Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,050,045	G→A	18.5%	intergenic (+17/‑124)	PP_2662 → / → PP_2663	hypothetical protein/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,050,045	0	G	A	18.5%	47.2 / 5.3	27	intergenic (+17/‑124)	PP_2662/PP_2663	hypothetical protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (8/14);  new base A (3/2);  total (11/16)
Fisher's exact test for biased strand distribution p-value = 3.70e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.24e-01

CCATGACATCAACGACAACCTGAAACTGGTGGCCGAGTACAACCAGTTTTCCATCGACGGGCAT‑GACACCAGTGCGCAGAACGAAGACACCGATACCTTTGCGGTGGGCGCGGTGTTGACCTGGTAAGCGGCCGGGGCCGCTAGGCGGCCCCGAATGACACGGTCTTTTACGCCCATGGAACCGCCCACCCGCTACCCAAGTAGCATTCG‑TCACCCACCACCACCTCCTTAAACTGATCACTCAGCCACCCCGTGCCGGAGACCACGATGCAGCAGGCT  >  NC_002947/3049902‑3050180                                                                                                                                                 |                                                                                                                                         ccATGACATCAACGACAACCTGAAACTGGTGGCCGAGTACAACCAGTTTTCCATCGACGGGCAT‑GACACCAGTGCGCAGAACGAAGACACCGATACCTTTGCGGTGGGCGCGGTGTTGACCTGGTAAGCGGCCGGGGCCGCTAggcgg                                                                                                                                      <  2:235595/148‑1 (MQ=255)        aTCAACGACAACCTGAAACTGGTGGCCGAGTACAACCAGTTTTCCATCGACGGGCAT‑GACACCAGTGCGCAGAACGAAGACACCGATACCTTTGCGGTGGGCGCGGTGTTGACCTGGTAAGCGGTCGGGGCCGCCTAGCGGCCCCggcc                                                                                                                              <  7:79309/149‑4 (MQ=255)        aTCAACGACAACCTGAAACTGGTGGCCGAGTACAACCAGTTTTCCATCGACGGGCAT‑GACACCAGTGCGCAGAACGAAGACACCGATACCTTTGCGGTGGGCGCGGTGTTGACCTGGTAAGCGGCCGGGGCCGCTAggc                                                                                                                                        <  6:182503/139‑1 (MQ=255)        aTCAACGACAACCTGAAACTGGTGGCCGAGTACAACCAGTTTTCCATCGACGGGCAT‑GACACCAGTGCGCAGAACGAAGACACCGATACCTTTGCGGTGGGCGCGGTGTTGACCTGGTAAGCGGCCGGGGCCGCTAggc                                                                                                                                        >  5:182503/1‑139 (MQ=255)        aTCAACGACAACCTGAAACTGGTGGCCGAGTACAACCAGTTTTCCATCGACGGGCAT‑GACACCAGTGCGCAGAACGAAGACACCGATACCTTTGCGGTGGGCGCGGTGTTGACCTGGTAAGCGGCCGGGGCCGCTAGGCGGCCCCGAAt                                                                                                                              <  1:53182/149‑1 (MQ=255)                    cTGAAACTGGTGGCCGAGTACAACCAGTTTTCCATCGACGGGCATAGACACCAGTGCGCAGAACGAAGACACCGATACCTTTGCGGTGGGCGCGGTGTTGACCTGGTAAGCGGCCGGGGCCGCTAGGCGGCCCCGAATGACACCGACtt                                                                                                                   >  1:233692/1‑149 (MQ=255)                       aaaCTGGTGGCCGAGTACAACCAGTTTTCCATCGACGGGCAT‑GACACCAGTGCGCAGAACGAAGACACCGATACCTTTGCGGTGGGCGCGGTGTTGACCTGGTAAGCGGCCGGGGCCGCTAGGCGGCCCCGAATGACACGGTCTTTTa                                                                                                                <  1:59144/148‑1 (MQ=255)                        aaCTGGTGGCCGAGTACAACCAGTTTTCCATCGACGGGCAT‑GACACCAGTGCGCAGAACGAAGACACCGATACCTTTGCGGTGGGCGCGGTGTTGACCTGGTAAGCGGCCGGGGCCGCTAGGCGGCCCCGAATGACACGGTCTTTTACg                                                                                                              >  7:277958/1‑149 (MQ=255)                                     