Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,368,464	G→A	8.7%	R576H (CGC→CAC)	PP_2964 →	transposase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,368,464	0	G	A	8.7%	123.8 / 2.9	46	R576H (CGC→CAC)	PP_2964	transposase
Reads supporting (aligned to +/- strand):  ref base G (20/22);  new base A (2/2);  total (22/24)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.67e-01

GGAGGAAACCGCGCAACAACTGGACGAGAAATTCCCATCATGCCGAGGGGACGTATCGATTAACGAAGCTGGAGAACCGGTGTTGCGCCGAGTAGCGGCGCGGGACATCCCCCCTTCGGCCATCTCGCTGCAGACGGCGCTTATGCAGCGCATGCC‑GGCCAGGCATGTGCTCGATATCATGGCTAACATCGAGCATTGGATTCAGTTCACGCGGCATTTCGGGCCCATGTCCGGTAACGAGCCGAAGCTCAAAGAGCCTGCCGAGCGCTACCTGATGACGATCTTCGCCATGGGCT  >  NC_002947/3368315‑3368610                                                                                                                                                      |                                                                                                                                                    ggaggaAACCGCGCAACAACTGGACGAGAAATTCCCATCATGCCGAGGGGACGTATCGATTAACGAAGCTGGAGAACCGGTGTTGCGCCGAGTAGCGGCGCGGGACATCCCCCCTTCGGCCATCTCGCTGCAGACGGCGCTTATGCAgcg                                                                                                                                                     >  1:1284976/1‑150 (MQ=255)        aCCGCGCAACAACTGGACGAGAAATTCCCATCATGCCGAGGGGACGTATCGATTAACGAAGCTGGAGAACCGGTGTTGCGCCGAGTAGCGGCGCGGGACATCCCCCCTTCGGCCATCTCGCTGCAGACGGCGCTTATGCAGCGCATGcc                                                                                                                                               >  2:1061224/1‑149 (MQ=255)        aCCGCGCAACAACTGGACGAGAAATTCCCATCATGCCGAGGGGACGTATCGATTAACGAAGCTGGAGAACCGGTGTTGCGCCGAGTAGCGGCGCGGGACATCCCCCCTTCGGCCATCTCGCTGCAGACGGCGCTTATGCAGCGCATGcc                                                                                                                                               <  1:1061224/149‑1 (MQ=255)            cgcAACAACTGGACGAGAAATTCCCATCATGCCGAGGGGACGTATCGATTAACGAAGCTGGAGAACCGGTGTTGCGCCGAGTAGCGGCGCGGGACATCCCCCCTTCGGCCATCTCGCTGCAGACGGCGCTTATGCAGCGCATGCC‑GGCCa                                                                                                                                         <  1:208932/150‑1 (MQ=255)               aacaacTGGACGAGAAATTCCCATCATGCCGAGGGGACGTATCGATTAACGAAGCTGGAGAACCGGTGTTGCGCCGAGTAGCGGCGCGGGACATCCCCCCTTCGGCCATCTCGCTGCAGACGGCGCTTATGCAGCGCATGCC‑GGCCAGGc                                                                                                                                      >  2:226143/1‑150 (MQ=255)                 caacTGGACGAGAAATTCCCATCATGCCGAGGGGACGTATCGATTAACGAAGCTGGAGAACCGGTGTTGCGCCGAGTAGCGGCGCGGGACATCCCCCCTTCGGCCATCTCGCTGCAGACGGCGCTTATGCAGCGCATGCC‑GGCCAGGCAt                                                                                                                                    >  1:191773/1‑150 (MQ=255)                 caacTGGACGAGAAATTCCCATCATGCCGAGGGGACGTATCGATTAACGAAGCTGGAGAACCGGTGTTGCGCCGAGTAGCGGCGCGGGACATCCCCCCTTCGGCCATCTCGCTGCAGACGGCGCTTATGCAGCGCATGCC‑GGCCAGGCAt                                                                                                                                    <  2:1353826/150‑1 (MQ=255)                      