Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_014034	2,185,841	+C	92.5%	intergenic (+114/‑391)	mtlK → / → RCAP_rcc02028	mannitol 2‑dehydrogenase/FeoA family protein

Read alignment evidence...
	seq id	position		change	freq	score	reads	annotation	genes	product
*	NC_014034	2,185,841	1	.→C	92.5%	5.4 ‑4.0 ‑1.7	53	intergenic (+114/‑391)	mtlK/RCAP_rcc02028	mannitol 2‑dehydrogenase/FeoA family protein
Reads supporting (aligned to +/- strand):  new base (7/42):  ref base (3/1):  total (10/43)
Fisher's exact test strand distribution p-value = 1.83e-02
Kolmogorov-Smirnov test that lower quality scores support polymorphism than reference p-value = 1.95e-02

GCCCCGGAACAGGCGGCCCCGCTCCCTCCCGGGCGGGGCCGCCTGATGTGCAAAGCGGTTTCGCCTCGGCGGTGCCGAGGCGACCCTGC..GGGGGCT.CCG.CCCC.GCACCCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTT.GCCCCGAAGGCCTTGTTTTTGATGGCACAAGAAACGCCGAACCGCCC  >  NC_014034/2185743‑2185933                                                                                                       |                                                                                               gCCCCGGAACAGGCGGCCCCGCTCCCTCCCGGGCGGGGCCGCCTGATGTGCAAAGCGGTTTCGCCTCGGCGGTGCCGAGGCGACCCTGC..GGGGGCT.CCG.cc                                                                                              <  1:2830816/101‑1 (MQ=255)    ccGGAACAGGCGGCCCCGCTCCCTCCCGGGCGGGGCCGCCTGATGTGCAAAGCGGTTTCGCCTCGGCGGTGCCGAGGCGACCCTGC..GGGGGCT.CCG.ccccc                                                                                           <  1:2436781/101‑2 (MQ=255)     cGGAACAGGCGGCCCCGCTCCCTCCCGGGCGGGGCCGCCTGATGTGCAAAGCGGTTTCGCCTCGGCGGTGCCGAGGCGACCCTGC..GGGGGGG.GCG.cccccc                                                                                          >  2:4145332/1‑99 (MQ=255)     cGGAACAGGCGGCCCCGCTCCCTCCCGGGCGGGGCCGCCTGATGTGCAAAGCGGTTTCGCCTCGGCGGTGCCGAGGCGACCCTGC..GGGGGCT.CCG.cccccg                                                                                          <  2:3877003/101‑3 (MQ=255)          cAGGCGGCCCCGCTCCCTCCCGGGCGGGGCCGCCTGATGTGCAAAGCGGTTTCGCCTCGGCGGTGCCGAGGCGACCCTGC..GGGGGCT.CCGCCCCC.GCAccc                                                                                     <  2:3377848/101‑1 (MQ=255)            ggcggcCCCGCTCCCTCCCGGGCGGGGCCGCCTGATGTGCAAAGCGGTTTCGCCTCGGCGGTGCCGAGGCGACCCTGC..GGGGGCT.CCGCCCCC.GCAccccc                                                                                   <  1:2555353/101‑1 (MQ=255)             gcggcCCCGCTCCCTCCCGGGCGGGGCCGCCTGATGTGCAAAGCGGTTTCGCCTCGGCGGTGCCGAGGCGACCCTGC..GGGGGCT.CCGCCCCC.GCAcccccg                                                                                  <  1:3285711/101‑2 (MQ=255)             gcggcCCCGCTCCCTCCCGGGCGGGGCCGCCTGATGTGCAAAGCGGTTTCGCCTCGGCGGTGCCGAGGCGACCCTGC..GGGGGCT.CCGCCCCC.GCAcccccg                                                                                  <  1:557377/101‑2 (MQ=255)             gcggcCCCGCTCCCTCCCGGGCGGGGCCGCCTGATGTGCAAAGCGGTTTCGCCTCGGCGGTGCCGAGGCGACCCTGC..GGGGGCT.CCGCCCCC.GCAcccccg                                                                                  <  1:4257584/101‑2 (MQ=255)               ggcCCCGCTCCCTCCCGGGCGGGGCCGCCTGATGTGCAAAGCGGTTTCGCCTCGGCGGTGCCGAGGCGACCCTGC..GGGGGGG.GCG.CCCC.CCCccccccccc                                                                               >  2:1933330/1‑98 (MQ=255)                gcCCCGCTCCCTCCCGGGCGGGGCCGCCTGATGTGCAAAGCGGTTTCGCCTCGGCGGTGCCGAGGCGACCCTGC..GGGGGCT.CCGCCCCC.GCAcccccggcg                                                                               <  2:805735/101‑5 (MQ=255)                     gCTCCCTCCCGGGCGGGGCCGCCTGATGTGCAAAGCGGTTTCGCCTCGGCGGTGCCGAGGCGACCCTGCG.GGGGGGG.CCG.CCCC.CCCCCCCCCCGccgggt                                                                          >  2:319873/1‑96 (MQ=255)                     gCTCCCTCCCGGGCGGGGCCGCCTGATGTGCAAAGCGGTTTCGCCTCGGCGGTGCCGAGGCGACCCTGC..GGGGGCT.CCGCCCCC.GCA.CCCCCGGCGGAttt                                                                         >  2:2888930/1‑101 (MQ=37)                      ttccctcccGGGCGGGGCCGCCTGATGTGCAAAGCGGTTTCGCCTCGGCGGTGCCGAGGCGACCCTGC..GGGGGCT.CCGCCCCC.GCA.CCCCCGGCGTATTTa                                                                        <  1:2073907/100‑1 (MQ=37)                      ctccctccCGGGCGGGGCCGCCTGATGTGCAAAGCGGTTTCGCCTCGGCGGTGCCGAGGCGACCCTGC..GGGGGCT.CCGCCCCC.GCA.CCCCCGGCGTATTTa                                                                        <  2:225053/101‑1 (MQ=255)                      ctccctccCGGGCGGGGCCGCCTGATGTGCAAAGCGGTTTCGCCTCGGCGGTGCCGAGGCGACCCTGC..GGGGGCT.CCGCCCCC.GCA.CCCCCGGCGTATTTa                                                                        <  1:1990407/101‑1 (MQ=255)                       tccctcccGGGCGGGGCCGCCTGATGTGCAAAGCGGTTTCGCCTCGGCGGTGCCGAGGCGACCCTGC..GGGGGCT.CCGCCCCC.GCA.CCCCCGGCGTATTTAt                                                                       <  2:2022875/101‑1 (MQ=255)                        ccctcccGGGCGGGGCCGCCTGATGTGCAAAGGGGTTTCGCCTCGGCGGTGCCGAGGCGACCCTGC..GGGGGCT.CCGCCCCC.GCA.CCCCCGGCGTATTTATc                                                                      <  1:1286189/101‑1 (MQ=25)                         cctcccGGGCGGGGCCGCCTGATGTGCAAAGCGGTTTCGCCTCGGCGGTGCCGAGGCGACCCTGC..GGGGGCT.CCGCCCCC.GCA.CCCCCGGCGTATTTATcc                                                                     <  1:3065749/101‑1 (MQ=255)                         cctcccGGGCGGGGCCGCCTGATGTGCAAAGCGGTTTCGCCTCGGCGGTGCCGAGGCGACCCTGC..GGGGGCT.CCGCCCCC.GCA.CCCCCGGCGTATTTATcc                                                                     >  1:1734431/1‑101 (MQ=255)                             ccGGGCGGGGCCGCCTGATGTGCAAAGCGGTTTCGCCTCGGCGGTGCCGAGGCGACCCTGC..GGGGGCT.CCGCCCCC.GCA.CCCCCGGCGTATTTATCCCAAg                                                                 <  1:1781537/101‑1 (MQ=255)                              cgggcgggGCCGCCTGATGTGCAAAGCGGTTTCGCCTCGGCGGTGCCGAGGCGACCCTGC..GGGGGCT.CCGCCCCC.GCA.CCCCCGGCGTATTTATCCCAAGa                                                                <  2:697691/101‑1 (MQ=255)                               gggcgggGCCGCCTGATGTGCAAAGCGGTTTCGCCTCGGCGGTGCCGAGGCGACCCTGC..GGGGGGT.CCC.CCCC.CCCCCCCCCGGCGCCTTTTTccccaaaa                                                               >  1:3658266/1‑96 (MQ=255)                                ggcgggGCCGCCTGATGTGCAAAGCGGTTTCGCCTCGGCGGTGCCGAGGCGACCCTGC..GGGGGCT.CCGCCCCC.GCA.CCCCCGGCGCATTTATCCCCAGaaa                                                              >  2:41047/1‑101 (MQ=25)                                  cgggGCCGCCTGATGTGCAAAGCGGTTTCGCCTCGGCGGTGCCGAGGCGACCCTGC..GGGGGCT.CCGCCCCC.GCA.CCCCCGGCGTATTTATCCCAAGaaaaa                                                            <  1:3124769/101‑1 (MQ=255)                                   ggggCCGCCTGATGTGCAAAGCGGTTTCGCATCGGCGGTGCCGAGGCGACCCTGCG.GGGGGCC.CCC.CCCC.CCCCCCCCCGCGGCTTTTTTCCCAAAaaaaa                                                            >  2:2583137/1‑101 (MQ=255)                                    gggCCGCCTGATGTGCAAAGCGGTTTCGCCTCGGCGGTGCCGAGGCGACCCTGC..GGGGGCT.CCGCCCCC.GCA.CCCCCGGCGTATTTATCCCAAGAAAAagc                                                          <  1:2016186/101‑1 (MQ=255)                                     ggCCGCCTGATGTGCAAAGCGGTTTCGCCTCGGCGGTGCCGAGGCGACCCTGC..GGGGGCT.CCGCCCCC.GCA.CCCCCGGCGTATTTATCCCAAGAAAAagca                                                         <  1:1508812/101‑1 (MQ=255)                                          ccTGATGTGCAAAGCGGTTTCGCCTCGGCGGTGCCGAGGCGACCCTGC..GGGGGCT.CCGCCCCC.GCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGc                                                    <  1:1784125/101‑1 (MQ=255)                                           cTGATGTGCAAAGCGGTTTCGCCTCGGCGGTGCCGAGGCGACCCTGC..GGGGGCT.CCGCCCCC.GCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCt                                                   >  2:1106948/1‑101 (MQ=255)                                           cTGATGTGCAAAGCGGTTTCGCCTCGGCGGTGCCGAGGCGACCCTGC..GGGGGCT.CCG.CCCC.CGCCCCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCt                                                   <  1:64465/101‑1 (MQ=255)                                            tGATGTGCAAAGCGGTTTCGCCTCGGCGGTGCCGAGGCGACCCTGC..GGGGGCT.CCGCCCCC.GCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCtt                                                  <  2:4144781/101‑1 (MQ=255)                                                gtgCAAAGCGGTTTCGCCTCGGCGGTGCCGAGGCGACCCTGC..GGGGGCT.CCGCCCCC.GCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTT.Gccc                                             <  1:639144/101‑1 (MQ=255)                                                  gCAAAGCGGTTTCGCCTCGGCGGTGCCGAGGCGACCCTGC..GGGGGCT.CCGCCCCC.GCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTT.GCCCCg                                           <  2:261506/101‑1 (MQ=255)                                                    aaaGCGGTTTCGCCTCGGCGGTGCCGAGGCGACCCTGC..GGGGGGC.CCG.CCCC.CCCCCCCCCGGCGGATTTATCCCCAGAAAAAACAGCGGCTTCGccccca                                          >  1:4253265/1‑99 (MQ=255)                                                     aaGCGGTTTCGCCTCGGCGGTGCCGAGGCGACCCTGC..GGGGGCT.CCGCCCCC.GCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTT.GCCCCGAAg                                        <  2:3113970/101‑1 (MQ=255)                                                        cGGTTTCGCCTCGGCGGTGCCGAGGCGACCCTGC..GGGGGCT.CCGCCCCC.GCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTT.GCCCCGAAGGcc                                     <  1:4225437/101‑1 (MQ=255)                                                        cGGTTTCGCCGCGGCGGTGCCGAGGCGACCCTGC..GGGGGCT.CCGCCCCC.GCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTT.GCCCCGAAGGcc                                     <  2:2243179/101‑1 (MQ=37)                                                           tttCGCCTCGGCGGTGCCGAGGCGACCCTGC..GGGGGCT.CCGCCCCC.GCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTT.Tccccccagggcctt                                  >  1:3885566/1‑91 (MQ=21)                                                              cGCCTCGGCGGTGCCGAGGCGACCCTGC..GGGGGCT.CCGCCCCC.GCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTT.GCCCCGAAGGCCTTGttt                               <  2:1924428/101‑1 (MQ=255)                                                               gCCTCGGCGGTGCCGAGGCGACCCTGC..GGGGGCT.CCGCCCCC.GCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTT.GCCCCGAAGGCCTTGtttt                              <  2:2471362/101‑1 (MQ=255)                                                                ccTCGGCGGTGCCGAGGCGACCCTGC..GGGGGCT.CCGCCCCC.GCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTT.GCCCCGAAGGCCTTGttttg                             <  2:1553172/101‑2 (MQ=37)                                                                  tCGGCGGTGCCGAGGCGACCCTGCGGGGGGGCC.CCC.CCCC.CCCCCCCCCCGCGGTTTTTTCCAAAAAAAAAAAAGGGGTTT.CCCCCCCGGCCCTTGttttt                             >  2:2844254/1‑101 (MQ=255)                                                                      cggTGCCGAGGCGACCCTGC..GGGGGCT.CCGCCCCC.GCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTT.GCCCCGAAGGCCTTG.TTTTGATGGca                      <  1:2978375/101‑1 (MQ=37)                                                                      cggTGCCGAGGCGACCCTGC..GGGGGCT.CCGCCCCC.GCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTT.GCCCCGAAGGCCTTG.TTTTGATGGca                      <  2:166896/101‑1 (MQ=37)                                                                        gTGCCGAGGCGACCCTGC..GGGGGCT.CCGCCCCC.GCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTT.GCCCCGAAGGCCTTG.TTTTGATGGcaca                    <  1:2327872/101‑1 (MQ=37)                                                                          gCCGAGGCGCCCCTGC..GGGGGCT.CCGCCCCC.GCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTT.GCCCCGAAGGCCTTG.TTTTGATGGCACAAg                  <  1:403761/101‑1 (MQ=25)                                                                           cctgtgCGTCCTTGC..GGGGGCTCCCC.CCCC.GCA.CCCCCGGCTTATTTATCCCAAGTAAATGCAGCGGCTT.GCCCCTAAGGCCTTG.TTTTGATGGCACAAGa                 <  2:3569230/96‑1 (MQ=16)                                                                            cGAGGCGACCCTGC..GGGGGCT.CCGCCCCC.GCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTT.GCCCCGAAGGCCTTG.TTTTGATGGCACAAGaa                <  1:2699962/101‑1 (MQ=37)                                                                             gAGGCGACCCTGC..GGGGGCT.CCGCCCCC.GCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTT.GCCCCGAAGGCCTTG.TTTTGATGGCACAAGaaa               <  1:4188859/101‑1 (MQ=37)                                                                              aGGCGACCCTGC..GGGGGCT.CCGCCCCC.GCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTT.GCCCCGAAGGCCTTG.TTTTGATGGCACAAGAAAc              <  2:2249634/101‑1 (MQ=37)                                                                                