Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,408,679	C→A	25.5%	P35P (CCC→CCA)	PP_3014 →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,408,679	0	C	A	25.5%	45.5 / 2.5	19	P35P (CCC→CCA)	PP_3014	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (11/3);  new base A (3/2);  total (14/5)
Fisher's exact test for biased strand distribution p-value = 5.70e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AAAATGCAGCCTATCCATAACGGCCGATTGCAAATGCCTGACTTTCGTATTTTTATCGCTACTGTGTTGGTTGCCTGCCTCGCCGGTTGCGCAACCCCCGGCAAACCCACTGCCAGCCAACTGACCAGGAAATCGCCGCAGCAGTACGCCGCCTGTGTCCTGCCGAAATGGCAGGCGCTGGCGCCACAGGCCACGCAGAAGTCGATAGCCCACGGCTACCGGCTCACGGC  >  NC_002947/3408572‑3408801                                                                                                            |                                                                                                                           aaaaTGCAGCCTATCCATAACGGCCGATTGCAAATGCCTGACTTTCGTATTTTTATCGCTACTGTGTTGGTTGCCTGCCTCGCCGGTTGCGCAACCCCCGGCAAACCCACTGCCAGCCAACTGACCAGGAAATcgc                                                                                                >  2:491082/1‑136 (MQ=255)                       gCCGATTGCAAATGCCTGACTTTCGTATTTTTATCGCTACTGTGTTGGTTGCCTGCCTCGCCGGTTGCGCAACCCCCGGCAAACCCACTGCCAGCCAACTGACCAGGAAATCGCCGCAGCAGTACGCCGCCTgtgt                                                                          >  2:275353/1‑136 (MQ=255)                       gCCGATTGCAAATGCCTGACTTTCGTATTTTTATCGCTACTGTGTTGGTTGCCTGCCTCGCCGGTTGCGCAACCCCCGGCAAACCCACTGCCAGCCAACTGACCAGGAAATCGCCGCAGCAGTACGCCGCCTgtgt                                                                          >  2:254334/1‑136 (MQ=255)                       gCCGATTGCAAATGCCTGACTTTCGTATTTTTATCGCTACTGTGTTGGTTGCCTGCCTCGCCGGTTGCGCAACCCCCGGCAAACCAACTGCCAGCCAACTGACCAGGAAATCGCCGCAGCAGTACGCCGCCTgtgt                                                                          >  2:106518/1‑136 (MQ=255)                       gCCGATTGCAAATGCCTGACTTTCGTATTTTTATCGCTACTGTGTTGGTTGCCTGCCTCGCCGGTTGCGCAA‑CCCCGGCAAACCAACTGCCAGCCAACTGACCAGGAAATCGCCGCAGCAGTACGCCGCCTGTGTc                                                                         >  2:284170/1‑136 (MQ=255)                           aTTGCAAATGCCTGACTTTCGTATTTTTATCGCTACTGTGTTGGTTGCCTGCCTCGCCGGTTGCGCAACCCCCGGCAAACCCACTGCCAGCCAACTGACCAGGAAATCGCCGCAGCAGTACGCCGCCTGTGTCCTg                                                                      >  1:111827/1‑136 (MQ=255)                           aTTGCAAATGCCTGACTTTCGTATTTTTATCGCTACTGTGTTGGTTGCCTGCCTCGCCGGTTGCGCAACCCCAGGCAAACCAACTGCCAGCCAACTGACCAGGAAATCGCCGCAGCAGTACGCCGCCTGTGTCCTg                                                                      >  1:146971/1‑136 (MQ=255)                                                 aTTTTTATCGCTACTGTGTTGGTTGCCTGCCTCGCCGGTTGCGCAACCCCCGGCAAACCCACTGCCAGCCAACTGACCAGGAAATCGCCGCAGCAGTACGCCGCCTGTGTCCTGCCGAAATGGCAGGCGCTGgcgc                                                >  2:204571/1‑136 (MQ=255)                                                    tttATCGCTACTGTGTTGGTTGCCTGCCTCGCCGGTTGCGCAACCCCCGGCAAACCCACTGCCAGCCAACTGACCAGGAAATCGCCGCAGCAGTACGCCGCCTGTGTCCTGCCGAAATGGCAGGCGCTGGCGCcac                                             <  2:314655/136‑1 (MQ=255)                                                        tCGCTACTGTGTTGGTTGCCTGCCTCGCCGGTTGCGCAACCCCCGGCAAACCCACTGCCAGCCAACTGACCAGGAAATCGCCGCAGCAGTACGCCGCCTGTGTCCTGCCGAAATGGCAGGCGCTGGCGCCACAGGc                                         >  2:527323/1‑136 (MQ=255)                                                          gCTACTGTGTTGGTTGCCTGCCTCGCCGGTTGCGCAACCCCCGGCAAACCCACTGCCAGCCAACTGACCAGGAAATCGCCGCAGCAGTACGCCGCCTGTGTCCTGCCGAAATGGCAGGCGCTGGCGCCACAGGCCa                                       >  2:317076/1‑136 (MQ=255)                                                                      gttgCCTGCCTCGCCGGTTGCGCAACCCCCGGCAAACCCACTGCCAGCCAACTGACCAGGAAATCGCCGCAGCAGTACGCCGCCTGTGTCCTGCCGAAATGGCAGGCGCTGGCGCCACAGGCCACGCAGAAGTCGa                           >  1:510879/1‑136 (MQ=255)                                                                      gttgCCTGCCTCGCCGGTTGCGCAACCCCCGGCAAACCCACTGCCAGCCAACTGACCAGGAAATCGCCGCAGCAGTACGCCGCCTGTGTCCTGCCGAAATGGCAGGCGCTGGCGCCACAGGCCACGCAGAAGTCGa                           >  1:374070/1‑136 (MQ=255)                                                                         gcctgcctCGCCGGTTGCGCAACCCCCGGCAAACCCACTGCCAGCCAACTGACCAGGAAATCGCCGCAGCAGTACGCCGCCTGTGTCCTGCCGAAATGGCAGGCGCTGGCGCCACAGGCCACGCAGAAGTCGATa                         >  1:386762/1‑135 (MQ=255)                                                                         gcctgcctCGCCGGTTGCGCAACCCCCGGCAAACCCACTGCCAGCCAACTGACCAGGAAATCGCCGCAGCAGTACGCCGCCTGTGTCCTGCCGAAATGGCAGGCGCTGGCGCCACAGGCCACGCAGAAGTCGATa                         <  2:386762/135‑1 (MQ=255)                                                                         gcctgcctCGCCGGTTGCGCAA‑CCCCGGCAAACCAACTGCCAGCCAACTGACCAGGAAATCGCCGCAGCAGTACGCCGCCTGTGTCCTGCCGAAATGGCAGGCGCTGGCGCCACAGGCCACGCAGAAGTCGATAGc                       <  1:284170/136‑1 (MQ=255)                                                                          cctgcctCGCCGGTTGCGCAACCCCCGGCAAACCAACTGCCAGCCAACTGACCAGGAAATCGCCGCAGCAGTACGCCGCCTGTGTCCTGCCGAAATGGCAGGCGCTGGCGCCACAGGCCACGCAGAAGTCGATAGc                       <  1:106518/136‑1 (MQ=255)                                                                                 cGCCGGTTGCGCAACCCCCGGCAAACCCACTGCCAGCCAACTGACCAGGAAATCGCCGCAGCAGTACGCCGCCTGTGTCCTGCCGAAATGGCAGGCGCTGGCGCCACAGGCCACGCAGAAGTCGATAGCCCACGGc                <  2:440643/136‑1 (MQ=255)                                                                                               cccccGGCAAACCCACTGCCAGCCAACTGACCAGGAAATCGCCGCAGCAGTACGCCGCCTGTGTCCTGCCGAAATGGCAGGCGCTGGCGCCACAGGCCACGCAGAAGTCGATAGCCCACGGCTACCGGCTCACGgc  >  2:522699/1‑136 (MQ=255)                                                                                                            |                                                                                                                           AAAATGCAGCCTATCCATAACGGCCGATTGCAAATGCCTGACTTTCGTATTTTTATCGCTACTGTGTTGGTTGCCTGCCTCGCCGGTTGCGCAACCCCCGGCAAACCCACTGCCAGCCAACTGACCAGGAAATCGCCGCAGCAGTACGCCGCCTGTGTCCTGCCGAAATGGCAGGCGCTGGCGCCACAGGCCACGCAGAAGTCGATAGCCCACGGCTACCGGCTCACGGC  >  NC_002947/3408572‑3408801

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: ‑