ggACGAGAAATTCCCATCATGCCGAGGGGACGTATCGATTAACGAAGCTGGAGAACCGGTGTTGCGCCGAGTAGCGGCGCGGGACATCCCCCCTTCGGCCATCTCGCTGCAGACGGCGCTTATGCAGCACATGCCTGGCC‑GGCATGCGCt                                                                                                                               <  2:1103969/150‑1 (MQ=255)                       gACGAGAAATTCCCATCATGCCGAGGGGACGTATCGATTAACGAAGCTGGAGAACCGGTGTTGCGCCGAGTAGCGGCGCGGGACATCCCCCCTTCGGCCATCTCGCTGCAGACGGCGCTTATGCAGCGCATGCC‑GGCCAGGCATGTGCTc                                                                                                                              <  2:1284976/150‑1 (MQ=255)                       gACGAGAAATTCCCATCATGCCGAGGGGACGTATCGATTAACGAAGCTGGAGAACCGGTGTTGCGCCGAGTAGCGGCGCGGGACATCCCCCCTTCGGCCATCTCGCTGCAGACGGCGCTTATGCAGCGCATGCC‑GGCCAGGCATGTGCTc                                                                                                                              <  2:1262795/150‑1 (MQ=255)                          gagaAATTCCCATCATGCCGAGGGGACGTATCGATTAACGAAGCTGGAGAACCGGTGTTGCGCCGAGTAGCGGCGCGGGACATCCCCCCTTCGGCCATCTCGCTGCAGACGGCGCTTATGCAGCACATGCCTGGCC‑GGCATGCGCtgcat                                                                                                                           >  2:170659/1‑146 (MQ=255)                            gaAATTCCCATCATGCCGAGGGGACGTATCGATTAACGAAGCTGGAGAACCGGTGTTGCGCCGAGTAGCGGCGCGGGACATCCCCCCTTCGGCCATCTCGCTGCAGACGGCGCTTATGCAGCACATGCCTGGCC‑GGCATGCGCtgcataa                                                                                                                         <  1:170659/150‑7 (MQ=255)                               aTTCCCATCATGCCGAGGGGACGTATCGATTAACGAAGCTGGAGAACCGGTGTTGCGCCGAGTAGCGGCGCGGGACATCCCCCCTTCGGCCATCTCGCTGCAGACGGCGCTTATGCAGCGCATGCC‑GGCCAGGCATGTGCTCGATATc                                                                                                                        <  1:684899/148‑1 (MQ=255)                               aTTCCCATCATGCCGAGGGGACGTATCGATTAACGAAGCTGGAGAACCGGTGTTGCGCCGAGTAGCGGCGCGGGACATCCCCCCTTCGGCCATCTCGCTGCAGACGGCGCTTATGCAGCGCATGCC‑GGCCAGGCATGTGCTCGATATc                                                                                                                        >  2:684899/1‑148 (MQ=255)                                    catcatGCCGAGGGGACGTATCGATTAACGAAGCTGGAGAACCGGTGTTGCGCCGAGTAGCGGCGCGGGACATCCCCCCTTCGGCCATCTCGCTGCAGACGGCGCTTATGCAGCGCATGCC‑GGCCAGGCATGTGCTCGATATCATGGCTa                                                                                                                 >  2:1101534/1‑150 (MQ=255)                                         tGCCGAGGGGACGTATCGATTAACGAAGCTGGAGAACCGGTGTTGCGCCGAGTAGCGGCGCGGGACATCCCCCCTTCGGCCATCTCGCTGCAGACGGCGCTTATGCAGCGCATGCC‑GGCCAGGCATGTGCTCGATATCATGGCTAACATc                                                                                                            <  1:226143/150‑1 (MQ=255)                                           ccGAGGGGACGTATCGATTAACGAAGCTGGAGAACCGGTGTTGCGCCGAGTAGCGGCGCGGGACATCCCCCCTTCGGCCATCTCGCTGCAGACGGCGCTTATGCAGCGCATGCC‑GGCCAGGCATGTGCTCGATATCATGGCTAACATCGa                                                                                                          <  2:111862/150‑1 (MQ=255)                                                     gTATCGATTAACGAAGCTGGAGAACCGGTGTTGCGCCGAGTAGCGGCGCGGGACATCCCCCCTTCGGCCATCTCGCTGCAGACGGCGCTTATGCAGCGCATGCC‑GGCCAGGCATGTGCTCGATATCATGGCTAACATCGAGCATTGGAtt                                                                                                >  2:95738/1‑150 (MQ=255)                                                          gATTAACGAAGCTGGAGAACCGGTGTTGCGCCGAGTAGCGGCGCGGGACATCCCCCCTTCGGCCATCTCGCTGCAGACGGCGCTTATGCAGCGCATGCC‑GGCCAGGCATGTGCTCGATATCa                                                                                                                       <  1:526859/122‑1 (MQ=255)                                                          gATTAACGAAGCTGGAGAACCGGTGTTGCGCCGAGTAGCGGCGCGGGACATCCCCCCTTCGGCCATCTCGCTGCAGACGGCGCTTATGCAGCGCATGCC‑GGCCAGGCATGTGCTCGATATCa                                                                                                                       >  2:526859/1‑122 (MQ=255)                                                                    gCTGGAGAACCGGTGTTGCGCCGAGTAGCGGCGCGGGACATCCCCCCTTCGGCCATCTCGCTGCAGACGGCGCTTATGCAGCGCATGCC‑GGCCAGGGATGTGCTCGATATGGTGGCTGTCATGGGGTATTTGAGTCGGTTCACGCGGCAt                                                                                 >  2:654258/1‑150 (MQ=255)                                                                        gagaACCGGTGTTGCGCCGAGTAGCGGCGCGGGACATCCCCCCTTCGGCCATCTCGCTGCAGACGGCGCTTATGCAGCGCATGCC‑GGCCAGGCATGTGCTCGATATCATGGCTAACATCGAGCATTGGATTCAGTTCACGCGGCATTTCg                                                                             >  1:346438/1‑150 (MQ=255)                                                                          gaACCGGTGTTGCGCCGAGTAGCGGCGCGGGACATCCCCCCTTCGGCCATCTCGCTGCAGACGGCGCTTATGCAGCGCATGCC‑GGCCAGGCATGTGCTCGATATCATGGCTAACATCGAGCATTGGATTCAGTTCACGCGGCATTTCggg                                                                           <  1:848434/150‑1 (MQ=255)                                                                           aaCCGGTGTTGCGCCGAGTAGCGGCGCGGGACATCCCCCCTTCGGCCATCTCGCTGCAGACGGCGCTTATGCAGCGCATGCC‑GGCCAGGCATGTGCTCGATATCATGGCTAACATCGAGCATTGGATTCAGTTCACGCGGCATTTCGGGc                                                                          >  1:538926/1‑150 (MQ=255)                                                                                gtgtTGCGCCGAGTAGCGGCGCGGGACATCCCCCCTTCGGTCATCTCGCTGCAGACGGCGCTTATGCAGCGCATGCC‑GGCCAGGCATGTGCTCGATATCATGGCTAACATCGAGCATTGGATTCAGTTCACGCGGCATTTCGGGCCCATg                                                                     >  2:25696/1‑150 (MQ=255)                                                                                             tAGCGGCGCGGGACATCCCCCCTTCGGCCATCTCGCTGCAGACGGCGCTTATGCAGCGCATGCC‑GGCCAGGCATGTGCTCGATATCATGGCTAACATCGAGCATTGGATTCAGTTCACGCGGCATTTCGGGCCCATGTCCGGTAACGAGc                                                        <  2:425625/150‑1 (MQ=255)                                                                                                 ggcgCGGGACATCCCCCCTTCGGCCATCTCGCTGCAGACGGCGCTTATGCAGCGCATGCC‑GGCCAGGCATGTGCTCGATATCATTGCTAACATCGAGCATTGGATTCAGTTCACGCGGCATTTCGGGCCCATGTCCGGTAACGAGCCGaa                                                    <  2:90881/150‑1 (MQ=255)                                                                                                  gcgcGGGACATCCCCCCTTCGGCCATCTCGCTGCAGACGGCGCTTATGCAGCGCATGCC‑GGCCAGGCATGTGCTCGATATCATGGCTAACATCGAGCATTGGATTCAGTTCACGCGGCATTTCGGGCCCATGTCCGGTAACGAGCAGAAg                                                   >  2:714488/1‑150 (MQ=255)                                                                                                            