Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,630,703	C→A	28.1%	A427A (GCC→GCA)	PP_3200 →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,630,703	0	C	A	28.1%	16.2 / 2.5	14	A427A (GCC→GCA)	PP_3200	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (7/3);  new base A (2/2);  total (9/5)
Fisher's exact test for biased strand distribution p-value = 5.80e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.86e-01

GTTGTCAACCCGCTGGAACCAGCCGTTGGCCTCGACCAACCAGCATGCGTTGGCCGTGGGCGAGGCGATCGACAATGACGATAACCCGGTTTATGCCACCGGCCGCACGCTGCACGCCAACGTCTCCTGGCTTGCCAGCCTGGAGCCGAACTTCATCGCTGCCGAGTCGAGCTTCCTCGGCGAAATCGCCTGGAACCGGGTGATGAGCGTGAGCAAGAACGCCGATGCCGTTGACCCTAACGCCGACCGTGACGCCACCAGCCTGCGCCTGGTGTTCGAGCCGAT  >  NC_002947/3630568‑3630852                                                                                                                                        |                                                                                                                                                      gTTGTCAACCCGCTGGAACCAGCCGTTGGCCTCGACCAACCAGCATGCGTTGGCCGTGGGCGAGGCGATCGACAATGACGATAACCCGGTTTATGCCACCGGCCGCACGCTGCACGCCAACGTCTCCAGGCTGGCAAGCCAGGa                                                                                                                                               <  1:413/144‑1 (MQ=255) gTTGTCAACCCGCTGGAACCAGCCGTTGGCCTCGACCAACCAGCATGCGTTGGCCGTGGGCGAGGCGATCGACAATGACGATAACCCGGTTTATGCCACCGGCCGCACGCTGCACGCCAACGTCTCCAGGCTGGCAAGCCAGGa                                                                                                                                               >  2:413/1‑144 (MQ=255)                                                   tGGCCGTGGGCGAGGCGATCGACAATGACGATAACCCGGTTTATGCCACCGGCCGCACGCTGCACGCCAACGTCTCCTGGCTTGCCAGCCTGGAGCCGAACTTCATCGCTGCCGAGTCGAGCTTCCTCGGCGAAATCGCCTGGAACCggg                                                                                       <  1:251224/150‑1 (MQ=255)                                                       cGTGGGCGAGGCGATCGACAATGACGATAACCCGGTTTATGCCACCGGCCGCACGCTGCACGCCAACGTCTCCTGGCTTGCCAGCCTGGAGCCGAACTTCATCGCTGCCGAGTCGAGCTTCCTCGGCGAAATCGCCTGGAACCGGGtgat                                                                                   >  1:2372/1‑150 (MQ=255)                                                          gggCGAGGCGATCGACAATGACGATAACNNGGTTTATGCCACCGNCNGNACGCTGCACGCCAACGTCTCCTGGCTTGCCGGCCTGGAGCCGAACTTCATCGCTGCCGAGTCGAGCTTCCTCGGCGAAATCGGCTGGAAGCGGGttgtgtg                                                                                >  1:320860/1‑144 (MQ=255)                                                                       gACAATGACGATAACCCGGTTTATGCCACCGGCCGCACGCTGCACGCCAACGTCTCCTGGCTTGCCAGCCTGGAGCCGAACTTCATCGCTGCCGAGTCGAGCTTCCTCGGCGAAATCGCCTGGAACCGGGTGATGAGCGTGAGCAAGAAc                                                                   >  1:42946/1‑150 (MQ=255)                                                                             gACGATAACCCGGTTTATGCCACCGGCCGCACGCTGCACGCCAACGTCTCCTGGCTTGCCAGCCTGGAGCCGAACTTCATCGCTGCCGAGTCGAGCTTCCTCGGCGAAATCGCCTGGAACCGGGTGATGAGCGTGAGCAAGAACGCCGAt                                                             >  1:336566/1‑150 (MQ=255)                                                                                      aaggTTTATGCCACCGGCCGCACGTTGAACGCCAACGTCTCCTGGCTTGCCAGCCTGGAGCCGAACTTCATCGCTGCCGAGTCGAGCTTCCTCGGCGAAATCGCATGGGACCGGGTGATGAGGGTGAGCAAGAACGCCGATGCCGTTGAc                                                    >  2:469835/3‑150 (MQ=255)                                                                                                                      gttcggctcCAGGCTGGCAAGCCAGGAGCCGAACTTCATCGCTGCCGAGTCGAGCTTCCTCGGCGAAATCGCCTGGAACCGGGTGATGAGCGTGAGCAAGAACGCCGATGCCGTTGACCCTAACGCCGACCGTGACGcca                              >  1:5749/7‑140 (MQ=255)                                                                                                                      gttcggctcCAGGCTGGCAAGCCAGGAGCCGAACTTCATCGCTGCCGAGTCGAGCTTCCTCGGCGAAATCGCCTGGAACCGGGTGATGAGCGTGAGCAAGAACGCCGATGCCGTTGACCCTAACGCCGACCGTGACGcca                              <  2:5749/134‑1 (MQ=255)                                                                                                                        aCGTCTCCTGGCTTGCCAGCCTGGAGCCGAACTTCATCGCTGCCGAGTCGAGCTTCCTCGGCGAAATCGCCTGGAACCGGGTGATGAGCGTGAGCAAg                                                                      >  1:221694/1‑98 (MQ=255)                                                                                                                        aCGTCTCCTGGCTTGCCAGCCTGGAGCCGAACTTCATCGCTGCCGAGTCGAGCTTCCTCGGCGAAATCGCCTGGAACCGGGTGATGAGCGTGAGCAAg                                                                      <  2:221694/98‑1 (MQ=255)                                                                                                                               cTGGCTTGCCAGCCTGGAGCCGAACTTCATCGCTGCCGAGTCGAGCTTCCTCGGCGAAATCGCCTGGAACCGGGTGATGAGCGTGAGCAAGAACGCCGATGCCGTTGACCCTAACGCCGCCCGTGACGCCACCAGCCTGCGCCTGGTGtt           >  1:87460/1‑150 (MQ=255)                                                                                                                                  gCTTGCCAGCCTGGAGCCGAACTTCATCGCTGCCGAGTCGAGCTTCCTCGGCGAAATCGCCTGGAACCGGGTGATGAGCGTGAGCAAGAACGCCGATGCCGTTGACCCTAACGCCGACCGTGACGCCACCAGCCTGCGCCTGGTGTTCGa        <  2:2372/150‑1 (MQ=255)                                                                                                                                        cAGCCTGGAGCCGAACTTCATCGCTGCCGAGTCGAGCTTCCTCGGCGAAATCGCCTGGAACCGGGTGATGAGCGTGAGCAAGAACGCCGATGCCGTTGACCCTAACGCCGACCGTGACGCCACCAGCCTGCGCCTGGTGTTCGAGCCGAt  >  2:310559/1‑150 (MQ=255)                                                                                                                                        |                                                                                                                                                      GTTGTCAACCCGCTGGAACCAGCCGTTGGCCTCGACCAACCAGCATGCGTTGGCCGTGGGCGAGGCGATCGACAATGACGATAACCCGGTTTATGCCACCGGCCGCACGCTGCACGCCAACGTCTCCTGGCTTGCCAGCCTGGAGCCGAACTTCATCGCTGCCGAGTCGAGCTTCCTCGGCGAAATCGCCTGGAACCGGGTGATGAGCGTGAGCAAGAACGCCGATGCCGTTGACCCTAACGCCGACCGTGACGCCACCAGCCTGCGCCTGGTGTTCGAGCCGAT  >  NC_002947/3630568‑3630852

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