gTACAACCAGTTTTCCTTCGCCGGCCAT‑GACTCCAGTGCGCAGAACGACGACACCGATTCCTTTGCGGTGGGCGGGGTTTTGACCTGGTAAGCGGCCGGGGCCGCTAGGCGGCCCCGAATGACACGGTCTTTTACGCCCATGGAACCGc                                                                                                 <  2:305351/149‑1 (MQ=255)                                         aaCCAGTTTTCCATCGACGGGCAT‑GACACCAGTGCGCAGAACGAAGACACCGATACCTTTGCGGT‑GGCGCGGTGTTGACCTGGTAAGCGGCCGGGGCCGCTAGGCGGCCCCGAATGACACGGTCTTTTTCCCCCAAGGAACCCCCCAcc                                                                                            >  2:6986/1‑149 (MQ=255)                                                     aTCGACGGGCAT‑GACACCAGTGCGCATAACGAAGACACCGATACCTTTGCGGTGGGCGCGGTGTTGACCTGGTAAGCGGCCGGGGCCGCTAGGCGGCCCCGAATGACACGGTCTTTTACGCCCATGGAACCGCCCAc                                                                                             <  1:311295/137‑1 (MQ=255)                                                      tCGACGGGCAT‑GACACCAGTGCGCAGAACGAAGACACCGATACCTTTGCGGTGGGCGCGGTGTTGACCTGGTAAGCGGCCGGGGCCGCTAGGCGGCCCCGAATGACACGGTCTTTTACGCCCATGGAACCGCCCACCCGCTACCCAAGt                                                                                <  6:138542/149‑1 (MQ=255)                                                        gACGGGCAT‑GACACCAGTGCGCAGAACGAAGACACCGATACCTTTGCGGGGGGCGCGGTGTTGACCTGGTAAGCGGCCGGGGCCGCTAGGCGGCCCCGAATGACACGGTCTTTTACGCCCATGGAACCGCCCACCCGCTACCCAAGTa                                                                               <  2:233692/148‑1 (MQ=255)                                                                     acCAGTGCGCAGAACGAAGACACCGATACCTTTGCGGTGGGCGCGGTGTTGACCTGGTAAGCGGCCGGGGCCGCTAGGCGGCCCCGAATGACACGGTCTTTTACGCCCATGGAACCGCCCACCCGCTACCCAAGTAGCATTCG‑Tcaccc                                                                 <  8:54615/149‑1 (MQ=255)                                                                                gAACGAAGACACCGATACCTTTGCGGTGGCCGCGGTGTTGACCTGGTAAGCGGCCGGGGCCCCTAGGCGGCCCCCAAAGACAAGGGCATTTTAGCCCCAGGAACCCCCCACCCCCGACCCCAGAATGATTAG‑TCACCCACCACCCcctc                                                      >  1:84436/1‑149 (MQ=255)                                                                                                  cTTTGCGGTGGGCGCGGTGTTGACCTGGTAAGCGGCCGGGGCCGCTAGGCGGCCCCGAATGACACGGGCGTTTTCGCCCATGGGACCGCCCCCCCCCGACCCAAGTAGCCATAG‑GCACCCACCCCCACCGCCGTAAACTGATCACACAg                                    >  2:263591/1‑149 (MQ=255)                                                                                                                 ggTGTTGACCTGGTAAGCGGCCGGGGCCGCTAGGCGGCCCCGAATGACACGGTCTTTTACGCCCATGGAACCGCCCACCCGCTACCCAAGTAGCATTCG‑TCACCCACCACCACCTCCTTATACTGATCACTCAGCCACCCCGTGCCGga                     <  6:8427/149‑1 (MQ=255)                                                                                                                  gtgtTGACCTGGTAAGCGGCCGGGGCCGCTAGGCGGCCCCGAATGACACGGTCTTTTACGCCCATGGAACCGCCCACCCGCTACCCAAGTAGCATTCG‑TCACCCACCACCACCTCCTTAAACTGATCACTCAGCCACCCCGTGCCGgag                    <  5:59744/149‑1 (MQ=255)                                                                                                                   tgtTGACCTGGTAAGCGGCCGGGGCCGCTAGGCGGCCCCGAATGACACGGTCTTTTACGCCCATGGAACCGCCCACCCGCTACCCAAGTAGCTTTCG‑TCACCCACCACCACCTCCTTAAACTGATCACTCAGCCACCCCGTGCCGgaga                   <  8:277958/149‑1 (MQ=255)                                                                                                                             gTAAGCGGCCGGGGCCGCTAGGCGGCCCCGAATGACACGGTCTTTTACGCCCATGGAACCGCCCACCCGCTACCCAAGTAGCATTCG‑TCACCCACCACCACCTCCTTAAACTGATCACTCAGCCACCCCGTGCCGGAGACCACGATgca         <  1:6986/149‑1 (MQ=255)                                                                                                                             