTCAACGGATGCAACACCCTGAACCCCCGCGCTTCTTCCAccagc                                                            >  2:17875/1‑107 (MQ=255)                                                                                                                                gTAAGCAGGCTTATTGAGCGAAGCGCTCCTGCTTCAAGCGCGCCCAGCTGGTTATTCCTTGTTCAACGGATGCAACACCCTGAACCCCCGCGCTTCTTCCACCAGCCAGTCATGCACCGCCCGCGCACCTGGCTGGTTCAAGCCGCCTg                 <  5:253302/149‑1 (MQ=255)                                                                                                                                   aGCAGGCTTATTGGGCGAAGCGCTCCTGCTTCAAGCGCGCCCAGCTGGTTATTCCTTGTTCAACGGATGCAACACCCTGAACCCCCGCGCTTCTTCCACCAGCCAGTCATGCACCGCCCGCGCACCTGGCTGGTTCAAGCCGCCTGGc               <  2:260991/148‑1 (MQ=255)                                                                                                                                        gCTTATTGAGCGAAGCGCTCCTGCTTCAAGCGCGCCCAGCTGGTTATTCCTTGTTCAACGGATGCAACACCCTGAACCCCCGCGCTTCTTCCACCAGCCAGTc                                                       >  7:146114/1‑103 (MQ=255)                                                                                                                                        gCTTATTGAGCGAAGCGCTCCTGCTTCAAGCGCGCCCAGCTGGTTATTCCTTGTTCAACGGATGCAACACCCTGAACCCCCGCGCTTCTTCCACCAGCCAGTc                                                       <  8:146114/103‑1 (MQ=255)                                                                                                                                        gCTTATTGAGCGAAGCGCTCCTGCTTCAAGCGCGCCCAGCTGGTTATTCCTTGTTCAACGGATGCAACACCCTGAACCCCCGCGCTTCTTCCACCAGCCAGTCATGCACCGCCCGCGCACCTGGCTGGTTCAAGCCGCCTGGCGGGTaa         <  6:14142/149‑1 (MQ=255)                                                                                                                                               gAGCGAAGCGCTCCTGCTTCAAGCGCGCCCAGCTGGTTATTCCTTGTTCAACGGATGCAACACCCTGAACCCCCGCGCTTCTTCCACCAGCCAGTCATGCACCGCCCGCGCACCTGGCTGGTTCAAGCCGCCTGGCGGGTAATGcacca  >  5:134225/1‑149 (MQ=255)                                                                                                                                                |                                                                                                                                                    TTCAGGGGGGAGACCAAGGATATCGAGCAAATGATCCAGCGAGTCGACTCGGACATCGAGTACATCAACAACTGGTCGTTGTGGCTGGACTTCGTGATCCTGGTGCGCACGCTTAATGCCTTCACCGGTAAGCAGGCTTATTGAGCGAAGCGCTCCTGCTTCAAGCGCGCCCAGCTGGTTATTCCTTGTTCAACGGATGCAACACCCTGAACCCCCGCGCTTCTTCCACCAGCCAGTCATGCACCGCCCGCGCACCTGGCTGGTTCAAGCCGCCTGGCGGGTAATGCACCA  >  NC_002947/3558980‑3559270

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