Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	4,258,198	G→A	10.5%	S47L (TCG→TTG)	PP_3731 ←	TetR family transcriptional regulator

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	4,258,198	0	G	A	10.5%	102.3 / 3.1	38	S47L (TCG→TTG)	PP_3731	TetR family transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base G (19/15);  new base A (2/2);  total (21/17)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.76e-01

CGCTCGCGGGCATTGGGCGCGGCCTGGGCCATGGCCTCACGCAACAGGCCCATCACCCGACCGGTGACGGCCATGTAAGCCTCTGCCACCAGTTCGTCCTTGCCCGCGTAATGGTGGCTG‑ATCAGCCCGACCGAGACCCCGGCCTCGGCCGAAATCTTGCGGATCGACGCCCCCTGGAAACCATGGCGTTTGAGGCACACCAGGGTCGCCTCGACCAGGTTGGCTTTGCGCAATTCCGGCAGCATGCGGTGGTAGCGGGCTTCCTGAGTCATCGGTGG  >  NC_002947/4258066‑4258343                                                                                                                                      |                                                                                                                                                  cGCTCGCGGGCATTGGGCGCGGCCTGGGCCATGGCCTCACGCAACAGGCCCATCACCCGACCGGTGACGGCCATGTAAGCCTCTGCCACCAGTTCGTCCTTGCCCGCGTAATGGTGGCTG‑ATCAGCCCGGCCGAGGCCGGGGTCTCggt                                                                                                                                   >  7:204902/1‑148 (MQ=255)    tCGCGGGCATTGGGCGCGGCCTGGGCCATGGCCTCACGCAACAGGCCCATCACCCGACCGGTGACGGCCATGTAAGCCTCTGCCACCAGTTCGTCCTTGCCCGCGTAATGGTGGCTG‑ATCAGCCCGACCAAGACCCCGGCCTCGGCCg                                                                                                                                 >  3:81435/1‑148 (MQ=255)     cgcgGGCATTGGGCGCGGCCTGGGCCATGGCCTCACGCAACAGGCCCATCACCCGACCGGTGACGGCCATGTAAGCCTCTGCCACCAGTTCGTCCTTGCCCGCGTAATGGTGGCTG‑ATCAGCCCGGCCGAGGCCGGGGTCTCGGTCggg                                                                                                                               <  8:204902/149‑3 (MQ=255)      gcgGGCATTGGGCGCGGCCTGGGCCATGGCCTCACGCAACAGGCCCATCACCCGACCGGTGACGGCCATGTAAGCCTCTGCCACCAGTTCGTCCTTGCCCGCGTAATGGTGGCTG‑ATCAGCCCGACCGAGACCCCGGCCTCGGCCGaa                                                                                                                               <  5:251679/148‑1 (MQ=255)      gcgGGCATTGGGCGCGGCCTGGGCCATGGCCTCACGCAACAGGCCCATCACCCGACCGGTGACGGCCATGTAAGCCTCTGCCACCAGTTCGTCCTTGCCCGCGTAATGGTGGCTG‑ATCAGCCCGACCAAGACCCCGGCCTCGGCCGaa                                                                                                                               <  4:81435/148‑1 (MQ=255)       cgGGCATTGGGCGCGGCCTGGGCCATGGCCTCACGCAACAGGCCCATCACCCGACCGGTGACGGCCATGTAAGCCTCTGCCACCAGTTCGTCCTTGCCCGCGTAATGGTGGCTGCATCAGCCCGACCGAGACCCCGGCCTCGGCCGaaa                                                                                                                              <  1:172705/149‑1 (MQ=255)            aTTGGGCGCGGCCTGGGCCATGGCCTCACGCAACAGGCCCATCACCCGACCGGTGACGGCCATGTAAGCCTCTGCCACCAGTTCGTCCTTGCCCGCGTAATGGTGGCTG‑ATCAGCCCGACCGAGACCCCGGCCTCGGCCGAAATCTTGc                                                                                                                        <  2:144836/149‑1 (MQ=255)               gggCGCGGCCTGGGCCATGGCCTCACGCAACAGGCCCATCACCCGACCGGTGACGGCCATGTAAGCCTCTGCCACCAGTTCGTCCTTGCCCGCGTAATGGTGGCTG‑ATCAGCCCGACCGAGACCCCGGCCTCGGCCGAAATCTTGCGGa                                                                                                                     >  6:210813/1‑149 (MQ=255)                                     tCACGCAACAGGCCCATCACCCGACCGGTGACGGCCATGTAAGCCTCTGCCACCAGTTCGTCCTTGCCCGCGTAATGGTGGCTG‑ATCAGCCCGACCGAGACCCCGGCCTCGGCCGAAATCTTGCGGATCGACGCCCCCTGGAAACCATg                                                                                               >  2:270923/1‑149 (MQ=255)                                     tCACGCAACAGGCCCATCACCCGACCGGTGACGGCCATGTAAGCCTCTGCCACCAGTTCGTCCTTGCCCGCGTAATGGTGGCTG‑ATCAGCCCGACCGAGACCCCGGCCTCGGCCGAAATCTTGCGGATCGACGCCCCCTGGAAACCATg                                                                                               >  1:99657/1‑149 (MQ=255)                                       aCGCAACAGGCCCATCACCCGACCGGTGACGGCCATGTAAGCCTCTGCCACCAGTTCGTCCTTGCCCGCGTAATGGTGGCTG‑ATCAGCCCGACCGAGACCCCGGCCTCGGCCGAAATCTTGCGGATCGACGCCCCCTGGAAACCATg                                                                                               <  6:183290/147‑1 (MQ=255)                                         gCAACAGGCCCATCACCCGACCGGTGACGGCCATGTAAGCCTCTGCCACCAGTTCGTCCTTGCCCGCGTAATGGTGGCTG‑ATCAGCCCGACCGAGACCCCGGCCTCGGCCGAAATCTTGCGGATCGACGCCCCCTGGAAACCATGGc                                                                                             >  6:120424/1‑147 (MQ=255)                                         gCAACAGGCCCATCACCCGACCGGTGACGGCCATGTAAGCCTCTGCCACCAGTTCGTCCTTGCCCGCGTAATGGTGGCTG‑ATCAGCCCGACCGAGACCCCGGCCTCGGCCGAAATCTTGCGGATCGACGCCCCCTGGAAACCATGGc                                                                                             <  5:120424/147‑1 (MQ=255)                                               ggCCCATCACCCGACCGGTGACGGCCATGTAAGCCTCTGCCACCAGTTCGTCCTTGCCCGCGTAATGGTGGCTG‑ATCAGCCCGACCGAGACCCCGGCCTCGGCCGAAATCTTGCGGATCGACGCCCCCTGGAAACCATGGCGTTTGAgg                                                                                     <  1:270923/149‑1 (MQ=255)                                                gCCCATCACCCGACCGGTGACGGCCATGTAAGCCTCTGCCACCAGTTCGTCCTTGCCCGCGTAATGGTGGCTG‑ATCAGCCCGACCGAGACCCCGGCCTCgg                                                                                                                                    <  2:252708/101‑1 (MQ=255)                                                gCCCATCACCCGACCGGTGACGGCCATGTAAGCCTCTGCCACCAGTTCGTCCTTGCCCGCGTAATGGTGGCTG‑ATCAGCCCGACCGAGACCCCGGCCTCgg                                                                                                                                    >  1:252708/1‑101 (MQ=255)                                                gCCCATCACCCGACCGGTGACGGCCATGTAAGCCTCTGCCACCAGTTCGTCCTTGCCCGCGTAATGGTGGCTG‑ATCAGCCCGACCGAGACCCCGGCCTCGGCCGAAATCTTGCGGATCGACGCCCCCTGGAAACCATGGCGTTTGAgg                                                                                     >  5:166441/1‑148 (MQ=255)                                                    aTCACCCGACCGGTGACGGCCATGTAAGCCTCTGCCACCAGTTCGTCCTTGCCCGCGTAATGGTGGCTG‑ATCAGCCCGACCGAGACCCCGGCCTCGGCCGAAATCTTGCGGATCGACGCCCCCTGGAAACCATGGCGTTTGAGGCacac                                                                                >  4:24400/1‑149 (MQ=255)                                                         ccGACCGGTGACGGCCATGTAAGCCTCTGCCACCAGTTCGTCCTTGCCCGCGTAATGGTGGCTG‑ATCAGCCCGACCGAGACCCCGGCCTCGGCCGAAATCTTGCGGATCGACGCCCCCTGGAAACCATGGCGTTTGAGGCACACCAggg                                                                           <  2:99657/149‑1 (MQ=255)                                                                         aTGTAAGCCTCTGCCACCAGTTCGTCCTTGCCCGCGTAATGGTGGCTG‑ATCAGCCCGACCGAGACCCCGGCCTCGGCCGAAATCTTGCGGATCGACGCCCCCTGGAAACCATGGCGTTTGAGGCACACCAGGGTCGCCTCGACCAGGtt                                                           <  6:166441/149‑1 (MQ=255)                                                                           