Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	335,433	C→T	13.1%	intergenic (‑38/+166)	PP_0277 ← / ← PP_5437	hypothetical protein/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	335,433	0	C	T	13.1%	91.0 / 5.5	38	intergenic (‑38/+166)	PP_0277/PP_5437	hypothetical protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (19/14);  new base T (2/3);  total (21/17)
Fisher's exact test for biased strand distribution p-value = 6.40e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.66e-01

GGGGTGGTTCCAGCCCAGGTTGCTGTTGGGGTGGGGCGAGGTGCCGCCGGCGCAGCCGGTCAGGGCCAGGGCGAAGGTCAACAGGGCGAGGGGGTTGGCTCGGGTCACGATGCTCAGGTCCGGTGGTCCATTGTCGGTTCTGGCGCAACGCCAGAAGGTCGCGGGGCTGGCGGGCAGCGCGCGACGTCACTTTTTAATGATTTGGGGGGGCGGATGATACACCGTTGCGGGGGTGGAGCATTAGCCTTGTGTTGTCTGGTATGGCCTCTTCGCGGGTGAACCCGCTCCTACAC  >  NC_002947/335288‑335580                                                                                                                                                  |                                                                                                                                                    ggggTGGTCCCAGCCCTGGTTGGTGTTGGGGGGGGGCGAGGGGCCGCCGGCGCAGCCGGTCAGGGCCAGGGCTATGGTCACCCGGGCGTGGGGGTTGGGGCGGGTCACGATGCTCCGGCCCGGTGGGCCATTGTCGGTTCGGGCGCAAc                                                                                                                                                  <  2:155035/149‑1 (MQ=255)        gctcAGCCCAGGTTGCTGTTGGGGTGGGGCGAGGTGGCGCCGGCGCAGCGGGTCAGGGCCAGGGCGAAGGTCAACAGGGCGAGGGGGTTGGCTCGGGTCACGATGCTCAGGTCCGGTGGTCCATTGTCGGTTCTGGCGTTGCGCCAGaa                                                                                                                                           <  5:336872/146‑1 (MQ=255)         tCCAGCCCAGGTTGCTGTTGGGGTGGGGCGAGGTGCCGCCGGCGCAGCCGGTCAGGGCCAGGGCGAAGGTCAACAGGGCGAGGGGGTTGGCTCGGGTCACGATGCTCAGGTCCGGTGGTCCATTGTCGGTTCTGGCGCAACGCCAGAAg                                                                                                                                          >  8:123878/1‑149 (MQ=255)          ccAGCCCAGGTTGCTGTTGGGGTGGGGCGAGGTGCCGCCGGCGCAGCCGGTCAGGGCCAGGGCGAAGGTCAACAGGGCGAGGGGGTTGGCTCGGGTCACGATGCTCAGGTCCGGTGGTCCATTGTCGGTTCTGGCGTTGCGCCAGaac                                                                                                                                          <  4:380604/148‑2 (MQ=255)            aGCCCAGGTTGCTGTTGGGGTGGGGCGAGGTGCCGCCGGCGCAGCCGGTCAGGGCCAGGGCGAAGGTCAACAGGGCGAGGGGGTTGGCTCGGGTCACGATGCTCAGGTCCGGTGGTCCATTGTCGGTTCTGGCGTTGCGCCAgca                                                                                                                                           >  6:336872/1‑143 (MQ=255)                cAGGTTGCTGTTGGGGTGGGGCGAGGTGCCGCCGGCGCAGCCGGTCAGGGCCAGGGCGAAGGTCAACAGGGCGAGGGGGTTGGCTCGGGTCACGATGCTCAGGTCCGGTGGTCCATTGTCGGTTCTGGCGCAACGCCAGAAGGTCGCgg                                                                                                                                   <  8:181336/149‑1 (MQ=255)                       cTGTTGGGGTGGGGCGAGGTGACGCCGGCGCAGCCGGTCAGGTCCAGGGCGAAGGTCAACAGGGCGAGGGGGTTGGCTCGGGTCACGATGCTCATTTCCGGTGGTCCATTGTCGGTTCTGGCGCAACGCCAGAAGGTCGCGGGGCTGGc                                                                                                                            >  1:404718/1‑149 (MQ=255)                        tGTTGGGGTGGGGCGAGGTGCCGCCGGCGCAGCCGGTCAGGGCCAGGGCGAAGGTCAACAGGGCGAGGGGGTTGGCTCGGGTCACGATGCTCAGGTCCGGTGGTCCATTGTCGGTTCTGGCGCAACGCCAGAAGGTCGCGGGGCTGGCg                                                                                                                           >  7:154734/1‑149 (MQ=255)                        tGTTGGGGTGGGGCGAGGTGCCGCCGGCGCAGCCGGTCAGGGCCAGGGCGAAGGTCAACAGGGCGAGGGGGTTGGCTCGGGTCACGATGCTCAGGTCCGGTGGTCCATTGTCGGTTCTGGCGCAACGCCAGAAGGTCGCGGGGCTGGCg                                                                                                                           >  1:383040/1‑149 (MQ=255)                          ttGGGGTGGGGCGAGGTGCCGCCGGCGCAGCCGGTCAGGGCCAGGGCGAAGGTCAACAGGGCGAGGGGGTTGGCTCGGGTCACGATGCTCAGGTCCGGTGGTCCATTGTCGGTTCTGGCGCAACGCCAGAAGGTCGCgg                                                                                                                                   >  3:109953/1‑139 (MQ=255)                          ttGGGGTGGGGCGAGGTGCCGCCGGCGCAGCCGGTCAGGGCCAGGGCGAAGGTCAACAGGGCGAGGGGGTTGGCTCGGGTCACGATGCTCAGGTCCGGTGGTCCATTGTCGGTTCTGGCGCAACGCCAGAAGGTCGCgg                                                                                                                                   <  4:109953/139‑1 (MQ=255)                          ttGGGGTGGGGCGAGGTGCCGCCGGCGCAGCCGGTCAGGGCCAGGGCGAAGGTCAACAGGGCGAGGGGGTTGGCTCGGGTCACGATGCTCAGGTCCGGTGGTCCATTGTCGGTTCTGGCGCAACGCCAGAAGGTCGCGGGGCTGGCgg                                                                                                                          <  8:154734/148‑1 (MQ=255)                             gggtggggCGAGGTGCCGCCGGCGCAGCCGGTCAGGGCCAGGGCGAAGGTCAACAGGGCGAGGGGGTTGGCTCGGGTCACGATGCTCAGGTCCGGTGGTCCATTGTCGGTTCTGGCGCAACGCCAGAAGGTCGCGGGGCTGGCGGGCa                                                                                                                       <  7:123878/148‑1 (MQ=255)                                    gCGAGGTGCCGCCGGCGCAGCCGGTCAGGGCCAGGGCGAAGGTCAACAGGGCGAGGGGGTTGGCTCGGGTCACGATGCTCAGGTCCGGTGGTCCATTGTCGGTTCTGGCGCAACGCCAGAAGGTCGCGGGGCTGGCGGGCAGCGCGCGa                                                                                                               >  7:282726/1‑149 (MQ=255)                                      gAGGTGCCGCCGGCGCAGCCGGTCAGGGCCAGGGCGAAGGTCAACAGGGCGAGGGGGTTGGCTCGGGTCACGATGCTCAGGTCCGGTGGTCCATTGTCGGTTCTGGCGCAACGCCAGAAGGTCGCGGGGCTGGCGGGCAGCGCGCGACg                                                                                                             >  3:367857/1‑149 (MQ=255)                                                  gcgcAGCCGGTCAGGGCCAGGGCGAAGGTCAACAGGGCGAGGGGGTTGGCTCGGGTCATGATGCTCAGGTCCGGTGGTCCATTGTCGGTTCTGGCGCAACGCCAGAAGGTCGCGGGGCTGGCGGGCAGCGCGCGACGt                                                                                                            >  2:234900/1‑138 (MQ=255)                                                  gcgcAGCCGGTCAGGGCCAGGGCGAAGGTCAACAGGGCGAGGGGGTTGGCTCGGGTCATGATGCTCAGGTCCGGTGGTCCATTGTCGGTTCTGGCGCAACGCCAGAAGGTCGCGGGGCTGGCGGGCAGCGCGCGACGt                                                                                                            <  1:234900/138‑1 (MQ=255)                                                  gcgcAGCCGGTCAGGGCCAGGGCGAAGGTCAACAGGGCGAGGGGGTTGGCTCGGGTCACGATGCTCAGGTCCGGTGGTCCATTGTCGGTTCTGGCGCAACGCCAGAAGGTCGCGGGGCTGGCGGGCa                                                                                                                       >  2:291276/1‑127 (MQ=255)                                                  gcgcAGCCGGTCAGGGCCAGGGCGAAGGTCAACAGGGCGAGGGGGTTGGCTCGGGTCACGATGCTCAGGTCCGGTGGTCCATTGTCGGTTCTGGCGCAACGCCAGAAGGTCGCGGGGCTGGCGGGCa                                                                                                                       <  1:291276/127‑1 (MQ=255)                                                       gCCGGTCAGGGCCAGGGCGAAGGTCAACAGGGCGAGGGGGTTGGCTCGGGTCACGATGCTCAGGTCCGGTGGTCCATTGTCGGTTCTGGCGCAACGCCAGAAGGTCGCGGGGCTGGCGGGCAGCGCGCGACGTCACTTTTTAATGAttt                                                                                            >  2:328104/1‑149 (MQ=255)                                                          ggTCAGGGCCAGGGCGAAGGTCAACAGGGCGAGGGGGTTGGCTCGGGTCACGATGCTCAGGTCCGGTGGTCCATTGTCGGTTCTGGCGCAACGCCAGAAGGTCGCGGGGCTGGCGGGCAGCGCGCGACGTCACTTTTTAATGATTTggg                                                                                         <  1:328104/149‑1 (MQ=255)                                                           gTCAGGGCCAGGGCGAAGGTCAACAGGGCGAGGGGGTTGGCTCGGGTCACGATGCTCAGGTCCGGTGGTCCATTGTCGGTTCTGGCGCAACGCCAGAAGGTCGCGGGGCTGGCGGGCAGCGCGCGACGTCACTTTTTAATGATTTgggg                                                                                        <  2:345605/149‑1 (MQ=255)                                                                 gccagggcGAAGGTCAACAGGGCGAGGGGGTTGGCTCGGGTCACGATGCTCAGGTCCGGTGGTCCATTGTCGGTTCTGGCGCAACGCCAGAAGGTCGCGGGGCTGGCGGGCAGCGCGCGACGTCACTTTTTAATGATTTGGGGGGGCg                                                                                   >  3:124706/1‑148 (MQ=255)                                                                  ccagggcGAAGGTCAACAGGGCGAGGGGGTTGGCTCGGGTCACGATGCTCAGGTCCGGTGGTCCATTGTCGGTTCTGGCGTTGCGCCAGaac                                                                                                                                          <  2:28591/92‑2 (MQ=255)                                                                  ccagggcGAAGGTCAACAGGGCGAGGGGGTTGGCTCGGGTCACGATGCTCAGGTCCGGTGGTCCATTGTCGGTTCTGGCGTTGCGCCAGaac                                                                                                                                          >  1:28591/1‑91 (MQ=255)                                                                  ccagggcGAAGGTCAACAGGGCGAGGGGGTTGGCTCGGGTCACGATGCTCAGGTCCGGTGGTCCATTGTCGGTTCTGGCGCAACGCCAGAAGGTCGCGGGGCTGGCGGGCAGCGCGCGACGTCACTTTTTAATGATTTGGGGGGGCGga                                                                                 <  4:367857/149‑1 (MQ=255)                                                                   cagggcGAAGGTCAACAGGGCGAGGGGGTTGGCTCGGGTCACGATGCTCAGGTCCGGTGGTCCATTGTCGGTTCTGGCGCAACGCCAGAAGGTCGCGGGGCTGGCGGGCAGCGCGCGACGTCACTTTTTAATGATTTGGGGGGGCGgat                                                                                <  8:282726/149‑1 (MQ=255)                                                                          aaGGTCAACAGGGCGAGGGGGTTGGCTCGGGTCACGATGCTCAGGTCCGGTGGTCCATTGTCGGTTCTGGCGCAACGCCAGAAGGTCGCGGGGCTGGCGGGCAGCGCGCGACGTCACTTTTTAATGATTTGGGGGGGCGGATGATacac                                                                         <  6:229649/149‑1 (MQ=255)                                                                             gTCAACAGGGCGAGGGGGTTGGCTCGGGTCACGATGCTCAGGTCCGGTGGTCCATTGTCGGTTCTGGCGCAACGCCAGAAGGTCGCGGGGCTGGCGGGCAGCGCGCGACGTCACTTTTTAATGATTTGGGGGGGCGGATGATACACCGt                                                                      >  4:180833/1‑149 (MQ=255)                                                                                  cAGGGCGAGGGGGTTGGCTCGGGTCACGATGCTCAGGTCCGGTGGTCCATTGTCGGTTCTGGCGCAACGCCAGAAGGTCGCGGGGCTGGCGGGCAGCGCGCGACGTCACTTTTTAATGATTTGGGGGGGCGGATGATACACCGTTGCgg                                                                 <  