Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	4,366,723	G→A	100%	R4R (CGC→CGT)	PP_3843 ←	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	4,366,723	0	G	A	100.0%	114.1 / NA	35	R4R (CGC→CGT)	PP_3843	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (17/18);  total (17/18)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

GGGCGTACACCCCGATGAACATCTGCGTTTTGCCTGTCCGCGACAGCCGCGTCTGAACATCAATGTATGTCCCATCGTCGAGTGTCTCGTCGTGAGTTCGGTGATGAAGCGTCGGGTCAGCCCAGGCCCAGAAAACATCACCGCGTATTCTCATGAGACGCTCCTACGACTTTAGTTGTAGTCAGGTGGTTTATTGCCACCATAGCGAACGTGCAGTTTTACGCAAATTCGTCTGACTCATCTGTGAGCTGAATCGGACAATCGGCTATTCAGCAGCCC  >  NC_002947/4366581‑4366859                                                                                                                                               |                                                                                                                                         gggCGTACACCCCGATGAACATCTGCGTTTTGCCTGTCCGCGACAGCCGCGTCTGAACATCAATGTATGTCCCATCGTCGAGTGTCTCGTCGTGAGTTCGGTGATGAAGCGTCGGGTCAGCCCAGGCCCAGAAAACATCACCACGTAtt                                                                                                                                    >  5:196566/1‑149 (MQ=255) gggCGTACACCCCGATGAACATCTGCGTTTTGCCTGTCCGCGACAGCCGCGTCTGAACATCAATGTATGTCCCATCGTCGAGTGTCTCGTCGTGAGTTCGGTGATGAAGCGTCGGGTCAGCCCAGGCCCAGAAAACATCACCACGTAtt                                                                                                                                    <  7:222359/149‑1 (MQ=255)    cGTACACCCCGATGAACATCTGCGTTTTGCCTGTCCGCGACAGCCGCGTCTGAACATCAATGTATGTCCCATCGTCGAGTGTCTCGTCGTGAGTTCGGTGATGAAGCGTCGGGTCAGCCCAGGCCCAGAAAACATCACCACGTATtctc                                                                                                                                 <  1:163115/149‑1 (MQ=255)        cacCCCGATGAACATCTGCGTTTTGCCTGTCCGCGACAGCCGCGTCTGAACATCAATGTATGTCCCATCGTCGAGTGTCTCGTCGTGAGTTCGGTGATGAAGCGTCGGGTCAGCCCAGGCCCAGAAAACATCACCACGTATTCTCATga                                                                                                                             <  3:131428/149‑1 (MQ=255)           cccGATGAACATCTGCGTTTTGCCTGTCCGCGACAGACGCGTCTGAACATCAATGTATCTCCCATCGTCGAGTGTCTCGTCGAGAGTTCGGTGATGAAGCGTCGGGTCAGCCCAGGCACAGAAAACATCACCACGTATTCTCATGAGAc                                                                                                                          >  1:21819/1‑149 (MQ=255)               aTGAACATCTGCGTTTTGCCTGTCCGCGACAGCCGCGTCTGAACATCAATGTATGTCCCATCGTCGAGTGTCTCGTCGTGAGTTCGGTGATGAAGCGTCGGGTCAGCCCAGGCCCAGAAAACATCACCACGTATTCTCATGAGACGCTc                                                                                                                      <  3:162533/149‑1 (MQ=255)                tGAACATCTGCGTTTTGCCTGTCCGCGACAGCCGCGTCTGAACATCAATGTATGTCCCATCGTCGAGTGTCTCGTCGTGAGTTCGGTGATGAAGCGTCGGGTCAGCCCAGGCCCAGAAAACATCACCACGTATTCTCATGAGACGCTcc                                                                                                                     >  2:245825/1‑149 (MQ=255)                       cTGCTTTTTGCCGGGCCGGGACATCCGCGTCTGAACCTCAATGTATGTCCCATCGTCGAGTGGCTCGTCGGGAGTTCGGTGATGAAGCGTCGGGGCAGCCCAGGCCCAGAAAACATCACCACGTATTCTCATGAGACGCTCCTACGAc                                                                                                               <  6:229195/148‑1 (MQ=255)                         gCGTTTTGCCTGTCCGCGACAGCCGCGTCTGAACATCAATGTATGTCCCATCGTCGAGTGTCTCGTCGTGAGTTCGGTGATGAAGCGTCGGGTCAGCCCAGGCCCAGAAAACATCACCACGTATTCTCATGAGAc                                                                                                                          >  6:5356/1‑135 (MQ=255)                         gCGTTTTGCCTGTCCGCGACAGCCGCGTCTGAACATCAATGTATGTCCCATCGTCGAGTGTCTCGTCGTGAGTTCGGTGATGAAGCGTCGGGTCAGCCCAGGCCCAGAAAACATCACCACGTATTCTCATGAGAc                                                                                                                          <  5:5356/135‑1 (MQ=255)                                               