Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	2,407,899	G→T	15.2%	Q113H (CAG→CAT) ‡	alaA →	glutamate‑‑pyruvate aminotransferase AlaA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,407,899	0	G	T	15.2%	107.2 / 13.5	52	Q113H (CAG→CAT) ‡	alaA	glutamate‑‑pyruvate aminotransferase AlaA
Reads supporting (aligned to +/- strand):  ref base G (23/20);  new base T (3/5);  total (27/25)
Fisher's exact test for biased strand distribution p-value = 4.65e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.35e-01

AAGGGTATTGCGATTCCAAAGGTCTTTACTCCGCGCGTAAAGCCATCATGCAGCACTACCAGGCTCGTGGCATGCGTGATGTTACCGTGGAAGATATTTACATCGGCAATGGTGTATCGGAGCTTATCGT‑TCAGGCAATGCAGGCATTG‑CTGAACAGCGGGGACGAAATGTTGGTTCCTGCACCAGATTACCCACTCTGGACCGCGGCGGTTTCGCTTTCCAGCGGTAAAGCGGTGCATTATCTTTGCGATGAATCCTCTGACTGGTTCCCGGACCTCGATGAT  >  NC_000913/2407757‑2408040                                                                                                                                                |                                                                                                                                               atgggTATAGCGAGTCGGAAGTGCTGTAGTCCGTGCGTAAAGCCATCATGGAGCACTACCTGGCTTGTGTCATGCTTGATGTTACCGTGGAAGATATTTACATCGTCAATGGTGTATCGGAGCTTATCGT‑TCAGGCAATGCAg                                                                                                                                                <  2:630563/141‑1 (MQ=255)    ggTATTGCGATTCCAAAGGTCTTTACTCCGCGCGTAAAGCCATCATGCAGCACTACCAGGCTCGTGGCATGCGTGATGTTACCGTGGAAGATATTTACATCGGCAATGGTGTATCGGAGCTTATCGT‑TCAGGCAATGCAGGCa                                                                                                                                             >  1:921726/1‑143 (MQ=255)     gTATTGCGATTCCAAAGGTCTTTACTCCGCGCGTAAAGCCATCATGCAGCACTACCAGGCTCGTGGCATGCGTGATGTTACCGTGGAAGATATTTACATCGGCAATGGTGTATCGGAGCTTATCGT‑TAAGGCAATGCAGGCAt                                                                                                                                            >  2:620679/1‑143 (MQ=255)        ttGCGATTCCAAAGGTCTTTACTCCGCGCGTAAAGCCATCATGCAGCACTACCAGGCTCGTGGCATGCGTGATGTTACCGTGGAAGATATTTACATCGGCAATGGCGTATCGGACCTTATCGT‑TCAGGCAATGCACGCATCG‑c                                                                                                                                        >  2:207189/1‑143 (MQ=255)         tGCGATTCCAAAGGTCTTTACTCCGCGCGTAAAGCCATCATGCAGCACTACCAGGCTCGTGGCATGCGTGATGTTACCGTGGAAGATATTTACATCGGCAATGGTGTATCGGAGCTTATCGT‑TCAGGCAATGCCTGCATTG‑cc                                                                                                                                       <  1:772639/143‑2 (MQ=255)         tGCGATTCCAAAGGGCAGTACGGCGCGCGTAAAGCCAGCATGCAGCACTGCTAGGCTCGTGGCATGCGTTATGTTACCGTGGAAGATATTTACATCGGCAATGGTGTATCGGAGCTTATCGT‑TCAGGCAATGCAGGCATTG‑Ct                                                                                                                                       <  2:590931/143‑1 (MQ=255)         tGCGAGTCCAAAGGTCTTTACTCCGCGCGTAAAGCCATCATGCAGCACTACCAGGCTCGTGGCATGCGTGATGTTACCGTGGAAGATATTTACATCGGCAATGGTGTATCGGAGCTTATCGT‑TCAGGCAATGCCTGCATTG‑cc                                                                                                                                       <  1:910417/143‑2 (MQ=255)          gCGATGCCAAAGGTCTTTACTCCGCGCGTAAAGCCATCATGCAGCACTACCAGGCTCGTGGCATGCGTGATGTTACCGTGGAAGATATTTACATCGGCAATGGTGTATCGGAGCTTATCGT‑TCAGGCAATGCAGGCATTG‑CTg                                                                                                                                      <  1:964982/143‑1 (MQ=255)            