3:180833/149‑1 (MQ=255)                                                                                  cAGGGCGAGGGGGTTGGCTCGGGTCACGATGCTCAGGTCCGGTGGTACATTGTCGGTTCTGGCGCAACGCCAGAAGGTCGCGGGGCTGGCGGGCAGCGCGCGACGTCACTTTTTAATGATTTGGGGGGGCGGATGATACACCGTTGCgg                                                                 >  1:294171/1‑149 (MQ=255)                                                                                     ggggtggggggTGGCTCGGGTCTCGATGCTCAGGTCCGGTGGGCCATTGTCGGTTCTGGCGCAACGCCAGATGGTCGCGGGGCTGGCGGGCAGCGCGCGACGTCACTTTTTAATGGTTTGGGGGGGCGGATGATACACCGTTGCgggg                                                               <  2:383040/143‑1 (MQ=255)                                                                                      gCGAGGGGGTTGGCTCGGGTCACGATGCTCAGGTCCGGTGGTCCATTGTCGGTTCTGGCGCAACGCCAGAAGGTCGCGGGGCTGGCGGGCAGCGCGCGACGTCACTTTTTAATGATTTGGGGGGGCGGATGATACACCGTTGCGGGGGt                                                             >  5:106009/1‑149 (MQ=255)                                                                                          gggggTTGGCTCGGGTCACGATGCTCAGGTCCGGTGGTCCATTGTCGGTTCTGGCGCAACGCCAGAAGGTCGCGGGGCTGGCGGGCAGCGCGCGACGTCACTTTTTAATGATTTGGGGGGGCGGATGATACACCGTTGCGGGGGTGGAg                                                         >  3:71609/1‑149 (MQ=255)                                                                                                   cTCGGGTCACGATGCTCAGGTCCGGTGGTCCATTGTCGGTTCTGGCGCAACGCCAGAAGGTCGCGGGGCTGGCGGGCAGCGCGCGACGTCACTTTTTAATGATTTGGGGGGGCGGATGATACACCGTTGCGGGGGTGGAGCATTAGCCt                                                >  1:160597/1‑149 (MQ=255)                                                                                                    tCGGGTCACGATGCTCAGGTCCGGTGGTCCATTGTCGGTTCTGGCGCAACGCCAGAAGGTCGCGGGGCTGGCGGGCAGCGCGCGACGTCCCTTTTTAATGATTTGGGGGGGCGGATGATACACCGTTGCGGGGGTGGAGCATTAGCCtt                                               >  5:398359/1‑149 (MQ=255)                                                                                                     cGGGTCACGATGCTCAGGTCCGGTGGTCCATTGTCGGTTCTGGCGCAACGCCAGAAGGTCGCGGGGCTGGCGGGCAGCGCGCGACGTCACTTTTTAATGATTTGGGGGGGCGGATGATACACCGTTGCGGGGGTGGAGCATTAGCCtta                                              >  1:123010/1‑148 (MQ=255)                                                                                                                  tCAGGTCCGGTGGTCCATTGTCGGTTCTGGCGCAACGCCAGAAGGTCGCGGGGCTGGCGGGCAGCGCGCGACGTCACTTTTTAATGATTTGGGGGGGCGGATGATACCCCGTTGCGGGGGTGGAGCTGTAGCCTTGTGTTGGCTGGTAt                                 >  8:285001/1‑149 (MQ=255)                                                                                                                                                 gcAACGCCAGAAGGTCGCGGGGCTGGCGGGCAGCGCGCGACGTCACTTTTTAATGATTTGGGGGGGCGGATGATACACCGTTGCGGGGGTGGAGCATTAGCCTTGTGTTGTCTGGTATGGCCTCTTCGCGGGTGAACCCGCTCCTacac  >  1:226500/1‑149 (MQ=255)                                                                                                                                                  |                                                                                                                                                    GGGGTGGTTCCAGCCCAGGTTGCTGTTGGGGTGGGGCGAGGTGCCGCCGGCGCAGCCGGTCAGGGCCAGGGCGAAGGTCAACAGGGCGAGGGGGTTGGCTCGGGTCACGATGCTCAGGTCCGGTGGTCCATTGTCGGTTCTGGCGCAACGCCAGAAGGTCGCGGGGCTGGCGGGCAGCGCGCGACGTCACTTTTTAATGATTTGGGGGGGCGGATGATACACCGTTGCGGGGGTGGAGCATTAGCCTTGTGTTGTCTGGTATGGCCTCTTCGCGGGTGAACCCGCTCCTACAC  >  NC_002947/335288‑335580

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: ‑