Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	5,033,297	G→A	10.8%	R2H (CGC→CAC)	PP_4437 →	transposase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	5,033,297	0	G	A	10.8%	98.2 / 3.5	37	R2H (CGC→CAC)	PP_4437	transposase
Reads supporting (aligned to +/- strand):  ref base G (19/14);  new base A (2/2);  total (21/16)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.00e-01

GGAACGCTCGTTGGACGCTCGCCAGGAATCACCATCGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTATTTTTAAGCGGACGCGATCACCCTTATCGCCAGGATTTCTATGCGCCAACGAAGCTCTTATCCGAAACCGTTCAAAGCCCAGGTCG  >  NC_002947/5033157‑5033338                                                                                                                                             |                                          ggAACGCTCGTTGGACGCTCGCCAGGAATCACCATCGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTATTTTTAAGCGGACGCGATCACCCTTATCGCCAGGATTTCTATGCGCCAACGAAg                                  <  1:1421009/150‑1 (MQ=255) ggAACGCTCGTTGGACGCTCGCCAGGAATCACCATCGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTATTTTTAAGCGGACGCGATCACCCTTATCGCCAGGATTTCTATGCGCCAACGAAg                                  <  1:86213/150‑1 (MQ=255)  gAACGCTCGTTGGACGCTCGCCAGGAATCACCATCGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTATTTTTAAGCGGACGCGATCACCCTTATCGCCAGGATTTCTATGCGCCAACGAAGc                                 >  2:964894/1‑150 (MQ=255)    aCGCTCGTTGGACGCTCGCCAGGAATCACCATCGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTATTTTTAAGCGGACGCGATCACCCTTATCGCCAGGATTTCTATGCGCCAACGAAGctc                               <  1:570132/150‑1 (MQ=255)    aCGCTCGTTGGACGCTCGCCAGGAATCACCATCGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTATTTTTAAGCGGACGCGATCACCCTTATCGCCAGGATTTCTATGCGCCAACGAAGctc                               <  1:224421/150‑1 (MQ=255)      gCTCGTTGGACGCTCGCCAGGAATCACCATCGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTATTTTTAAGCGGACGCGATCACCCTTATCGCCAGGATTTCTATGCGCCAACGAAGCTCtt                             <  1:865665/150‑1 (MQ=255)          gTTGGACGCTCGCCAGGAATCACCATCGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTATTTTTAAGCGGACGCGATCACCCTTATCGCCAGGATTTCTATGCGCCAACGAAGCTCTTATcc                         >  2:2187753/1‑150 (MQ=255)           ttGGACGCTCGCCAGGAATCACCATCGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTATTTTTAAGCGGACGCGATCACCCTTATCGCCAGGATTTCTATGCGCCAACGAAGCTCTTATCCg                        >  2:118880/1‑150 (MQ=255)              gACGCTCGCCAGGAATCACCATCGTAGGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTATTTTTAAGCGGACGCGATCACCCTTATCGCCAGGATTTCTATGCGCCAACGAAGCTCTTATCCGaaa                     <  1:202711/150‑1 (MQ=255)              gACGCTCGCCAGGAATCACCATCGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTATTTTTAAGCGGACGCGATCACCCTTATCGCCAGGATTTCTATGCGCCAACGAAGCTCTTATCCGaca                     <  1:2302043/150‑3 (MQ=255)              gACGCTCGCCAGGAATCACCATCGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTATTTTTAAGCGGACGCGATCACCCTTATCGCCAGGATTTCTATGCGCCAACGAAGCTCTTATCCGaaa                     >  2:1339800/1‑150 (MQ=255)                   tCGCCAGGAATCACCATCGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTATTTTTAAGCGGACGCGATCACCCTTCTCGCCAGGATTTCTATGCGCCAACGAAGCTCTTATCCGAAACCGtt                >  1:856874/1‑150 (MQ=255)                   tCGCCAGGAATCACCATCGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTATTTTTAAGCGGACGCGATCACCCTTATCGCCAGGATTTCTATGCGCCAACGAAGCTCTTATCCGAAACCGtt                >  1:2213396/1‑150 (MQ=255)                   tCGCCAGGAATCACCATCGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTATTTTTAAGCGGACGCGATCACCCTTATCGCCAGGATTTCTATGCGCCAACGAAGCTCTTATCCGAAACCGtt                >  2:1446864/1‑150 (MQ=255)                      ccAGGAATCACCATCGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTATTTTTAAGCGGACGCGATCACCCTTATCGCCAGGATTTCTATGCGCCAACGAAGCTCTTATCCGAAACCGTTCaa             >  1:270144/1‑150 (MQ=40)                       cAGNAATCACCATCGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTATTTTTAAGCGGACGCGATCACCCTTATCGCCAGGATTTCTATGCGCCAACGAAGCTCTTATCCGAAACCGTTCaaa            >  2:1504005/1‑150 (MQ=39)                       cAGGAATCACCATCGTAAGCGTCCGTCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTATTCTTAAGCGGACGCGATCACCCTTATCGCCAGGATTTCTATGCGCCAACGATGCTCTTATCCGAAACCGTTCaaa            <  2:1190920/150‑1 (MQ=255)                       cAGGAATCACCATCGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTATTTTTAAGCGGACGCGATCACCCTTATCGCCAGGATTTCTATGCGCCAACGAAGCTCTTATCCGAAACCGTTCaaa            >  2:2264896/1‑150 (MQ=40)                        aGGAATCACCATCGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTATTTTTAAGCGGACGCGATCACCCTTATCGCCAGGATTTCTATGCGCCAACGAAGCTCTTATCCGAAACCGTTCAAAg           <  1:964894/150‑1 (MQ=39)                         ggAATCACCATCGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTATTTTTAAGCGGACGCGATCACCCTTATCGCCAGGATTTCTATGCGCCAACGAAGCTCTTATCCGAAACCGTTCAAAGc          >  2:446497/1‑150 (MQ=38)                          gAATCACCATCGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTATTTTTAAGCGGACGCGATCACCCTTATCGCCAGGATTTCTATGCGCCAACGAAGCTCTTATCCGAAACCGTTCAAAGcc         >  2:946640/1‑150 (MQ=38)                            aTCACCATCGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTATTTTTAAGCGGACGCGATCACCCTTATCGCCAGGATTTCTATGCGCCAACGAAGCTCTTATCCGAAACCGTTc               >  1:1467954/1‑142 (MQ=35)                            aTCACCATCGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTATTTTTAAGCGGACGCGATCACCCTTATCGCCAGGATTTCTATGCGCCAACGAAGCTCTTATCCGAAACCGTTc               <  2:1467954/142‑1 (MQ=35)                            aTCACCATCGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTATTTTTAAGCGGACGCGATCACCCTTATCGCCAGGATTTCTATGCGCCAACGAAGCTCTTATCCGAAACCGTTCAAAGCCCa       <  1:1446864/150‑1 (MQ=35)                             tCACCATCGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTATTTTTAGGCGGACGCGATCACCCTTATCGCCAGGATTTCTATGCGCCAACGAAGCTCTTATCCGAAACCGTTCAAAGCCCAg      >  2:1814357/1‑150 (MQ=25)                             tCACCATCGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTATTTTTAAGCGGACGCGATCACCCTTATCGCCAGGATTTCTATGCGCCAACGAAGCTCTTATCCGAAACCGTTCAAAGCCCAg      <  1:312598/150‑1 (MQ=35)                             tCACCATCGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTATTTTTAAGCGGACGCGATCACCCTTATCGCCAGGATTTCTATGCGCCAACGAAGCTCTTATCCGAAACCGTTCAAAGCCCAg      >  1:579337/1‑150 (MQ=35)                              cACCATCGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTATTTTTAAGCGGACGCGATCACCCTTATCGCCAGGATTTCTATGCGCCAACGAAGCTCTTATCCGAAACCGTTCAAAGCCCAgg     <  1:316227/150‑1 (MQ=34)                                ccATCGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTATTTTTAAGCGGACGCGATCACCCTTATCGCCAGGATTTCTATGCGCCAACGAAGCTCTTATCCGAAACCGTTCAAAGCCCAGGTc   >  1:2230821/1‑150 (MQ=32)                                ccATCGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTATTTTTAAGCGGACGCGATCACCCTTATCGCCAGGATTTCTATGCACCAACGAAGCTCTTATCCGAAACCGtt                >  1:2146117/1‑137 (MQ=18)                                ccATCGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTATTTTTAAGCGGACGCGATCACCCTTATCGCCAGGATTTCTATGCACCAACGAAGCTCTTATCCGAAACCGtt                <  2:2146117/137‑1 (MQ=18)                                ccATCGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTATTTTTAAGCGGACGCGATCACCCTTATCGCCAGGATTTCTATGCACCAACGAAGCTCTTATCCGAAACCGtt                <  2:2151915/137‑1 (MQ=18)                                ccATCGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTATTTTTAAGCGGACGCGATCACCCTTATCGCCAGGATTTCTATGCACCAACGAAGCTCTTATCCGAAACCGtt                >  1:2151915/1‑137 (MQ=18)                                 cATCGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTATTTTTAAGCGGACGCGATCACCCTTATCGCCAGGATTTCTATGCGCCAACGAAGCTCTTATCCGAAACCGTTCAAAGCCCa       >  2:2072847/1‑145 (MQ=32)                                 cATCGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTATTTTTAAGCGGACGCGATCACCCTTATCGCCAGGATTTCTATGCGCCAACGAAGCTCTTATCCGAAACCGTTCAAAGCCCa       <  1:2072847/145‑1 (MQ=32)                                 cATCGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTATTTTTAAGCGGACGCGATCACCCTTATCGCCAGGATTTCTATGCGCCAACGAAGCTCTTATCCGAAACCGTTCAAAGCCCAGGTCg  >  1:958702/1‑150 (MQ=32)                                 cATCGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTATTTTTAAGCGGACGCGATCACCCTTATCGCCAGGATTTCTATGCGCCAACGAAGCTCTTATCCGAAACCGTTCAAAGCCCAGGTCg  >  2:460133/1‑150 (MQ=32)                                                                                                                                             |                                          GGAACGCTCGTTGGACGCTCGCCAGGAATCACCATCGTAAGCGTCCGGCGAACTCACCTTCCGAACTCCAGCATTAAGGGCGATGGTGTCCGCGTATTTTTAAGCGGACGCGATCACCCTTATCGCCAGGATTTCTATGCGCCAACGAAGCTCTTATCCGAAACCGTTCAAAGCCCAGGTCG  >  NC_002947/5033157‑5033338

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