Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	1,955,242	C→T	8.1%	intergenic (+29/‑164)	PP_1752 → / → PP_1753	hypothetical protein/DMT superfamily permease

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	1,955,242	0	C	T	8.1%	139.9 / 3.3	50	intergenic (+29/‑164)	PP_1752/PP_1753	hypothetical protein/DMT superfamily permease
Reads supporting (aligned to +/- strand):  ref base C (27/18);  new base T (2/2);  total (29/21)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.45e-01

AGCAGCGAGATTGCCCCTTGGACGCTGGTGGAGGCCAATGACAAGCGCTGGGCGCGGGTGAAGGTGGTGCGCACAATCAACCAGGCGCTTGAGGCGGCGTTTGCCA‑AGCACAAGAAATAGCCGAAGGTGAGGTTGCCTGTTCTGGCCGCTTCGCGGGTTTACCCGCGAAAGGGTCAGCACAGGCAACACCTCCACCCAGCCATGCCCCAAAAGAATGACCTGATGAATTCTTTTCTCGGCACTCTCCACCGTCTCTGTCCTCCAACCCCGTAGAATTCAACAACCCCCACCACGGG  >  NC_002947/1955094‑1955389                                                                                                                                                      |                                                                                                                                                    agcagcGAGATTGCCCCTTGGACGCTGGTGGAGGCCAATGACAAGCGCTGGGCGCGGGTGAAGGTGGTGCGCACAATCAACCAGGCGCTTGAGGCGGCGTTTGCCA‑AGCACAAGAAATAGCCGAAGGTGAGGTTGCCTGTTCTGGCCGCt                                                                                                                                                    <  1:1105389/150‑1 (MQ=255)         gaTTGCCCCTTGGACGCTGGTGGAGGCCAATGACAAGCGCTGGGCGCGGGTGAAGGTGGTGCGCACAATCAACCAGGCGCTTGAGGCGGCGTTTGCCA‑AGCACAAGAAATAGCCGAAGGTGAGGTTGCCTGTTCTGGCCGCTTcgcg                                                                                                                                               >  2:1272938/1‑147 (MQ=255)         gaTTGCCCCTTGGACGCTGGTGGAGGCCAATGACAAGCGCTGGGCGCGGGTGAAGGTGGTGCGCACAATCAACCAGGCGCTTGAGGCGGCGTTTGCCA‑AGCACAAGAAATAGCCGAAGGTGAGGTTGCCTGTTCTGGCCGCTTcgcg                                                                                                                                               <  1:1272938/147‑1 (MQ=255)           ttGCCCCTTGGACGCTGGTGGAGGCCAATGACAAGCGCTGGGCGCGGGTGAAGGTGGTGCGCACAATCAACCAGGCGCTTGAGGCGGCGTTTGCCA‑AGCACAAGAAATAGCCGAAGGTGAGGTTGCCTGTTCTGGCCGCTTCGCGGGttt                                                                                                                                          <  2:1093263/150‑1 (MQ=255)                ccTTGGACGCTGGTGGAGGCCAATGACAAGCGCTGGGCGCGGGTGAAGGTGGTGCGCACAATCAACCAGGCGCTTGAGGCGGCGTTTGCCA‑AGCACAAGAAATAGCCGAAGGTGAGGTTGCCTGTTCTGGCCGCTTCGCGGGTTTACCcg                                                                                                                                     >  2:606516/1‑150 (MQ=255)                 cTTGGACGCTGGTGGAGGCCAATGACAAGCGCTGGGCGCGGGTGAAGGTGGTGCGCACAATCAACCAGGCGCTTGAGGCGGCGTTTGCCA‑AGCACAAGAAATAGCCGAAGGTGAGGTTGCCTGTTCTGGCCGCTTCGCgg                                                                                                                                              >  1:1029589/1‑140 (MQ=255)                 cTTGGACGCTGGTGGAGGCCAATGACAAGCGCTGGGCGCGGGTGAAGGTGGTGCGCACAATCAACCAGGCGCTTGAGGCGGCGTTTGCCA‑AGCACAAGAAATAGCCGAAGGTGAGGTTGCCTGTTCTGGCCGCTTCGCgg                                                                                                                                              <  2:1029589/140‑1 (MQ=255)                 cTTGGACGCTGGTGGAGGCCAATGACAAGCGCTGGGCGCGGGTGAAGGTGGTGCGCACAATCAACCAGGCGCTTGAGGCGGCGTTTGCCA‑AGCACAAGAAATAGCCGAAGGTGAGGTTGCCTGTTCTGGCCGCTTCGCGGGTTTACCcgc                                                                                                                                    >  2:939981/1‑150 (MQ=255)                 cTTGGACGCTGGTGGAGGCCAATGACAAGCGCTGGGCGCGGGTGAAGGTGGTGCGCACAATCAACCAGGCGCTTGAGGCGGCGTTTGCCA‑AGCACAAGAAATAGCCGAAGGTGAGGTTGCCTGTTCTGGCCGCTTCGCGGGTTTACCcgc                                                                                                                                    >  2:515740/1‑150 (MQ=255)                         cTGGTGGAGGCCAATGACAAGCGCTGGGCGCGGGTGAAGGTGGTGCGCACAATCAACCAGGCGCTTGAGGCGGCGTTTGCCA‑AGCACAAGAAATAGCCGAAGGTGAGGTTGCCTGTTCTGGCCGTTTCGCGGGTAAACCCGCGaagcggc                                                                                                                            <  2:765012/150‑6 (MQ=255)                          tggtggAGGCCAATGACAAGCGCTGGGCGCGGGTGAAGGTGGTGCGCACAATCAACCAGGCGCTTGAGGCGGCGTTTGCCA‑AGCACAAGAAATAGCCGAAGGTGAGGTTGCCTGTTCTGGCCGCTTCGCGGGTTTACCGGCGAAAGGGTc                                                                                                                           >  2:1056417/1‑150 (MQ=255)                               gAGGCCAATGACAAGCGCTGGGCGCGGGTGAAGGTGGTGCGCACAATCAACCAGGCGCTTGAGGCGGCGTTTGCCA‑AGCACAAGAAATAGCCGAAGGTGAGGTTGCCTGTTCTGGCCGCTTCGCGGGTTTACCCGCGAAAGGGTCAGcac                                                                                                                      >  1:1038659/1‑150 (MQ=255)                                aGGCCAATGACAAGCGCTGGGCGCGGGTGAAGGTGGTGCGCACAATCAACCAGGCGCTTGAGGCGGCGTTTGCCA‑AGCACAAGAAATAGCCGAAGGTGAGGTTGCCTGTTCTGGCCGCTTCGCGGGTTTACCCGCGAAAGGGTCAGcaca                                                                                                                     >  1:891263/1‑150 (MQ=255)                                 ggCCAATGACAAGCGCTGGGCGCGGGTGAAGGTGGTGCGCACAATCAACCAGGCGCTTGAGGCGGCGTTTGCCA‑AGCACAAGAAATAGCCGAAGGTGAGGTTGCCTGTTCTGGCCGCTTCGCGGGTTTACCCGCGAAAGGGTCAGCACAg                                                                                                                    >  1:245751/1‑150 (MQ=255)                                 ggCCAATGACAAGCGCTGGGCGCGGGTGAAGGTGGTGCGCACAATCAACCAGGCGCTTGAGGCGGCGTTTGCCA‑AGCACAAGAAATAGCCGAAGGTGAGGTTGCCTGTTCTGGCCGCTTCGCGGGTTTACCCGCGAAAGGGTCAGCACAg                                                                                                                    <  1:515740/150‑1 (MQ=255)                                 ggCCAATGACAAGCGCTGGGCGCGGGTGAAGGTGGTGCGCACAATCAACCAGGCGCTTGAGGCGGCGTTTGCCA‑AGCACAAGAAATAGCCGAAGGTGAGGTTGCCTGTTCTGGCCGCTTCGCGGGTTTACCCGCGAAAGGGTCAGCACAg                                                                                                                    <  1:748123/150‑1 (MQ=255)                                    cAATGACAAGCGCTGGGCGCGGGTGAAGGTGGTGCGCACAATCAACCAGGCGCTTGAGGCGGCGTTTGCCA‑AGCACAAGAAATAGCCGAAGGTGAGGTTGCCTGTTCTGGCCGCTTCGCgg                                                                                                                                              >  1:318651/1‑121 (MQ=255)                                    cAATGACAAGCGCTGGGCGCGGGTGAAGGTGGTGCGCACAATCAACCAGGCGCTTGAGGCGGCGTTTGCCA‑AGCACAAGAAATAGCCGAAGGTGAGGTTGCCTGTTCTGGCCGCTTCGCgg                                                                                                                                              <  2:318651/121‑1 (MQ=255)                                    cAATGACAAGCGCTGGGCGCGGGTGAAGGTGGTGCGCACAATCAACCAGGCGCTTGAGGCGGCGTTTGCCA‑AGCACAAGAAATAGCCGAAGGTGAGGTTGCCTGTTCTGGCCGCTTCGCGGGTTTACCCGCGAAAGGGTCAGCACAGGCa                                                                                                                 >  1:165091/1‑150 (MQ=255)                                      aTGACAAGCGCTGGGCGCGGGTGAAGGTGGTGCGCACAATCAACCAGGCGCTTGAGGCGGCGTTTGCCA‑AGCACAAGAAATAGCCGAAGGTGAGGTTGCCTGTTCTGGCCGCTTCGCGGGTTTACCCGCGAAAGGGTCAGCACAGGCAac                                                                                                               <  2:891263/150‑1 (MQ=255)                                                               ggtggtGCGCACAATCAACCAGGCGCTTGAGGCGGCGTTTGCCA‑AGCACAAGAAATAGCCGAAGGTGAGGTTGCCTGTTCTGGCCGCTTCGCGGGTTTACCCGCGaagc                                                                                                                               >  1:308406/1‑107 (MQ=255)                                                               ggtggtGCGCACAATCAACCAGGCGCTTGAGGCGGCGTTTGCCA‑AGCACAAGAAATAGCCGAAGGTGAGGTTGCCTGTTCTGGCCGCTTCGCGGGTTTACCCGCGaagc                                                                                                                               <  2:308406/109‑3 (MQ=255)                                                               ggtggtGCGCACAATCAACCAGGCGCTTGAGGCGGCGTTTGCCA‑AGCACAAGAAATAGCCGAAGGTGAGGTTGCCTGTTCTGGCCGCTTCGCGGGTTTACCCGCGAAAGGGTCAGCACAGGCAACACCTCCACCCAGCCATGCCCCaaaa                                                                                      <  1:639778/150‑1 (MQ=255)                                                               ggtggtGCGCACAATCAACCAGGCGCTTGAGGCGGCGTTTGCCA‑AGCACAAGAAATAGCCGAAGGTGAGGTTGCCTGTTCTGGACGCCTCGCGGCTTCTCCCGCGAAAGGGTCATCACTGGCAACACCTCCACCCAGCCATGCCCCaaaa                                                                                      <  2:787933/150‑1 (MQ=255)                                                                   gtgCGCACAATCAACCAGGCGCTTGAGGCGGCGTTTGCCA‑AGCACAAGAAATAGCCGAAGGTGAGGTTGCCTGTTCTGGCCGCTTCGCGGGTTTACCCGCGAAAGGGTCAGCACAGGCAACACCTCCACCCAGCCATGCCCCAAAAGAAt                                                                                  >  1:832724/1‑150 (MQ=255)                                                                             tCAACCAGGCGCTTGAGGCGGCGTTTGCCA‑AGCACAAGAAATAGCCGAAGGTGAGGTTGCCTGTTCTGGCCGCTTCGCGGGTTTACCCGCGAAAGGGTCAGCACAGGCAACACCTCCACCCAGCCATGCCCCAAAAGAAt                                                                                  <  1:543338/140‑1 (MQ=255)                                                                             tCAACCAGGCGCTTGAGGCGGCGTTTGCCA‑AGCACAAGAAATAGCCGAAGGTGAGGTTGCCTGTTCTGGCCGCTTCGCGGGTTTACCCGCGAAAGGGTCAGCACAGGCAACACCTCCACCCAGCCATGCCCCAAAAGAAt                                                                                  >  2:543338/1‑140 (MQ=255)                                                                                agcAGGCGCTTGAGGCGGCGCTTCCCACAGC‑CGAGCACTAGCAAGCGGTGGGGTTCGCTGTTCTAGTCGATTCGCTGGTTTACCCGCGAAAGGGTCAGCACAGGCAACACCTCCACCCAGCCATGCCCCAAAAGAATGACCTGATGAAtt                                                                     <  2:908366/148‑1 (MQ=255)                                                                                aCCAGGCGCTTGAGGCGGCGTTTGCCA‑AGCACAAGAAATAGCCGAAGGTGAGGTTGCCTGTTCTGGCCGCTTCGCGGGTTTACCCGCGAAAGGGTCAGCACAGGCAACACCTCCACCCAGCCATGCCCCAAAAGAATGACCTGATGAAtt                                                                     <  2:165091/150‑1 (MQ=255)                                                                                 ccAGGCGCTTGAGGCGGCGTTTGCCA‑AGCACAAGAAATAGCCGAAGGTGAGGTTGCCTGTTCTGGCCGCTTCGCGGGTTTACCCGCGAAAGGGTCAGCACAg                                                                                                                    >  1:375014/1‑102 (MQ=255)                                                                                 ccAGGCGCTTGAGGCGGCGTTTGCCA‑AGCACAAGAAATAGCCGAAGGTGAGGTTGCCTGTTCTGGCCGCTTCGCGGGTTTACCCGCGAAAGGGTCAGCACAg                                                                                                                    <  2:375014/102‑1 (MQ=255)                                                                                  cAGGCGCTTGAGGCGGCGTTTGCCA‑AGCACAAGAAATAGCCGAAGGTGAGGTTGCCTGTTCTGGCCGCTTCGCGGGTTTACCCGCGAAAGGGTCAGCACAGGCAACACCTCCACCCAGCCATGCCCCAAAAGAATGACCTGATGAATTCt                                                                   >  1:110893/1‑150 (MQ=255)                                                                                   aGGCGCTTGAGGCGGCGTTTGCCA‑AGCACAAGAAATAGCCGAAGGTGAGGTTGCCTGTTCTGGCCGCTTCGCGGGTTTACCCGCGAAAGGGTCAGCACAGGCAACACCTCCACCCAGCCATGCCCCAAAAGAATGACCTGATGAATTCtt                                                                  <  2:110893/150‑1 (MQ=255)                                                                                    ggCGCTTGAGGCGGCGTTTGCCA‑AGCACAAGAAATAGCCGAAGGTGAGGTTGCCTGTTCTGGCCGCTTCGCGGGTTTACCCGCGAAAGGGTCAGCACAGGCAACACCTCCACCCAGCCATGCCCCAAAAGCATGACCTGATGACTTCttt                                                                 >  1:1145950/1‑150 (MQ=255)                                                                                    ggCGCTTGAGGCGGCGTTTGCCA‑AGCACAAGAAATAGCCGAAGGTGAGGTTGCCTGTTCTGGCCGCTTCGCGGGTTTACCCGCGAAAGGGTCAGCACAGGCAACACCTCCACCCAGCCATGCCCCAAAAGAATGa                                                                                >  2:1136804/1‑135 (MQ=255)                                                                                    ggCGCTTGAGGCGGCGTTTGCCA‑AGCACAAGAAATAGCCGAAGGTGAGGTTGCCTGTTCTGGCCGCTTCGCGGGTTTACCCGCGAAAGGGTCAGCACAGGCAACACCTCCACCCAGCCATGCCCCAAAAGAATGa                                                                                <  1:1136804/135‑1 (MQ=255)                                                                                                         cA‑AGCACAAGAAATAGCCGAAGGTGAGGTTGCCTGTTCTGGCCGCTTCGCGGGTTTACCCGCGAAAGGGTCAGCACAGGCAACACCTCCACCCAGCCATGCCCCAAAAGAATGACCTGATGAATTCTTTTCTCGGCACTCTCCACCGtct                                            >  2:364978/1‑150 (MQ=255)                                                                                                                caAGAAATAGCCGAAGGTGAGGTTGCCTGTTCTGACCCTTTCGCGGGTAAACCCGCGaagc                                                                                                                               <  2:1072277/61‑3 (MQ=11)                                                                                                                caAGAAATAGCCGAAGGTGAGGTTGCCTGTTCTGACCCTTTCGCGGGTAAACCCGCGaagc                                                                                                                               >  1:1072277/1‑59 (MQ=11)                                                                                                                      aTAGCCGAAGGTGAGGTTGCCTGTTCTGGCCGCTTCGCGGGTTTACCCGCGAAAGGGTCAGCACAGGCAACACCTCCACCCAGCCATGCCCCAAAAGAATGACCTGATGAATTCTTTTCTCGGCACTCTCCACCGTCTCTGTCCTCCAAc                                >  1:1080411/1‑150 (MQ=255)                                                                                                                          ccGAAGGTGAGGTTGCCTGTTCTGGCCGCTTCGCGGGTTTACCCGCGAAAGGGTCAGCACAGGCAACACCTCCACCCAGCCATGCCCCAAAAGAATGACCTGATGAATTCTTTTCTCGGCACTCTCCACCGTCTCTGTCCTCCAACCCCg                            >  2:411667/1‑150 (MQ=255)                                                                                                                            gAAGGTGAGGTTGCCTGTTCTGGCCGCTTCGCGGGTTTACCCGCGAAAGGGTCAGCACAGGCAACACCTCCACCCAGCCATGCCCCAAAAGAATGACCTGATGAATTCTTTTCTCGGCACTCTCCACCGTCTCTGTCCTCCAACCCCGTa                          <  2:1080411/150‑1 (MQ=255)                                                                                                                                    ggTTGCCTGTTCTGGCCGCTTCGCGGGTTTACCCGCGAAAGGGTCAGCACAGGCAACACCTCCACCCAGCCATGCCCCAAAAGAATGACCTGATGAATTCTTTTCTCGGCACTCTCCACCGTCTCTGTCCTCCAACCCCGTAGAATTcaa                  <  2:245751/150‑1 (MQ=255)                                                                                                                                     gTTGCCTGTTCTGGCCGCTTCGCGGGTTTACCCGCGAAAGGGTCAGCACAGGCAACACCTCCACCCAGCCATGCCCCAAAAGAATGACCTGATGAATTCTTTTCTCGGCACTCTCCACCGTCTCTGTCCTCCAACCCCGTAGAATTcaac                 >  1:583672/1‑150 (MQ=255)                                                                                                                                      ttGCCTGTTCTGGCCGCTTCGCGGGTTTACCCGCGAAAGGGTCAGCACAGGCAACACCTCCACCCAGCCATGCCCCAAAAGAATGACCTGATGAATTCTTTTCTCGGCACTCTCCACCGTCTCTGTCCTCCAACCCCGTAGAATTcaaca                >  2:1027890/1‑150 (MQ=255)                                                                                                                                      ttGCCTGTGCTGACCCTTTCGCGGGTAAACCCGCGAAGCGGCCAGAACAGGCAACACCTCCACCCAGCCATGCCCCAAAAGAATGACCTGATGAATTCTTTTCTCGGCACTCTCCACCGTCTCTGTCCTCCAACCCCGTAGAATTcaaca                >  1:189120/1‑150 (MQ=21)                                                                                                                                          cTGTTCTGGCCGCTTCGCGGGTTTACCCGCGAAAGGGTCAGCACAGGCAACACCTCCACCCAGCCATGCCCCAAAAGAATGACCTGATGAATTCTTTTCTCGGCACTCTCCACCGTCTCTGTCCTCCAACCCCGTAGAATTCAACAAccc            >  2:205725/1‑150 (MQ=255)                                                                                                                                                tGGCCGCTTCGCGGGTTTACCCGCGAAAGGGTCAGCACAGGCAACACCTCCACCCAGCCATGCCCCAAAAGAATGACCTGATGAATTCTTTTCTCGGCACTCTCCACCGTCTCTGTCCTCCAACCCCGTAGAATTCAACAACCCccacca      >  2:1281936/1‑150 (MQ=255)                                                                                                                                                  gCCGCTTCGCGGGTTTACCCGCGAAAGGGTCAGCACAGGCAACACCTCCACCCAGCCATGCCCCAAAAGAATGACCTGATGAATTCTTTTCTCGGCACTCTCCACCGTCTCTGTCCTCCAACCCCGTAGAATTCAACAACCCCCACCACg    >  2:662840/1‑150 (MQ=255)                                                                                                                                                    cGCTTCGCGGGTTTACCCGCGAAAGGGTCAGCACAGGCAACACCTCCACCCAGCCATGCCCCAAAAGAATGACCTGATGAATTCTTTTCTCGGCACTCTCCACCGTCTCTGTCCTCCAACCCCGTAGAATTCAACAACCCCCACCACggg  >  2:123366/1‑150 (MQ=255)                                                                                                                                                      |                                                                                                                                                    AGCAGCGAGATTGCCCCTTGGACGCTGGTGGAGGCCAATGACAAGCGCTGGGCGCGGGTGAAGGTGGTGCGCACAATCAACCAGGCGCTTGAGGCGGCGTTTGCCA‑AGCACAAGAAATAGCCGAAGGTGAGGTTGCCTGTTCTGGCCGCTTCGCGGGTTTACCCGCGAAAGGGTCAGCACAGGCAACACCTCCACCCAGCCATGCCCCAAAAGAATGACCTGATGAATTCTTTTCTCGGCACTCTCCACCGTCTCTGTCCTCCAACCCCGTAGAATTCAACAACCCCCACCACGGG  >  NC_002947/1955094‑1955389

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