gTAAGCCTCTGCCACCAGTTCGTCCTTGCCCGCGTAATGGTGGCTG‑ATCAGCCCGACCAAGACCCCGGCCTCGGCCGAAATCTTGCGGATCGACGCCCCCTGGAAACCATGGCGTTTGAgg                                                                                     <  6:170235/121‑1 (MQ=255)                                                                           gTAAGCCTCTGCCACCAGTTCGTCCTTGCCCGCGTAATGGTGGCTG‑ATCAGCCCGACCAAGACCCCGGCCTCGGCCGAAATCTTGCGGATCGACGCCCCCTGGAAACCATGGCGTTTGAgg                                                                                     >  5:170235/1‑121 (MQ=255)                                                                             aaGCCTCTGCCACCAGTTCGTCCTTGCCCGCGTAATGGTGGCTG‑ATCAGCCCGACCGAGACCCCGGCCTCGGCCGAAATCTTGCGGATCGACGCCCCCTGGAAACCATGGCGTTTGAGGCACACCAGGGTCGCCTCGACCAGGTTGGCt                                                       >  8:48182/1‑149 (MQ=255)                                                                              aGCCTCTGCCACCAGTTCGTCCTTGCCCGCGTAATGGTGGCTG‑ATCAGCCCGACCGAGACCCCGGCCTCGGCCGAAATCTTGCGGATCGACGCCCCCTGGAAACCATGGCGTTTGAGGCACACCAGGGTCGCCTCGACCAGGTTGGCtt                                                      >  2:40001/1‑149 (MQ=255)                                                                               gCCTCTGCCACCAGTTCGTCCTTGCCCGCGTAATGGTGGCTG‑ATCAGCCCGACCGAGACCCCGGCCTCGGCCGAAATCTTGCGGATCGACGCCCCCTGGAAACCATGGCGTTTGAGGCACACCAGGGTCGCCTCGACCAGGTTGGCttt                                                     <  8:120925/149‑1 (MQ=255)                                                                                ccTCTGCCACCAGTTCGTCCTTGCCCGCGTAATGGTGGCTG‑ATCAGCCCGACCGAGACCCCGGCCTCGGCCGAAATCTTGCGGATCGACGCCCCCTGGAAACCATGGCGTTTGAGGCACACCAGGGTCGCCTCGACCAGGTTGGCTTTg                                                    >  3:5181/1‑149 (MQ=255)                                                                                  tctGCCACCAGTTCGTCCTTGCCCGCGTAATGGTGGCTG‑ATCAGCCCGACCGAGACCCCGGCCTCGGCCGAAATCTTGCGGATCGACGCCCCCTGGAAACCATGGCGTTTGAGGCACACCAGGGTCGCCTCGACCAg                                                              <  4:244313/137‑1 (MQ=255)                                                                                  tctGCCACCAGTTCGTCCTTGCCCGCGTAATGGTGGCTG‑ATCAGCCCGACCGAGACCCCGGCCTCGGCCGAAATCTTGCGGATCGACGCCCCCTGGAAACCATGGCGTTTGAGGCACACCAGGGTCGCCTCGACCAg                                                              >  3:244313/1‑137 (MQ=255)                                                                                    tGCCACCAGTTCGTCCTTGCCCGCGTAATGGTGGCTG‑ATCAGCCCGACCGAGACCCCGGCCTCGGCCGAAATCTTGCGGATCGACGCCCCCTGGAAACCATGGCGTTTGAGGCACACCAGGGTCGCCTCGACCAGGTTGGCTTTGCGCa                                                >  7:237841/1‑149 (MQ=255)                                                                                      ccaccaGTTCGTCCTTGCCCGCGTAATGGTGGCTG‑ATCAGCCCGACCGAGACCCCGGCCTCGGCCGAAATCTTGCGGATCGACGCCCCCTGGAAACCATGGCGTTTGAGGCACACCAGGGTCGCCTCGACCAGGTTGGCTTTGCGCAAt                                              >  5:40389/1‑149 (MQ=255)                                                                                          caGTTCGTCCTTGCCCGCGTAATGGTGGCTG‑ATCAGCCCGACCGAGACCCCGGCCTCGGCCGAAATCTTGCGGATCGACGCCCCCTGGAAACCATGGCGTTTGAGGCACACCAGGGTCGCCTCGACCAGGTTGGCTTTGCGCAATTCCg                                          <  4:5181/149‑1 (MQ=255)                                                                                                        ccGCGTAATGGTGGCTG‑ATCAGCCCGACCGAGACCCCGGCCTCGGCCGAAATCTTGCGGATCGACGCCCCCTGGAAACCATGGCGTTTGAGGCACACCAGGGTCGCCTCGACCAGGTTGGCTTTGCGCAATTCCGGCAGCATGCggtgg                            <  7:48182/149‑1 (MQ=255)                                                                                                          