Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,466,841	T→G	15.1%	intergenic (‑16/+108)	PP_3081 ← / ← PP_5560	hypothetical protein/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,466,841	0	T	G	15.1%	58.9 / 4.1	32	intergenic (‑16/+108)	PP_3081/PP_5560	hypothetical protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (8/17);  new base G (2/3);  total (12/20)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GGCAGGTTGTCCCAGCTCAGTTGCGGGGTCCGCTCTTCACCGGCACCGCATGCCGGGTCCTGGCCGACCTGTTGCAGGGCAATGACGCCGCCATCAGTGAAAGACGAGGAACTGACCGACATCGCGCCTTGGCCGCCTGCGGCGGCCAACGCTGTGCAGGGCAGCAAAGCAGCGAACAGCCAGTGTCTGAGGTGCATGGTCAATCCTTGGCAGGGCGTCACGGCTCAGTCTAGCCCAGGTCTGCTTCAGCGGCTGTCCTGGTCCTCGGCAGTGCCTCCGCTGG  >  NC_002947/3466704‑3466986                                                                                                                                          |                                                                                                                                                  ggCAGGTTGTCCCAGCTCAGTTGCGGGGTCCGCTCTTCACCGGCACCGCATGCCGGGTCCTGGCCGACCTGTTGCAGGGCAATGACGCCGCCATCAGTGAAAGACGAGGAACTGACCGACATCGCGCCTTGGCCGCCGCAGGCGGCCaa                                                                                                                                        <  5:215990/149‑1 (MQ=255) ggCAGGTTGTCCCAGCTCAGTTGCGGGGTCCGCTCTTCACCGGCACCGCATGCCGGGTCCTGGCCGACCTGTTGCAGGGCAATGACGCCGCCATCAGTGAAAGACGAGGAACTGACCGACATCGCGCCTTGGCCGCCGCAGGCGGCCaa                                                                                                                                        <  3:265169/149‑1 (MQ=255)   cAGGTTGTCCCAGCTAAGTTGCGGGGTCCGCTCTTCACCGGCTCCGGATGCCGGGTCCTGGCCGACCTGTTGCAGGGCAATGACGCCGCCATCAGTGAAAGACTAGGAACTGACCGACATCGCGCCTTGGCCGCCTGCGGCGGCCAACg                                                                                                                                      <  4:212757/149‑1 (MQ=255)      gTTGTCCCAGCTCAGTTGCGGGGTCCGCTCTTCACCGGCACCGCATGCCGGGTCCTGGCCGACCTGTTGCAGGGCAATGACGCCGCCATCAGTGAAAGACGAGGAACTGACCGACATCGCGCCTTGGCCGCCTGCGGCGGCCAACGCtg                                                                                                                                   >  7:5014/1‑149 (MQ=255)           cccAGCTCAGTTGCGGGGTCCGCTCTTCACCGGCACCGCATGCCGGGTCCTGGCCGACCTGTTGCAGGGCAATGACGCCGCCATCAGTGAAAGACGAGGAACTGACCGACATCGCGCCTTGGCCCCCAGAGGCGGCCAACCCAGTGCAg                                                                                                                              >  8:219210/1‑149 (MQ=255)                               cGCTCTTCACCGGCACCGCATGCCGGGTCCTGGCCGACCTGTTGCAGGGCAATGACGCCGCCATCAGTGAAAGACGAGGAACTGACCGACATCGCGCCTTGGCCGCCTGCGGCGGCCAACGCTGTGCAGGGCAGCAAAGCAGCGAACAg                                                                                                          >  5:234319/1‑149 (MQ=255)                                gCTCTTCACCGGCACCGCATGCCGGGTCCTGGCCGACCTGTTGCAGGGCAATGACGCCGCCATCAGTGAAAGACGAGGAACTGACCGACATCGCGCCTTGGCCGCCTGCGGCGGCCAACGCTGTGCAGGGCAGCAAAGCAGCGAACAGc                                                                                                         <  7:219210/149‑1 (MQ=255)                                 ctctTCACCGGCACCGCATGCCGGGTCCTGGCCGACCTGTTGCAGGGCAATGACGCCGCCATCAGTGAAAGACGAGGAACTGACCGACATCGCGCCTTGGCCGCCTGCggcggc                                                                                                                                           <  7:159777/114‑1 (MQ=255)                                 ctctTCACCGGCACCGCATGCCGGGTCCTGGCCGACCTGTTGCAGGGCAATGACGCCGCCATCAGTGAAAGACGAGGAACTGACCGACATCGCGCCTTGGCCGCCTGCggcggc                                                                                                                                           >  8:159777/1‑114 (MQ=255)                                      