tCCCCCCTTCGGCCATCTCGCTGCAGACGGCGCTTATGCAGCGCATGCC‑GGCCAGGCATGTGCTTGATATCATGGCTAACATCGAGCATTGGATTCAGTTCACGCGGCATTTCGGGCCCATGTCCGGTAACGAGCCGAAGCTCAAAGAGc                                         <  2:24701/150‑1 (MQ=255)                                                                                                              cccccTTCGGCCATCTCGCTGCAGACGGCGCTTATGCAGCGCATGCC‑GGCCAGGCATGTGCTCGATATCATGGCTAACATCGAGCATTGGATTCAGTTCACGCGGCATTTCg                                                                             >  1:286439/1‑112 (MQ=255)                                                                                                              cccccTTCGGCCATCTCGCTGCAGACGGCGCTTATGCAGCGCATGCC‑GGCCAGGCATGTGCTCGATATCATGGCTAACATCGAGCATTGGATTCAGTTCACGCGGCATTTCg                                                                             <  2:286439/112‑1 (MQ=255)                                                                                                               ccccTTCGGCCATCTCGCTGCAGACGGCGCTTATGCAGCGCATGCC‑GGCCAGGCATGTGCTCGATATCATGGCTAACATCGAGCATTGGATTCAGTTCACGCGGCATTTCGGGc                                                                          <  1:639552/114‑1 (MQ=255)                                                                                                               ccccTTCGGCCATCTCGCTGCAGACGGCGCTTATGCAGCGCATGCC‑GGCCAGGCATGTGCTCGATATCATGGCTAACATCGAGCATTGGATTCAGTTCACGCGGCATTTCGGGc                                                                          >  2:639552/1‑114 (MQ=255)                                                                                                                   ttCGGCCATCTCGCTGCAGACGGCGCTTATGCAGCGCATGCC‑GGCCAGGCATGTGCTCGATATCATGGCTAACATCGAGCATTGGATTCAGTTCACGCGGCATTTCGGGCCAATGTCCGGTAACGAGCCGAAGCTCAAAGAGCCTGCCGa                                  <  1:1101534/150‑1 (MQ=255)                                                                                                                     cGGCCATCTCGCTGCAGACGGCGCTTATGCAGCGCATGCC‑GGCCAGGCATGTGCTCGATATCATGGCTAACATCGAGCATTGGATTCAGTTCACGCGGCATTTCGGGCCCATGTCCGGTAAc                                                            >  1:831328/1‑122 (MQ=255)                                                                                                                     cGGCCATCTCGCTGCAGACGGCGCTTATGCAGCGCATGCC‑GGCCAGGCATGTGCTCGATATCATGGCTAACATCGAGCATTGGATTCAGTTCACGCGGCATTTCGGGCCCATGTCCGGTAAc                                                            <  2:831328/122‑1 (MQ=255)                                                                                                                                   cAGACGGCGCTTATGCAGCGCATGCC‑GGCCAGGCATGCGCTCGATATCATGGCTAACATCGAGCATTGGATTCAGTTCACGCGGCATTTCGGGCCCATGTCCGGTAACGAGCCGAAGCTCAAAGAGCCTGCCGAGCGCTACCtga                       >  2:484031/1‑145 (MQ=255)                                                                                                                                   cAGACGGCGCTTATGCAGCGCATGCC‑GGCCAGGCATGCGCTCGATATCATGGCTAACATCGAGCATTGGATTCAGTTCACGCGGCATTTCGGGCCCATGTCCGGTAACGAGCCGAAGCTCAAAGAGCCTGCCGAGCGCTACCtga                       <  1:484031/145‑1 (MQ=255)                                                                                                                                           