gcgTAATGGTGGCTG‑ATCAGCCCGACCGAGACCCCGGCCTCGGCCGAAATCTTGCGGATCGACGCCCCCTGGAAACCATGGCGTTTGAGGCACACCAGGGTCGCCTCGACCAGGTTGGCTTTg                                                    <  5:197296/123‑1 (MQ=255)                                                                                                          gcgTAATGGTGGCTG‑ATCAGCCCGACCGAGACCCCGGCCTCGGCCGAAATCTTGCGGATCGACGCCCCCTGGAAACCATGGCGTTTGAGGCACACCAGGGTCGCCTCGACCAGGTTGGCTTTg                                                    >  6:197296/1‑123 (MQ=255)                                                                                                           cgTAATGGTGGCTG‑ATCAGCCCGACCGAGACCCCGGCCTCGGCCGAAATCTTGCGGATCGACGCCCCCTGGAAACCATGGCGTTTGAGGCACACCAGGGTCGCCTCGACCAGGTTGGCTTTGCGCAATTCCGGCAGCATGCGGTGGTAg                         >  1:222942/1‑149 (MQ=255)                                                                                                              aaTGGTGGCTG‑ATCAGCCCGACCGAGACCCCGGCCTCGGCCGAAATCTTGCGGATCGACGCCCCCTGGAAACCATGGCGTTTGAGGCACACCAGGGTCGCCTCGACCAGGTTGGCTTTGCGCAATTCCGGCAGCATGCGGTGGTAGCgg                      >  1:64068/1‑149 (MQ=255)                                                                                                                  gtggCTG‑ATCAGCCCGACCGAGACCCCGGCCTCGGCCGAAATCTTGCGGATCGACGCCCCCTGGAAACCATGGCGTTTGAGGCACACCAGGGTCGCCTCGACCAGGTTGGCTTTGCGCAATTCCGGCAGCATGCGGTGGTAGCGGGCtt                  >  2:209224/1‑149 (MQ=255)                                                                                                                               cccGACCGAGACCCCGGCCTCGGCCGAAATCTTGCGGATCGACGCCCCCTGGAAACCATGGCGTTTGAGGCACACCAGGGTCGCCTCGACCAGGTTGGCTTTGCGCAATTCCGGCAGCATGCGGTGGTAGCGGGCTTCCTGAGTCATCg      >  5:120730/1‑149 (MQ=255)                                                                                                                                 cgaccgaGACCCCGGCCTCGGCCGAAATCTTGCGGATCGACGCCCCCTGGAAACCATGGCGTTTGAGGCACACCAGGGTCGCCTCGACCAGGTTGGCTTTGCGCAATTCCGGCAGCATGCGGTGGTAGCGGGCTTCCTGAGTCATCGGt    <  1:40001/149‑1 (MQ=255)                                                                                                                                  gaccgaGACCCCGGCCTCGGCCGAAATCTTGCGGATCGACGCCCCCTGGAAACCATGGCGTTTGAGGCACACCAGGGTCGCCTCGACCAGGTTGGCTTTGCGCAATTCCGGCAGCATGCGGTGGTAGCGGGCTTCCTGAGTCATCGGTg   <  5:210813/149‑1 (MQ=255)                                                                                                                                   accgaGACCCCGGCCTCGGCCGAAATCTTGCGGATCGACGCCCCCTGGAAACCATGGCGTTTGAGGCACACCAGGGTCGCCTCGACCAGGTTGGCTTTGCGCAATTCCGGCAGCATGCGGTGGTAGCGGGCTTCCTGAGTCATCGGTgg  <  6:40389/149‑1 (MQ=255)                                                                                                                                     cgaGACCCCGGCCTCGGCCGAAATCTTGCGGATCGACGCCCCCTGGAAACCATGGCGTTTGAGGCACACCAGGGTCGCCTCGACCAGGTTGGCTTTgc                                                   <  2:170824/98‑1 (MQ=255)                                                                                                                                      |                                                                                                                                                  CGCTCGCGGGCATTGGGCGCGGCCTGGGCCATGGCCTCACGCAACAGGCCCATCACCCGACCGGTGACGGCCATGTAAGCCTCTGCCACCAGTTCGTCCTTGCCCGCGTAATGGTGGCTG‑ATCAGCCCGACCGAGACCCCGGCCTCGGCCGAAATCTTGCGGATCGACGCCCCCTGGAAACCATGGCGTTTGAGGCACACCAGGGTCGCCTCGACCAGGTTGGCTTTGCGCAATTCCGGCAGCATGCGGTGGTAGCGGGCTTCCTGAGTCATCGGTGG  >  NC_002947/4258066‑4258343

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