cACCGGCACCGCATGCCGGGTCCTGGCCGACCTGTTGCAGGGCATTGACGCCGCCATCAGTGAAAGACGAGGAACTGACCGACTTCGCGCGTTGGCGGCCTGCGGCGGCCAACGCTGTGCAGGGCAGCAAAGCAGCGAACAGCCAgt                                                                                                     <  2:3447/147‑1 (MQ=255)                                      cACCGGCACCGCATGCCGGGTCCGGGCCGACCTGTTGCAGGGCAATGACGCCGCCATCAGTGAAAGACGAGGAACTGACCGACATCGCGCCTTGGCCGCCTGCGGCGGCCAACGCTGTGCAGGGCAGCAAAGCAGCGAACAGCCAgt                                                                                                     <  2:224603/147‑1 (MQ=255)                                           gCACCGCATGCCGGGTCCTGGCCGACCTGTTGCAGGGCAATGACGCCGCCATCAGTGAAAGACGAGGAACTGACCGACATCGAGCCTTGGCCCCCGTAGGCCGCCAACGAGTAGCAAGCCAGCCAAGCAGCGAACAGCCAGAGTCTggg                                                                                              >  8:155276/1‑147 (MQ=255)                                                 cATGCCGGGTCCTGGCCGACCTGTTGCAGGGCAATGACGCCGCCATCAGTGAAAGACGAGGAACTGACCGACATCGCGCCTTGGCCGCCTGCGGCGGCCAACGCTGTGCAGGGCAGCAAAGCAGCGAACAGCCAGTGTCTGAGGTGCAt                                                                                        <  6:138585/149‑1 (MQ=255)                                                      cGGGTCCTGGCCGACCTGTTGCATGGCAATGACGCGGCCATCTGTGAAAGACGAGTAACTGACCGACATCGCGCCTTGGCCGCCTGGGGCGGCCAACGCTGTGCAGGGCAGCAAAGCAGCGAACa                                                                                                           <  4:33315/125‑1 (MQ=255)                                                               gCCGACCTGTTGCAGGGCAATGACGCCGCCATCAGTGAAAGACGAGGAACTGACCGACATCGCGCCTTGGCCGCCTGCGGCGGCCAACGCTGTGCAGGGCAGCAAAGCAGCGAACAGCCAGTGTCTGAGGTGCATGGTCAATCCTTgg                                                                           >  5:245806/1‑148 (MQ=255)                                                                 cGACCTGTTGCAGGGCAATGACGCCGCCATCAGTGAAAGACGAGGAACTGACCGACATCGCGCCTTGGCCCCCTGCGGCGGCCAACGCTGTGCAGGGCAGCAAAGCAGCGAACAGCCAGTGTCTGAGGTGCATGGTCAATCCTTGGCAg                                                                        >  8:29215/1‑149 (MQ=255)                                                                       gTTGCAGGGCAATGACGCCGCCATCAGTGAAAGACGAGGAACTGACCGACATCGCGCCTTGGCCGCCTgcggcg                                                                                                                                             >  4:113018/1‑74 (MQ=255)                                                                       gTTGCAGGGCAATGACGCCGCCATCAGTGAAAGACGAGGAACTGACCGACATCGCGCCTTGGCCGCCTgcggcg                                                                                                                                             <  3:113018/74‑1 (MQ=255)                                                                               gCAATGACGCCGCCATCAGTGAAAGACGAGGAACTGACCGACATCGCGCCTTGGCCGCCTGCGGCGGCCAACGCTGTGCAGGGCAGCAAAGCAGCGAACAGCCAGTGTCTGAGGTGCATGGTCAATCCTTGGCAGGGCGTCACGGCTCa                                                          <  5:203618/149‑1 (MQ=255)                                                                                          gacATCAGTTAAAGACGATGAACTGACCGACATCGCGCCTTGGCCGCCTGCGGCTTCCAACGCTGTGCAGGGCAGCAAAGCAGCGATCAGCCAGTGTCTGAGGTGCATGTTCAATCCTTGGCAGGGCGTCACGGCTCAGTCTAGCCCAg                                               <  7:155276/147‑1 (MQ=255)                                                                                                aGTGAAAGACGAGGAACTGACCGACATCGCGCCTTGGCCACCTGCGGCGGCCAACGCTGTGCAGGGCAGCAAAGCAGCGAACAGCCAGTGTCTGAGGTGCATGGTCAATCCTTGGCAg                                                                        >  8:22290/1‑118 (MQ=255)                                                                                                aGTGAAAGACGAGGAACTGACCGACATCGCGCCTTGGCCACCTGCGGCGGCCAACGCTGTGCAGGGCAGCAAAGCAGCGAACAGCCAGTGTCTGAGGTGCATGGTCAATCCTTGGCAg                                                                        <  7:22290/118‑1 (MQ=255)                                                                                                        aCGAGGAACTGACCGACATCGCGCATTGGCCGCCTGCGGCGGCCAACGCTGTGCAGGGCAGCAAAGCAGCGAACAGCCAGTGTCTGAGGTGCATGGTCAATCCTTGGCAGGGCGTCACGGCTCAGTCTAGCCCAGGTCTGCTTCAGCgg                                 <  3:63726/149‑1 (MQ=255)                                                                                                                cTGACCGACATCGCGCCTTGGGCCCCAGCGGCGGCCAACCCGGTGGAGGGCAGCAAAGCAGCGACAAGCCAGTGTCGGGGGTGCATGGGCAATACATGGCAGGGCGTAACCGCGCAGTCTAGCCCCGGGCTGCTTAAGCGGCGGTCGTg                         >  8:9791/1‑149 (MQ=255)                                                                                                                       acacCGCCCCTTGCCCGCCTGCGGCGGCCAACGCTGTGCAGGGCAGCAAAGCAGCGAACAGCCAGTGTCTGAGGTGCATGGTCAATCCTTGGCAGGGCGTCACGGCTCAGTCTAGCCCAGGTCTGCTTCAGCGGCTGTCCTGGTCCTCg                  <  3:20989/149‑1 (MQ=255)                                                                                                                        cATCGCGCCTTGGCCGCCTGCGGCGGCCAACGCTGTGCAGGGCAGCAAAGCAGCGAACAGCCAGTGTCTGAGGTGCATGGTCAATCCTTGGCAGGGCGTCACGGCTCAGTCTAGCCCAGGTCTGCTTCAGCGGCTGTCCTGGTCCTCgg                 <  6:234319/149‑1 (MQ=255)                                                                                                                          tCGCGCCTTGGCCGCCTGCGGCGGCCAACGCTGTGCAGGGCAGCAAAGCAGCGAACAGCCAGTGTCTGAGGTGCATGGTCAATCCTTGGCAGGGCGTCACGGCTCAGTCTAGCCCAGGTCTGCTTCAGCGGCTGTCCTGGTCCTCGGCa               <  7:234223/149‑1 (MQ=255)                                                                                                                            gcgcCTTGGCCGCCTGCGGCGGCCAACGCTGTGCAGGGCAGCAAAGCAGCGAACAGCCAGTGTCTGAGGTGCATGGTCAATCCTTGGCAGGGCGTCACGGCTCAGTCTAGCCCa                                                <  7:111960/114‑1 (MQ=255)                                                                                                                            gcgcCTTGGCCGCCTGCGGCGGCCAACGCTGTGCAGGGCAGCAAAGCAGCGAACAGCCAGTGTCTGAGGTGCATGGTCAATCCTTGGCAGGGCGTCACGGCTCAGTCTAGCCCAGGTCTGCTTCAGCGGCTGTCCTGGTCCTCGGCAGt             <  6:245806/149‑1 (MQ=255)                                                                                                                             ttgttgggCCGCCGCTGGTGGCCAACGCTGTGCAGGGCAGCAAAGCAGCGAACAGCCAGTGTCTGAGGTGCATGGTCAATCCTTGGCAGGGCGTCACGGCTCAGTCTAGCCCAGTTCTGCTTCAGCGGCTGTCCTGGTCCTCGGCAGt             <  7:52233/142‑1 (MQ=255)                                                                                                                               cgttGGCCGCCGCAGGCGGCCAACGCTGTGCAGGGCAGCAAAGCAGCGAAAAGCCAGTGTCTGAGGTGCATGGTAAAACCTTGCCAGGCCGTCACCCCTCACTCTAGCCCACGTCTACTTCAGAGGCTATCCTGGTCCTAGGCAGt             >  8:52233/3‑146 (MQ=255)                                                                                                                                       gccTGCGGCGGCCAACGCTGTGCAGGGCAGCAAAGCAGCGAACAGCCAGTGTCTGAGATGCATGGTCAATCCTTGGCAGGGCGTCACGGCTCAGTCTAGCCCAGGTCTGCTTCAGCGGCTGTCCTGGTCCTCGGCAGTGCCTCCGCTgg  >  1:74542/1‑149 (MQ=255)                                                                                                                                          |                                                                                                                                                  GGCAGGTTGTCCCAGCTCAGTTGCGGGGTCCGCTCTTCACCGGCACCGCATGCCGGGTCCTGGCCGACCTGTTGCAGGGCAATGACGCCGCCATCAGTGAAAGACGAGGAACTGACCGACATCGCGCCTTGGCCGCCTGCGGCGGCCAACGCTGTGCAGGGCAGCAAAGCAGCGAACAGCCAGTGTCTGAGGTGCATGGTCAATCCTTGGCAGGGCGTCACGGCTCAGTCTAGCCCAGGTCTGCTTCAGCGGCTGTCCTGGTCCTCGGCAGTGCCTCCGCTGG  >  NC_002947/3466704‑3466986

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: ‑