gcTTATGCAGCGCATGCC‑GGCCAGGCATGTGCTCGATATCATGGCTAACATCGAGCATTGGATTCGGTTCACGCGGCATTTCGGGCCCATGTCCGGTAACGAGCCGAAGCTCAAAGAGCCTGCCGAGCGCTACCTGATGACGATCTTCGc          >  1:719506/1‑150 (MQ=255)                                                                                                                                           gcTTATGCAGCGCATGCC‑GGCCAGGCATGTGCTCGATATCATGGCTAACATCGAGCATTGGATTCAGTTCACGCGGCATTTCGGGCCCATGTCCGGTAACGAGCCGAAGCTCAAAGAGCCTGCCGAGCGCTACCTGATGACGATCTTCGc          >  1:377187/1‑150 (MQ=255)                                                                                                                                           gcTTATGCAGCGCACGCC‑GGCCAAGCGTGTGCTTGGTATCATGGCTAACATCGACCATTGGATTCACTCCACGCGGCATTTCGGGCCCATGTCCGGTAACGAGCCGAAGCTCAAAGAGCCTGCCGAGCGCTACCTGATGACGATCTTCGc          <  1:25696/150‑1 (MQ=255)                                                                                                                                             ttATGCAGCGCATGCC‑GGCCAGGCATGTGCTCGATATCATGGCTAACATCGAGCATTGGATTCAGTTCACGCGGCATTTCGGGCCCATGTCCGGTAACGAGCCGAAGCTCAAAGAGCCTGCCGAGCGCTACCTGATGACGATCTTCGCCa        >  2:1066861/1‑150 (MQ=255)                                                                                                                                               aTGCAGCGCATGCC‑GGCCAGGCATGTGCTCGATATCATGGCTAACATCGAGCATTGGATTCAGTTCACGCGGCATTTCGGGCCCATGTCCGGTAACGAGCCGAAGCTCAAAGAGCCTGCCGAGCGCTACCTGATGACGATCTTCGCCATg      <  1:95738/150‑1 (MQ=255)                                                                                                                                                tGCAGCGCATGCC‑GGCCAGGCATGTGCTCGATATCATGGCTAACATCGAGCATTGGATTCAGTTCACGCGGCATTTCGGGCCCATGTCCGGTAACGAGCCGAAGCTCAAAGAGCCTGCCGAGCGCTACCTGATGACGATCTTCGCCATgg     <  2:346438/150‑1 (MQ=255)                                                                                                                                                tGCAGCGCATGCC‑GGCCAGGCATGTGCTCGATATCATGGCTAACATCGAGCATTGGATTCAGTTCACGCGGCATTTCGGGCCCATGTCCGGTAACGAGCCGAAGCTCAAAGAGCCTGCCGAGCGCTACCTGATGACGATCTTCGCCATgg     <  1:1066861/150‑1 (MQ=255)                                                                                                                                                 gCAGCGCATGCC‑GGCCAGGCATGTGCTCGATATCATGGCTAACATCGCGCATTGGATTCAGTTCACGCGGCATTTCGGGCCCATGTCCGGTAACGAGCCGAAGCTCAAAGAGCCTGCCGAGCGCTACCTGATGACGATCTTCGCCATggg    >  2:8118/1‑150 (MQ=255)                                                                                                                                                   aGCACATGCC‑TGGCCGGCATGCGCTCGATATCATGGCTAACATCGAGCATTGGATTCAGTTCACGCGGCATTTCGGGCCCATGTCCGGTAACGAGCCGAAGCTCAAAGAGCCTGCCGAGCGCTACCTGATGACGATCTTCGCCATGGGCt  >  1:136620/1‑150 (MQ=255)                                                                                                                                                      |                                                                                                                                                    GGAGGAAACCGCGCAACAACTGGACGAGAAATTCCCATCATGCCGAGGGGACGTATCGATTAACGAAGCTGGAGAACCGGTGTTGCGCCGAGTAGCGGCGCGGGACATCCCCCCTTCGGCCATCTCGCTGCAGACGGCGCTTATGCAGCGCATGCC‑GGCCAGGCATGTGCTCGATATCATGGCTAACATCGAGCATTGGATTCAGTTCACGCGGCATTTCGGGCCCATGTCCGGTAACGAGCCGAAGCTCAAAGAGCCTGCCGAGCGCTACCTGATGACGATCTTCGCCATGGGCT  >  NC_002947/3368315‑3368610

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: ‑