gCGTCCATGC..GGGGGCT.CCGCCCCC.GCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTT.GCCCCGAAGGCCTTG.TTTTGATGGCACAAGAAACGc            <  1:736742/101‑1 (MQ=25)                                                                                gCGACCCTGC..GGGGGCT.CCGCCCCC.GCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTT.GCCCCGAAGGCCTTG.TTTTGATGGCACAAGAAACGc            <  2:1172199/101‑1 (MQ=37)                                                                                 cGACCCTGC..GGGGGCT.CCGCCCCC.GCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTT.GCCCCGAAGGCCTTG.TTTTGATGGCACAAGAAACGcc           <  1:423110/101‑1 (MQ=37)                                                                                  gACCCTGC..GGGGGCT.CCGCCCCC.GCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTT.GCCCCGAAGGCCTTG.TTTTGATGGCACAAGAAACGCCg          <  2:287363/101‑1 (MQ=37)                                                                                   aCCCTGC..GGGGGCT.CCGCCCCC.GCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTT.GCCCCGAAGGCCTTG.TTTTGATGGCACAAGAAACGCCGa         <  2:898529/101‑1 (MQ=37)                                                                                    cccTGC..GGGGGCT.CCGCCCCC.GCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTT.GCCCCGAAGGCCTTG.TTTTGATGGCACAAGAATCGCCGaa        <  2:917415/101‑1 (MQ=25)                                                                                    cccTGC..GGGGGCT.CCGCCCCC.GCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTT.GCCCCGAAGGCCTTG.TTTTGATGGCACAAGAAACGCCGaa        <  1:505184/101‑1 (MQ=37)                                                                                      cTGC..GGGGGCT.CCGCCCCC.GCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTT.GCCCCGAAGGCCCTG.TTTTGATGGGACAAGAAAAGCCGaaac      >  2:3504476/1‑99 (MQ=21)                                                                                       tGC..GGGGGCT.CCGCCCCC.GCA.CCCCCGGCGTATTTATCCCAAGGAAAAGCAGCGGCTT.GCCCCGAAGGCCTTG.TTTTGATGGCACAAGAAACGCCGAACCg     <  2:1059854/101‑1 (MQ=25)                                                                                        gC..GGGGGCT.CCG.CCCCAGCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTT.GCCCCGAAGGCCTTG.TTTTGATGGCACAAGAAACGCCGAACCGc    >  2:1030281/1‑101 (MQ=37)                                                                                         c..GGGGGCT.CCGCCCCC.GCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTT.GCCCCGAAGGCCTTG.TTTTGATGGCACAAGAAACGACGAACCGcc   >  2:778582/1‑101 (MQ=25)                                                                                            gggggCT.CCGCCCCC.GCA.CCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTT.GCCCCGAAGGCCTTG.TTTTGATGGCACAAGAAACGCCGAACCGccc  <  1:2844461/101‑1 (MQ=37)                                                                                                       |                                                                                               GCCCCGGAACAGGCGGCCCCGCTCCCTCCCGGGCGGGGCCGCCTGATGTGCAAAGCGGTTTCGCCTCGGCGGTGCCGAGGCGACCCTGC..GGGGGCT.CCG.CCCC.GCACCCCCCGGCGTATTTATCCCAAGAAAAAGCAGCGGCTT.GCCCCGAAGGCCTTGTTTTTGATGGCACAAGAAACGCCGAACCGCCC  >  NC_014034/2185743‑2185933 Base quality scores:  ATCG  < 3 ≤  ATCG  < 16 ≤  ATCG  < 26 ≤  ATCG  < 33 ≤  ATCG  < 41 ≤  ATCG