ccGCGTCTGAACATCAATGTATGTCCCATCGTCGAGTGTCTCGTCGTGAGTTCGGTGATGAAGCGTCGGGTCAGCCCAGGCCCAGAAAACATCACCACGTATTCTCATGAGACGCTCCTACGACTTTAGTTGTAGTCAGGTGGTTTAtt                                                                                      <  6:196566/149‑1 (MQ=255)                                                  cgTCTGAACATCAATGTATGTCCCATCGTCGAGTGTCTCGTCGTGAGTTCGGTGATGAAGCGTCGGGTCAGCCCACGCCCAGAAAACATCACCACGTATTCTCAAGAGACGCTCCTACGACTTTAGTTGTACTCAGGTGGTTTATTGc                                                                                    >  2:96046/1‑148 (MQ=255)                                                          cATCAATGTATGTCCCATCGTCGAGTGTCTCGTCGTGAGTTCGGTGATGAAGCGTCGGGTCAGCCCAGGCCCAGAAAACATCACCACGTATTCTCATGAGACGCTCCTACGACTTTAGTTGTAGTCAGGTGGTTTATTGCCACCATAGc                                                                           <  8:185022/149‑1 (MQ=255)                                                             cAATGTATGTCCCATCGTCGAGTGTCTCGTCGTGAGTTCGGTGATGAAGCGTCGGGTCAGCCCAGGCCCAGAAAACATCACCACGTATTCTCAt                                                                                                                               <  2:189181/94‑1 (MQ=255)                                                             cAATGTATGTCCCATCGTCGAGTGTCTCGTCGTGAGTTCGGTGATGAAGCGTCGGGTCAGCCCAGGCCCAGAAAACATCACCACGTATTCTCAt                                                                                                                               >  1:189181/1‑94 (MQ=255)                                                             cAATGTATGTCCCATCGTCGAGTGTCTCGTCGTGAGTTCGGTGATGAAGCGTCGGGTCAGCCCAGGCCCAGAAAACATCACCACGTATTCTCATGAGACGCTCCTACGACTTTAGTTGTAGTCAGGTGGTTTATTGCCACCATAGCGaa                                                                        >  4:135037/1‑149 (MQ=255)                                                                      tCCCATCGTCGAGTGTCTCGTCGTGAGTTCGGTGATGAAGCGTCGGGTCAGCCCAGGCCCAGAAAACATCACCACGTATTCTCATGAGACGCTCCTACGACTTTAGTTGTAGTCAGGTGGTTTATTGCCACCATAGCGAACGTGCAGtt                                                               >  3:61959/1‑149 (MQ=255)                                                                              tcgAGTGTCTCGTCGTGAGTTCGGTGATGAAGCGTCGGGTCAGCCCAGGCCCAGAAAACATCACCACGTATTATCATGAGACGCTCCTACGACTTTAGTTGTAGTCAGGTGGTTTATTTCCACCATAGCGAACGTGCAGTTTTACGCa                                                        >  4:34184/1‑148 (MQ=255)                                                                                     tctcGTCGTGAGTTCGGTGATGAAGCGTCGGGTCAGCCCAGGCCCAGAAAACATCACCACGTATTCTCATGAGACGCTCCTACGACTTTACTTGTAGTCAGGTGGTTTATTGCCACCATAGCGAACGTGCAGTTTTACGCAAATTCGTc                                                <  1:96046/149‑1 (MQ=255)                                                                                         gtcgtGAGTTCGGTGATGAAGCGTCGGGTCAGCCCAGGCCCAGAAAACATCACCACGTATTCTCATGAGACGCTCCTACGACTTTAGTTGTAGTCAGGTGGTTTATTGCCACCATAGCGAACGTGCAGTTTTACGCAAATTCGTCt                                               <  4:61959/146‑1 (MQ=255)                                                                                          tcgtGAGTTCGGTGATGAAGCGTCGGGTCAGCCCAGGCCCAGAAAACATCACCACGTATTCTCATGAGACGCTCCTACGACTTTAGTTGTAGTCAGGTGGTTTATTGCCACCATAGCGAACGTGCAGTTTTACGCAAATTCGTCTGAc                                            >  1:178826/1‑148 (MQ=255)                                                                                                    ggTGATGAAGCGTCGGGTCAGCCCAGGCCCAGAAAACATCACCACGTATTCTCATGAGACGCTCCTACGACTTTAGTTGTAGTGAGGTGGTTTATTGCCACCATAGCGAACGTGCAGTTTTACGCAAATTCGTCTGACTCATCTGTGAg                                 <  2:21819/149‑1 (MQ=255)                                                                                                    ggTGATGAAGCGTCGGGTCAGCCCAGGCCCAGAAAACATCACCACGTATTCTCATGAGACGCTCCTACGACTTTAGTTGTAGTCAGGTGGTTTATTGCCACCATAGCGAACGTGCAGTTTTACGCAAATTCGTCTGACTCATCt                                      <  2:210189/144‑1 (MQ=255)                                                                                                    ggTGATGAAGCGTCGGGTCAGCCCAGGCCCAGAAAACATCACCACGTATTCTCATGAGACGCTCCTACGACTTTAGTTGTAGTCAGGTGGTTTATTGCCACCATAGCGAACGTGCAGTTTTACGCAAATTCGTCTGACTCATCt                                      >  1:210189/1‑144 (MQ=255)                                                                                                        atgaAGCGTCGGGTCAGCCCAGGCACAGAAAACATCACCACGTATTCTCATGAGACGCTCCTACGACTTTAGTTGTAGTCAGGTGGTTTATTGCCAACATAGAGAACGTGCAGTTTTACGCAAATTCGTCTGACTCATCTTTGAGCTGa                             >  4:82319/1‑149 (MQ=255)                                                                                                         tgaAGCGTCGGGTCAGCCCAGGCCCAGAAAACATCACCACGTATTCTCATGAGACGCTCCTACGACTTTAGTTGTAGTCAGGTGGTTTATTGCCACCATAGCGAACGTGCAGTTTTACGCAAATTCGTCTGACTCATCTGTGAGCTGa                             <  2:178826/148‑1 (MQ=255)                                                                                                          gaAGCGTCGGGTCAGCCCAGGCCCAGAAAACATCACCACGTATTCTCATGAGACGCTCCTACGACTTTAGTTGTAGTCAGGTGGTTTATTGCCACCATAGCGAACGTGCAGTTTTACGCAAATTCGTc                                                >  5:26386/1‑128 (MQ=255)                                                                                                          gaAGCGTCGGGTCAGCCCAGGCCCAGAAAACATCACCACGTATTCTCATGAGACGCTCCTACGACTTTAGTTGTAGTCAGGTGGTTTATTGCCACCATAGCGAACGTGCAGTTTTACGCAAATTCGTc                                                <  6:26386/128‑1 (MQ=255)                                                                                                                    gTCAGCCCAGGCCCAGAAAACATCACCACGTATTCTCATGAGACGCTCCTACGACTTTAGTTGTAGTCAGGTGGTTTATTGCCACCATAGCGAACGTGCAGTTTTACGCAAATTCGTCTGACTCATCTGTGAGCTGAATCGGACAATCg                 >  8:154436/1‑149 (MQ=255)                                                                                                                       aGCCCAGGCCCAGAAAACATCACCACGTATTCTCATGAGACGCTCCTACGACTTTAGTTGTAGTCAGGTGGTTTATTGCCACCATAGCGAACGTGCAGTTTTACGCAAATTCGTCTGACTCATCTGTGAGCTGAATCGGACAATCGGc               <  1:245825/148‑1 (MQ=255)                                                                                                                          ccaggcccagAAAACATCACCACGTATTCTCATGAGACGCTc                                                                                                                      >  2:174289/1‑42 (MQ=255)                                                                                                                          ccaggcccagAAAACATCACCACGTATTCTCATGAGACGCTCCTACGACTTTAGTTGTAGTCAGGTGGTTTATTGCCACCATAGCGAACGTGCAGTTTTACGCAAATTCGTCTGACTCATCTGTGAGCTGAATCGGACAATCGGCTAtt           <  3:135037/149‑1 (MQ=255)                                                                                                                                 cagAAAACATCACCACGTATTCTCATGAGACGCTCCTACGACTTTAGTTGTAGTCAGGTGGTTTATTGCCACCATAGCGAACGTGCAGTTTTACGCAAATTCGTCTGACTCATCTGTGAGCTGAATCGGACAATCGGCTATTCagcagc    <  3:165102/149‑1 (MQ=255)                                                                                                                                 cagAAAACATCACCACGTATTCTCATGAGACGCTCCTACGACTTTAGTTGTAGTCAGGTGGTTTATTGCCACCATAGCGAACGTGCAGTTTTACGCAAATTCGTCTGACTAATCTGTGAGCTGAATCGGACAATCGGCTATTcagcatc    >  5:58916/1‑147 (MQ=255)                                                                                                                                   gAAAACATCACCACGTATTCTCATGAGACGCTCCTACGACTTTAGTTGTAGTCAGGTGGTTTATTGCCACCATAGCGAACGTGCAGTTTTACGCAAATTCGTCTGACTCATCTGTGAGCTGAATCGGACAATCGGCTATTCAGCAGccc  >  6:300795/1‑149 (MQ=255)                                                                                                                                               |                                                                                                                                         GGGCGTACACCCCGATGAACATCTGCGTTTTGCCTGTCCGCGACAGCCGCGTCTGAACATCAATGTATGTCCCATCGTCGAGTGTCTCGTCGTGAGTTCGGTGATGAAGCGTCGGGTCAGCCCAGGCCCAGAAAACATCACCGCGTATTCTCATGAGACGCTCCTACGACTTTAGTTGTAGTCAGGTGGTTTATTGCCACCATAGCGAACGTGCAGTTTTACGCAAATTCGTCTGACTCATCTGTGAGCTGAATCGGACAATCGGCTATTCAGCAGCCC  >  NC_002947/4366581‑4366859

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: ‑