gATTCCAAAGGTCTTTACTCCGCGCGTAAAGCCATCATGCAGCACTACCAGGCTCGTGGCATGCGTGATGTTACCGTGGAAGATATTTACATCGGCGATGGTGTATCGGAGCTTATCGT‑TCAGGCAATGCAGGCATTG‑CTGaa                                                                                                                                    >  1:997652/1‑143 (MQ=255)              ttCCAAAGGTCTTTACTCCGCGCGTAAAGCCATCATGCAGCACTACCAGGCTCGTGGCATGCGTGATATTACCGTGGAAGATATTTACATCGGCAATGGTGTATCGGAGCTTATCGT‑TCAGGCAATGCAGGCATTG‑CTGAACa                                                                                                                                  >  2:556754/1‑143 (MQ=255)              ttCCAAAGGTCTGTCCTCCGCGCGCAAAGCCATCATGCAGCACTACCAGGCTCGTGGCATGCGTGATGTTACCGTGGAAGATATTTACATCGGCAATGGTGTATCGGAGCTTATCGT‑TCAGGCAATGCCTGCATTGCCTGAAc                                                                                                                                   <  1:918330/143‑1 (MQ=255)               tCCAAAGGTCTTTACTCCGCGCGTAAAGCCATCATGCAGCACTACCAGGCTCGTGGCATGCGTGATGTTACCGTGGAAGATATTTACATCGGCAATGGTGTATCGGAGCTTATCGT‑TCAGGCAATGCAGGCATTG‑CTGAACAg                                                                                                                                 <  1:680905/143‑1 (MQ=255)                  aaaGGTCTTTACTCCGCGCGTAAAGCCATCATGCAGCACTACCAGGCTCGTGGCATGCGTGATGTTACCGTGGCAGATATTTACATCGGCACTGGTGTATCGGAGCTTATCGT‑TCCGGCAATGCAGGCATTG‑CTGAACAGCgg                                                                                                                              >  2:361559/1‑143 (MQ=255)                  aaaGGTCGTTGCTCCGGGCGTAAAGCCATCGTGCAGCACTACCAGGCTCGTGGCATGCGGGATGTTACCGTGGAAGATATTTACATCGGCAATGGTGTATCGGAGCTTATCGT‑TCAGGCAATGCAGGCATTG‑CTGAACAGCgg                                                                                                                              <  2:762768/143‑1 (MQ=255)                   aaGGCCTGTCCTCCCCGCGTAAAGCCATCATGCAGCACTACCAGGCTCGTGGCAGGCGTGATGTTACCGTGGAAGATATTTACATCGGCAATGGTGTATCGGAGCTTATCGT‑TCAGGCAATGCAGGCATTG‑CTGAACAGCggg                                                                                                                             <  1:178572/143‑1 (MQ=255)                     ggTCTTTACTCCGCGCGTAAAGCCATCATGCAGCACTACCAGGCTCGTGGCATGCGTGATGTTACCGTGGAAGATATTTACATCGGCAATGGTGTCTCGGAGCTTATCGT‑TCAGGCAATGCAGGCATTG‑CTGAACAGCGGGGa                                                                                                                           >  2:574602/1‑143 (MQ=255)                      gTCTTTACTCGGCGCGTAAAGCGATCATGCAGCACTACCAGGCTCGTGGCATGCGTGATGTTGCCGTGGGCGCTATTTCCATCGGCAATGGGGTATCGGAGCTTATCGT‑CCAGGCGATGGAGGCAGTG‑CTGGAGTGCGGGCAc                                                                                                                          >  2:764097/1‑143 (MQ=255)                       tcgttACTCCGCGCGTAAAGCCATCATGCAGCACTACCAGGCTCGTGGCATGCGTGATGTTACCGTGGAAGATATTTACATCGGCAATGGTGTATCGGAGCTTATCGT‑TCAGGCAATGCAGGCATTG‑CTGAACAGCGGGGACg                                                                                                                         <  2:649924/140‑1 (MQ=255)                        cTTTAAGCCGGGCGTAAAGCCATCATGCAGCACTACCAGGCTCGTGGCATGCGTGATGTTACCGTGGAAGATATTTACATCGGCAATGGTGTATCGGAGCTTATCGT‑TCAGGCAATGCAGGCATTG‑CTGAACAGCGGGGACGa                                                                                                                        <  1:730576/143‑1 (MQ=255)                              tCCGCGCGTAAAGCCATCATGCAGCACTACCAGGCTCGTGGCATGCGTGATGTTACCGTGGAAGATATTTACATCGGCAATGGTGTATCGGAGCTTATCGT‑TCAGGCAATGCAGGCATTG‑CTGAACAGCGGGGACGAAATGtt                                                                                                                  >  1:729129/1‑143 (MQ=255)                                      tagaGCCAGCATGCAGCACTCCCAGGCTCGTGGCATGCGTGATGTTACCGTGGAAGATATTTACATCGGCAATGGTGTATCGGAGCTTATCGT‑TCAGGCAATGCAGGCATTG‑CTGAACAGCGGGGACGAAATGTTGGTTCCTg                                                                                                          <  1:270178/140‑1 (MQ=255)                                      tAACGCCATCATGCAGTACGACCAGGCTCGTGGCATGCGGGATGGTACCGTGGAAGATATGTACATCGGCAATGGTGTATCGGAGCTTAGCGT‑TCAGGCAATGCAGGCATTG‑CTGAACAGCGGGGACGAAATGTTGGTTCCTg                                                                                                          <  2:308745/143‑1 (MQ=255)                                       aaaGCCATCATGCAGCACTACCAGGCTCGTGGCATGCGTGATGTTACCGTGGAAGATATTTACATCGGCAATGGTGTATCGGAGCTTATCGT‑TCAGGCAATGCAGGCATTG‑CTGAACAGCGGGGACGAAATGTTGGTTCCTGc                                                                                                         >  1:995376/1‑143 (MQ=255)                                           ccATCATGCAGCACTACCAGGCTCGTGGCATGCGTGATGTTACCGTGGAAGATATTTACATCGGCAATGGTGTATCGGAGCTTATCGT‑TCAGGCAATGCAGGCATTG‑CTGAACAGCGGGGACGAAATGTTGGTTCCTGCACCa                                                                                                     <  1:798345/143‑1 (MQ=255)                                                agtctgcaCGAGCAGGCTCGTGGCATGCGTGATGGTACCGTGGAAGAGATGTACATCGGCAATGGCGTCTGGTACCTTATCCTATCA‑TCATTGTATGCATTG‑CTGAACAGCGGGGACGAAATGTTGGTTCCTGCACCAGATTa                                                                                                <  2:392245/138‑1 (MQ=255)                                                  gcagcaCTACCCGGCTCGTGGCATGCGGGATGTTACCGTGGAAGATATTTACAGCGGCAATGGTGTATCGGAGCTTATCGT‑TCAGGCAATGCAGGCATTG‑CTGAACAGCGGGGACGAAATGTTGGTTCCTGCACCAGATTAcc                                                                                              <  2:295189/143‑1 (MQ=255)                                                         tACCAGGCTCTTGGCTTGCGTGATGTTACCGTGGAAGATATTTACATCGGCAATGGTGTATCGGAGCTTATCGT‑TCAGGCAATGCATGCATTG‑CTGAACAGCGGGGACGAAATGTTGGTTCCTGCACCAGATTACCCACTCTg                                                                                       <  2:440107/143‑1 (MQ=255)                                                            caagCTCGTGGCATGCGTGATGTTACCGTGGAAGATATTTACATCGGCAATGGTGTATCGGAGCTTATGGT‑TAAGGCAACACAGGCATTG‑CTGAACAGCGGGGGCGAAATGTTGGATGCGGGAGCCGATTACCCACACCGGag                                                                                    >  2:311134/4‑142 (MQ=255)                                                                            gTGATGTTACCGTGGAAGATATTTACATCGGCAATGGTGTATCGGAGCTTATCGT‑TCAGGCAATGCAGGCATTG‑CTGAACAGCGGGGACGAAATGTTGGTTCCTGCACCAGATTACCCACTCTGGACCGCGGCGGTTTCGCtt                                                                    >  1:797711/1‑143 (MQ=255)                                                                              gtgtgtACCGTGTAAGATATCTACATCGGGAAGGGTGGATGGGAGCTTATCGT‑TCAGGCAATGCAGGCATTG‑CGGAACAGCGGGGACGAAATGTTGGTTGCTGCACCAGAGTACCCACTCTGGACCGCGGCGGTTTCGCTTTc                                                                  <  2:339747/138‑1 (MQ=255)                                                                                 gTTACCGTGGAAGATATTTACATCGGCAAGGGTGTATCGGAGCTTATCGT‑TCAGGCAATGCAGGCATTG‑CTGAACAGCGGGGACGAAATGTTGGTTCCTGCACCAGATTACCCACTCTGGACCGCGGCGGTTTCGCTTTCCAg                                                               <  1:255140/143‑1 (MQ=255)                                                                                   gaCCGTGTAACATATTTACATGGGCAGTGGTGTATCGGAGCTTATCGT‑TCAGGCACTGCAGGCATTG‑CTGAACAGCGGGGACGAAATGTTGGTTCCTGCACCAGATTACCCACTCTGGACCGCGGCGTTTTCGCTTTCCAGCg                                                             <  2:102097/142‑1 (MQ=255)                                                                                    aCCGTGGAAGATATTTACATCGGCAATGGTGTATCGGAGCTTATCGT‑TCAGGCAATGCAGGCATTG‑CTGAACAGCGGGGACGAAATGTTGGTTCCTGCACCAGATTACCCACTCTGGACCGCGGCGGTTTCGCTTTCCAGCgg                                                            >  1:559033/1‑143 (MQ=255)                                                                                     ccGTGGAAGATATTTACATCGGCAATGGTGTATCGGAGCTTATCGT‑TCAGGCAATGCAGGCATTG‑CTGAACAGCGGGGACGAAATGTTGGTTCCTGCACCAGATTACCCACTCTGGACCGCGGCGGTTTCGCTTTCCAGCGGt                                                           >  1:728154/1‑143 (MQ=255)                                                                                      cGTGGAAGATATTTACATCGGCAATGGTGTATCGGAGCTTATCGT‑TCAGGCAATGCAGTCATTG‑CTGAACAGCGGGGACGAAATGTTGGTTCCTGCACCAGATTACCCACTCTGGACCGCGGCGGTTTCGCTTTCCAGCGGTa                                                          >  1:530571/1‑143 (MQ=255)                                                                                                atTTGCATCTGCAATCTGGTATCGGAGCTTGTCGT‑TCATGTATGTCAGGCATTG‑CTGAACAGCGGGGACGAAATGTTGGTTCCTGCATTAGATCACCCACTCTGGTCCTCGGCGGTTTCGCTTTTCACCGGTAAAGCGGTGCa                                                <  2:837790/143‑1 (MQ=255)                                                                                                  ttACATCGGCAATGGTGTATCGGAGCTTATCGT‑TCAGGCAATGCAGGCATTG‑CTGAACAGCGGGGACGAAATGTTGGTTCCTGCACCAGATTACCCACTCTGGACCGCGGCGGTTTCGCTTTCCAGCGGTAAAGCGGTGCAtt                                              >  1:45420/1‑143 (MQ=255)                                                                                                  ttACATCGGCAATGGTGTATCGGAGCTTATCGT‑TCAGGCAATGCAGACATTC‑ATGAACATGTGGGCCGACCCGTCGGGCCCGTCACCAGATTACCCACTCTGGACCGCGGCGGTTTCGCTTTCCAGCGGTAACGCGCTGCAta                                              >  1:1101756/1‑142 (MQ=255)                                                                                                  ttACACCGGCAATGGTGTATCGGAGCTTATCGT‑GCAGGCAATGCAGGCATTG‑CTGAACAGCGGGGACGAAATGTTGGTTCCTGCACCAGATTACCCACTCTGGACCGCGGCGGTTTCGCTTTCCAGCGGTAAAGCGGTGCAtt                                              <  1:598203/143‑1 (MQ=255)                                                                                                  tcacgtCGGCAATGGTGTATCGGGGCTTATCGT‑TCAGGCAATGCAGGCATTG‑CTGAACAGCGGGGACGAAATGTTTGTTCCTGCACCAGATTACCCACTCTGGACCGCGGCGGTTTCGCTTTCCAGCGGTAAAGCGGTGCAtt                                              <  2:347403/138‑1 (MQ=255)                                                                                                   cataccGGCAGTTGTGTGACGGAGCTTATCGT‑TCAGGCAATGCAGGCATTG‑CTGAACAGCGGGGACGAAATGTTGGTTCCTGCACCAGATTACCCACTCTGGACCGCGGCGGTTTCGCTTTCCAGCGGTAAAGCTGTGCATTa                                             <  2:1065436/138‑1 (MQ=255)                                                                                                        cGGCAATGGTGTATCGGAGCTTATCGT‑TCAGGCAATGCAGGCATTG‑CTGAACAGCGGGGACGAAATGTTGGTTCCTGCACCAGATTACCCACTCTGGACCGCGGCGGTTTCGCTTTCCAGCGGTAAAGCGGTGCATTATCttt                                        >  2:901796/1‑143 (MQ=255)                                                                                                         gtcAATGGTGTAGCGGAGCTTATCGT‑TCAGGCAATGCAGGCATTG‑TTGAACAGCGGGGACGAAATGTTGGTTCCTGCACCAGATTACCCACTCTGGACCGCGGCGGTTTCGCTTTCCAGCGGTAAAGCGGTGCATTATCTTTg                                       <  1:445490/141‑1 (MQ=255)                                                                                                          