gTAAGCGGCCGGGGCCGCTAGGCGGCCCCGAATGACAAGGTCTTTTACCCCCATGGAACCGCCCCCCCGCTACCCAAGTACGAATCG‑TGACCCACCACCCCCTCCTTAAACTGATCACTCAGCCACCCCCTGCCCGGGACCACGAAgca         >  6:150174/1‑149 (MQ=255)                                                                                                                                   ggCCGGGGCCGCTAGGCGGCCCCGAATGACACGGTCTTTTACGCCCATGGAACCGCCCACCCGCTACCCAAGTAGCATTCGTTCACCCACCACCACCTCCTTAAACTGATCACTCAGCCACCCCGTGCCGGAGACCACGATGCAGCAgg    <  1:263591/149‑1 (MQ=255)                                                                                                                                    ttcGGGGCCGCCTAGCGGCCCCGAATGACACGGTCTTTTACGCCCATGGAACCGCCCACCCGCTACCCAAGTAGCATTCG‑TCACCCACCACCACCTCCTTAAACTGATCACTCAGCCACCCCGTGCCGga                     <  4:319666/128‑1 (MQ=255)                                                                                                                                    ttcGGGGCCGCCTAGCGGCCCCGAATGACACGGTCTTTTACGCCCATGGAACCGCCCACCCGCTACCCAAGTAGCATTCG‑TCACCCACCACCACCTCCTTAAACTGATCACTCAGCCACCCCGTGCCGga                     >  3:319666/3‑130 (MQ=255)                                                                                                                                    ttcGGGGCCGCCTAGCGGCCCCGAATGACACGGTCTTTTACGCCCATGGAACCGCCCACCCGCTACCCAAGTAGCATTCG‑TCACCCACCACCACCTCCTTAAACTGATCACTCAGCCACCCCGTGCCGGAGACCACGATGCAGCAGGCt  >  3:153698/3‑149 (MQ=255)                                                                                                                                    ttcGGGGCCGCCTAGCGGCCCCGAATGACACGGTCTTTTACGCCCATGGAACCGCCCACCCGCTACCCAAGTAGCATTCG‑TCACCCACCACCACCTCCTTAAACTGATCACTCAGCCACCCCGTGCCGGAGACCACGATGCACCAGGCt  >  7:192858/3‑149 (MQ=255)                                                                                                                                            cGCTAGGCGGCCCCGAATGACACGGTCTTTTACGCCCATGGAACCGCGCAGCCGCTTCCCAAGTAGCATTCG‑TCACCCACCACCACCTCCTTAAACTGATCACTCAGCCACCCCGTGc                         <  2:242646/118‑1 (MQ=255)                                                                                                                                            cGCTAGGCGGCCCCGAATGACACGGTCGTTTACGCCCATGGAACCGCCCGCCCGCTAACCAAGTAGCATTCG‑TCACCCACCACCACCTCCTTAAACTGATAACTCAGCCACCCCGTGc                         >  1:242646/1‑118 (MQ=255)                                                                                                                                             gCTAGGCGGCCCCGAATGACACGGTCTTTTACGCCCATGGAACCGCCCACCCGCTACCCAAGTAGCATTCG‑TCACCCACCACCACCTCCTTAAACTGATCACTCAGCCACCCCGTGCCGGAGACCa                >  1:128649/1‑126 (MQ=255)                                                                                                                                             gCTAGGCGGCCCCGAATGACACGGTCTTTTACGCCCATGGAACCGCCCACCCGCTACCCAAGTAGCATTCG‑TCACCCACCACCACCTCCTTAAACTGATCACTCAGCCACCCCGTGCCGGAGACCa                <  2:128649/126‑1 (MQ=255)                                                                                                                                                 |                                                                                                                                         CCATGACATCAACGACAACCTGAAACTGGTGGCCGAGTACAACCAGTTTTCCATCGACGGGCAT‑GACACCAGTGCGCAGAACGAAGACACCGATACCTTTGCGGTGGGCGCGGTGTTGACCTGGTAAGCGGCCGGGGCCGCTAGGCGGCCCCGAATGACACGGTCTTTTACGCCCATGGAACCGCCCACCCGCTACCCAAGTAGCATTCG‑TCACCCACCACCACCTCCTTAAACTGATCACTCAGCCACCCCGTGCCGGAGACCACGATGCAGCAGGCT  >  NC_002947/3049902‑3050180

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: ‑