gCAATGGTGTATCGGAGCTTATCGT‑TCAGGCAATGCAGGCATTG‑CTGAACAGCGGGGACGAAATGTTGGTTCCTGCACCAGATTACCCACTCTGGACCGCGGCGGTTTCGCTTTCCCGCGGTAACGCGGTGCATTATCtttcc                                      >  2:995760/1‑141 (MQ=255)                                                                                                                        gAGCTTAACGT‑TCAGGCAATGCAGGCATTG‑CTGAACAGCGGGGACGAAATGTTGGTTCCTGCACCAGATTACCCACTCTGGACCGCGGCGGTTTCGCTTTCCAGCGGTAAAGCGGTGCATTATCTTTGCGATGAATCCTCTGa                        <  1:264205/143‑1 (MQ=255)                                                                                                                                 gT‑TCA‑GCAATGCCTGCATTGCCTGAACAGCGGGGACGAAATGTTGGTTCCTGCACCAGATTACCCACTCTGGACCGCGGCGGTTTCGCTTTCCAGCGGTAAAGCGGTGCATTATCTTTGCGATGAATCCTCTGACTGGTTccc               >  1:604104/1‑143 (MQ=255)                                                                                                                                      cagCAATGCCTGCATTGCCTGAACGGCGGGGACGAAATGTTGGTTCCTGCACCAGATTACCCACTCTGGACCGCGGCGGTTTCGCTTTCCAGCGGTAAAGCGGTGCATTATCTTTGCGGTGAATCCTCTGACTGGTTCCCGGa            >  1:817684/3‑143 (MQ=255)                                                                                                                                      cagCAATGCCTGCATTGCCTGAACAGCGGGGACGAAATGTTGGTTCCTGCACCAGATTACCCACTCTGGACCGCGGCGGTTTCGCTTTCCAGCGGTAAAGCGGTGCATTCTCTTTGCGATCAATCCTCTGCATGGGTCCCGGa            >  2:157254/3‑143 (MQ=255)                                                                                                                                      aGGCAATGCAGGCATTG‑CTGAACAGCGGGGACGAAATGTTGGTTCCTGCACCAGATTACCCACTCTGGACCGCGGCGGTTTCGCTTTCCAGCGGTAAAGCGGTGCATTATCTTTGCGCTGAATCCTCTGACTGGTTCCAGGAc           >  2:203612/1‑143 (MQ=255)                                                                                                                                       ggCAATGCAGGCATTG‑CTGAACAGCGGGGACGAAATGTTGGTTCCTGCACCAGATTACCCACGCTGGACCGCGGCGGTTTCGCTTTCCAGCGGTCAAGCGGTGCATTATCTTTGCGATGAATCCTCTGACTGGTTCCCGGccc          >  2:559924/1‑143 (MQ=255)                                                                                                                                              cAGGCATTG‑CTGAACAGCGGGGACGAAATGTTGGTTCCTGCACCAGATTACCCACTCTGGACCGCGGCGGTATCGCTTTCCCGCGGGAAAGCGGTGCATTATCTTCGCGATGAATCCTCTGACTGGCTCCCGGACCTCgatgc   >  2:148984/1‑142 (MQ=255)                                                                                                                                               aGGCATTG‑CTGAACAGCGGGGACGAAATGTTGGTTCCTGCAGTAGATTACCCACTCTGGACCGCGGCGGTTTCGCTTTCCAGCGGTAAAGCGGTGCATTATCTTTGCGATGTATCCTCTGACTGGTTCCCGGACCTCgatgat  >  1:701512/1‑143 (MQ=255)                                                                                                                                               aGGCATTG‑CTGAACAGCGGGGACGAAATGTTGGTTCCTGCACCAGATTACCCACTCTGGACCGCGGCGGGTTCGCTTTCCAGCGGCAAAGCGGTGCATTACCTTTGCGACGAATCCTCTGACCGCTTCCCCGACCTCgatgat  >  2:1108539/1‑143 (MQ=255)                                                                                                                                                |                                                                                                                                               AAGGGTATTGCGATTCCAAAGGTCTTTACTCCGCGCGTAAAGCCATCATGCAGCACTACCAGGCTCGTGGCATGCGTGATGTTACCGTGGAAGATATTTACATCGGCAATGGTGTATCGGAGCTTATCGT‑TCAGGCAATGCAGGCATTG‑CTGAACAGCGGGGACGAAATGTTGGTTCCTGCACCAGATTACCCACTCTGGACCGCGGCGGTTTCGCTTTCCAGCGGTAAAGCGGTGCATTATCTTTGCGATGAATCCTCTGACTGGTTCCCGGACCTCGATGAT  >  NC_000913/2407757‑2408040

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