Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	349,692	A→G	intergenic (+120/‑320)	prpB → / → prpC	2‑methylisocitrate lyase/2‑methylcitrate synthase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	349,692	0	A	G	86.8%	100.3 / 9.5	68	intergenic (+120/‑320)	prpB/prpC	2‑methylisocitrate lyase/2‑methylcitrate synthase
Reads supporting (aligned to +/- strand):  ref base A (7/2);  new base G (24/35);  total (31/37)
Fisher's exact test for biased strand distribution p-value = 6.87e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.82e-01

GACAGCCGATGCCTGATGCGTCGCTGACGCGACTTATCAGGCCTACGAGGTGCACTGAACTGTAGGTCGGATAAGACGGATGGCGTCGCATCCGACAACCGATGCCTGATGCGCCGCTGACGTGACTTATCAGGCCTACGGGGTGCACTGAACTGTAGGTCGGATAAGACGCATAGCGTCGCATCC  >  NC_000913/349595‑349780                                                                                                  |                                                                                         gACAGCCGATGCCTGATGCGTCGCTGACGCGACTTATCAGGCCTACGAGGTGCACTGAACTGTAGGTCGGATAAGACGCATGGCGTCGCATCCGACAAcc                                                                                        >  1:504418/1‑100 (MQ=255)   cAGCCGATGCCTGATGCGTCGCTGACGCGACTTATCAGGCCTACGAGGTGCACTGAACTGTAGGTCGGATAAGACGGATGGCGTCGCATCCGACAGCCGa                                                                                      <  1:201320/100‑1 (MQ=255)     gCCGATGCCTGATGCGTCGCTGACGCGACTTATCAGGCCTAGGAGGTGCACTGAACTGTAGATCGGATAAGACGGATGGCGTCGCATCCGACAGCCGATg                                                                                    >  1:991013/1‑100 (MQ=255)     gCCGATGCCTGATGCGTCGCTGACGCGACTTATCAGGCCTACGAGGTGCACTGAACTGTAGGTCGGATAAGACGGATGGCGTCGCATCCGACAGCCGATg                                                                                    >  1:1515425/1‑100 (MQ=255)     gCCGATGCCTGATGCGTCGCTGACGCGACTTATCAGGCCTACGAGGTGCACTGAACTGTAGGTCAGATAAGACGGATGGCGTCGCATCCGACAGCCGATg                                                                                    >  2:964616/1‑100 (MQ=255)       cGATGCCTGATGCGTCGCTGACGCGACTTATCACGCCTACGAGGTGCACTGAACTGTAGGTCGGATAAGACGGATGGCGTCGCATCCGACCGCCGATGcc                                                                                  >  1:1197965/1‑100 (MQ=255)         aTGCCTGATGCGTCGCTGACGCGACTTATCAGGCCTACGAGGTGCACTGAACTGTAGGTCGGATAAGACGGATGGCGTCGCATCCGACAGCCGATGCCTg                                                                                <  2:1638192/100‑1 (MQ=255)          tGCCTGATGCGTCGCTGACGCGACTTATCAGGCCTACGAGGTGCACTGAACTGTAGGTCGGATAAGACGGATGGCGTCGCATCCGACAGCCGATGCCTGa                                                                               >  1:935044/1‑100 (MQ=255)            ccTGATGCGTCGCTGACGCGACTTATCAGGCCTACGAGGTGCACTGAACTGTAGGTCGGATAAGACGGATGGCGTCGCATCCGACAGCCGATGCCTGATg                                                                             <  2:1152167/100‑1 (MQ=255)            ccTGATGCGTCGCTGACGCGACTTATCAGGCCTACGAGGTGCACTGAACTGTAGGTCGGATAAGACGGATAGCGTCGCATCCGACAGCCGATGCCTGATg                                                                             >  2:506482/1‑100 (MQ=255)             cTGATGCGTCGCTGACGCGACTTATCATGCCTACGAGGTGCACTGAACTGTAGGTCGGATAAGACGGATGGCGTCGCATCTGACAGCCGATGCCTGATg                                                                             <  1:909046/99‑1 (MQ=255)             cTGATGCGTCGCTGACGCGACTTATCAGGCCTACGAGGTGCACTGAACTGTAGGTCGGATAAGACGCATGGCGTCGCATCCGACAACCGATGCCtgctgc                                                                            >  2:1725123/1‑100 (MQ=255)              tGATGCGTCGCTGACGCGACTTATCAGGCCTACGAGGTGCACTGAACTGTAGGTCGGATAAGACGGATGGCGTCGCATCCGACAGCCGATGCCTGATgcg                                                                           >  2:427090/1‑100 (MQ=255)                aTGCGTCGCTGACGCGACTTATCAGGCCTACGAGGTGCACTGAACTGTAGGTCGGATAAGACGGATGGCGTCGCATCCGACAGCCGATGCCTGATgcgtc                                                                         <  2:1372949/100‑3 (MQ=255)                  gCGTCGCTGACGCGACTTATCAGGCCTACGAGGTGCACTGAACTGTAGGTCGGATAAGACGAATGGCGACGCATACGACAACCGATGCCTGATGcgtcgc                                                                       >  2:1515179/1‑100 (MQ=14)                          gACGCGACTTATCAGGCCTACGAGGTGCACTGAACTGTAGGTCGGATAAGACGGATGGCGTCGCATCCGACAGCCGATGCCTGATGCGTCGCTGACGCGa                                                               <  2:1021703/100‑1 (MQ=14)                           aCGCGACTTATCAGGCCTACGAGGTGCACTGAACTGTAGGTCGGATAAGACGGATGGCGTCGCATCCGACAGCCGATGCCTGATGCGTCGCTGACGCGAc                                                              <  2:1647024/100‑1 (MQ=14)                           aCGCGACTTATCAGGCCTACGAGGTGCACTGAACTGTAGGTCGGATAAGACGGATGGCGTCGCATCCGACAGCCGATGCCTGATGCGTCGCTGACGCGAc                                                              <  2:841814/100‑1 (MQ=14)                           aCGCGACTTATCAGGCCTACGAGGTGCACTGAACTGTAGGTCGGATAAGACGGATGGCGTCGCATCCGAAAGCCGATAACTGATGCGTCGCTGACgcca                                                               >  1:1647181/1‑96 (MQ=14)                            cgcgACTTATCAGGCCTACGAGGTGCACTGAACTGTAGGTCGGATAAGACGGATGGCGTCGCATCCGACAGCCGCTGCCTGATGCCTCGCTGACgccact                                                             >  2:796470/1‑95 (MQ=11)                            cgcgACTTATCAGGCCTACGAGGTGCACTGAACTGTAGGTCGGATAAGACGGATGGCGTCGCATCCGACAGCCGATGCCTGATGCGTCGCTGACGCGACt                                                             >  2:1012326/1‑100 (MQ=255)                              cgACTTATCAGGCCTACGAGGTGCACTGAACTGTAGGTCGGATAAGACGGATGGCGTCGCATCCGACAGCCGATGCCTGATGCGTCGCTGACGCGACTTa                                                           <  1:1442956/100‑1 (MQ=11)                               gACTTATCAGGCCTACGAGGTGCACTGAACTGTAGGTCGGATAAGACGGATGGCGTCGCATCCGACAGCCGATGCCTGATGCGTCGCTGACGCGACTTAt                                                          <  2:1411585/100‑1 (MQ=14)                                  ttATCAGGCCTACGAGGTGCACTGAACTGTAGGTCGGATAAGACGGATGGCGTCGCATCCGACAGCCGATGCCTGATGCGTCGCTGACGCGACTTATCAg                                                       <  1:964608/100‑1 (MQ=11)                                   tATCAGGCCTACGAGGTGCACTGAACTGTAGGTCGGATAAGACGGATGGCGTCGCATCCGACAGCCGATGCCTGATGCGTCGCTGACGCGACTTATCAgg                                                      >  1:367751/1‑100 (MQ=255)                                   tATCAGGCCTACGAGGTGCACTGAACTGTAGGTCGGATAAGACGGATGGCGTCGCATCCGACAGCCGATGCCTGATGCGTCGCTGACGCGACTTATCAgg                                                      >  2:1382304/1‑100 (MQ=255)                                   tATCAGGCCTACGAGGTGCACTGAACTGTAGGTCGGATAAGACGGATGGCGTCGCATCCGACAGCCGATGCCTGATGCGTCGCTGACGCGACTTATCAgg                                                      <  2:1293722/100‑1 (MQ=14)                                    aTCAGGCCTACGAGGTGCACTGAACTGTAGGTCGGATAAGACGGATGGCGTCGCATCCGACAGCCGATGCCTGATGCGTCGCTGACGCGACTTATCAGGc                                                     <  2:1597830/100‑1 (MQ=14)                                    aTCAGCCCTAGGAGGTGCACCAAACTTTACGTCTGATAATACGGATGGCATCGCATCCGACAGCCGATGCCTGATGCGTCGCTGACGCTACTTATCAgg                                                      <  1:144873/99‑1 (MQ=2)                                     tCAGGCCTACGAGGTGCACTGAACTGTAGGTCGGATAAGACGGATGGCGTCGCATCCGACAGCCGATGCCTGATGCGTCGCTGACGCGACTTATCAGGcc                                                    <  2:946263/100‑1 (MQ=11)                                     tCAGGCCTACGAGGTGCACTGAACTGTAGGTCGGATAAGACGGATGGCGTCGCATCCGACAGCCGATGCCTGATGCGTCGCTGACGCAGCTTATCAg                                                       >  1:1498545/1‑97 (MQ=14)                                      cAGGCCTACGAGGTGCACTGAACTGTAGGTCGGATAAGACGGATGGCGTCGCATCCGACAGCCGATGCCTGATGCGCCGCTGACGCGACTTATCAGGCCt                                                   >  1:118131/1‑100 (MQ=255)                                      cAGGCCTACGAGGTGCACTGAACTGTAGGTCGGATAAGACGGATGGCGTCGCATCCGACAACCGATGCCTGATGCGCCGCTGACGTGACTTATCAGGCCt                                                   >  1:564036/1‑100 (MQ=255)                                       aGGCCTACGAGGTGCACTGAACTGTAGGTCGGATAAGACGGATGGCGTCGCATCCGACAGCCGATGCCTGATGCGTCGCTGACGCGACTTATCAGGCCTa                                                  >  1:1353040/1‑100 (MQ=14)                                        ggCCTACGAGGTGCACTGAACTGTAGGTCGGATAAGACGGATGGCGTCGCATCCGACAGCCGATGCCTGATGCGTCGCTGACGCGACTTATCAGGCCTAc                                                 >  2:1809378/1‑100 (MQ=14)                                        ggCCTACGAGGTGCACTGAACTGTAGGTCGGATAAGACGGATGGCGTCGCATCCGACAGCCGATGCCTGATGCGTCGCTGACGCGACTTATCAGGCCTAc                                                 >  2:1535483/1‑100 (MQ=255)                                           cTACGAGGTGCACTGAACTGTAGGTCGGATAAGACGGATGGCGTCGCATCCGACAGCCGATGCCTGATGCGTCGCTGACGCGACTTATCAGGCCTACgg                                               <  2:901109/99‑1 (MQ=11)                                           cTACGAGGTGCACTGAACTGTAGGTCGGATAAGACGGATGGCGTCGCATCCGACAACCGATGCCTGATGCGCCGCTGACGTGACTTATCAGGCCTACgg                                               >  2:1749451/1‑99 (MQ=255)                                            tACTAGGTTCACTGAACTTTAGTTCGGATAATACGTATGGCGTCGCATCCGACAGCCGATGCCTGATGCGTCGCTGACGCGACTTATCAGGCCTACgg                                               <  2:785067/98‑1 (MQ=11)                                            tACGAGGTGCACTGAACTGTAGGTCGGATAAGACGGATGGCGTCGCATCCGACAGCCGATGCCTGATGCGTCGCTGACGCGACTTATCAGGCCTACgggg                                             <  2:701500/100‑1 (MQ=11)                                            tACGAGGTGCACTGAACTGTAGGTCGGATAAGACGGATGGCGTCGCATCCGACAGCCGATGCCTGATGCGTCGCTGACGCGACTTATCAGGCCTACgggg                                             <  2:209550/100‑1 (MQ=11)                                            tACGAGGTGCACTGAACTGTAGGTCGGATAAGACGGATGGCGTCGCATCCGACAGCCGATGCCTGATGCGTCGCTGACGCGACTTATCAGGCCTACgggg                                             <  1:427088/100‑1 (MQ=11)                                              cGAGGTGCACTGAACTGTAGGTCGGATAAGACGGATGGCGTCGCATCCGACAGCCGATGCCTGATGCGTCGCTGACGCGACTTATCAGGCCTACGGGGTg                                           <  1:218130/100‑1 (MQ=255)                                              cGAGGTGCACTGAACTGTAGGTCGGATAAGACGGATGGCGTCGCATCCGACAGCCGATGCCTGATGCGTCGCTGACGCGACTTATCAGGCCTACGGGGTg                                           <  2:1539576/100‑1 (MQ=11)                                               gAGGTGCACTGAACTGTAGGTCGGATAAGACGGATGGCGTCGCATCCGACAGCCGATGCCTGATGCGTCGCTGACGCGACTTATCAGGCCTACGGGGTGc                                          <  2:935050/100‑1 (MQ=11)                                               gAGGTGCACTGAACTGTAGGTCGGATAAGACGGATGGCGTCGCATCCGACAGCCGATGCCTGATGCGTCGCTGACGCGACTTATCAGGCCTACGGGGTGc                                          <  1:1012316/100‑1 (MQ=11)                                               gAGGTGCACTGAACTGTAGGTCGGATAAGACGGATGGCGTCGCATCCGACAGCCGATGCCTGATGCGTCGCTGACGCGACTTATCAGGCCTACGGGGTGc                                          <  2:1353050/100‑1 (MQ=11)                                                aGGTGCACTGAACTGTAGGTCGGATAAGACGGATGGCGTCGCATCCGACAGCCGATGCCTGATGCGTCGCTGACGCGACTTATCAGGCCTACGGGGTGCa                                         <  1:179621/100‑1 (MQ=11)                                                 ggTGCACTGAACTGTAGGTCGGATAAGACGGATGGCGTCGCATCCGACAGCCGATGCCTGATGCGTCGCTGACGCGACTTATCAGGCCTACGGGGTGCAc                                        <  1:1594639/100‑1 (MQ=11)                                                  ccgatcTGAACTGTAGGTCGGATAAGACGGATGGCGTCGCATCCGACAACCGATGCCTGATGCGCCGCTGACGTGACTTATCAGGCCTACGGGGTGCACt                                       <  2:989029/95‑1 (MQ=255)                                                    gCACTGAACTGTAGGTCGGATAAGACGGATGGCGTCGCATCCGACAGCCGATGCCTGATGCGTCGCTGACGCGACTTATCAGGCCTACGGGGTGCACTGa                                     >  1:373194/1‑100 (MQ=255)                                                      aCTGAACTGTATGTCGGTTAAGACGGATGGCGTCGCATCCGACAGCCGATGCCTGATGCGTCGCTGACGCGACTTATCAGGCCTACGGGGTGCACTGAAc                                   <  1:624695/100‑1 (MQ=11)                                                      aCTGAACTGTAGGTCGGATAAGACGGATGGCGTCGCATCCGACAGCCGATGCCTGATGCGTCGCTGACGCGACTTATCAGGCCTACGGGGTGCACTGAAc                                   <  2:962958/100‑1 (MQ=11)                                                      aCTGAACTGTAGGTCGGATAAGACGGATGGCGTCGCATCCGACAGCCGATGCCTGATGCGTCGCTGACGCGACTTATCAGGCCTACGGGGTGCACTGAAc                                   <  2:1410113/100‑1 (MQ=11)                                                      aCTGAACTGTAGGTCGGATAAGACGGATGGCGTCGCATCCGACAGCCGATGCCTGATGCGTCGCTGACGCGACTTATCAGGCCTACGGGGTGCACTGAAc                                   <  2:1365498/100‑1 (MQ=11)                                                      aCTGAACTGTAGGTCGGATAAGACGGATGGCGTCGCATCCGACAGCCGATGCCTGATGCGTCGCTGACGCGACTTATCAGGCCTACGGGGTGCACTGAAc                                   >  1:487018/1‑100 (MQ=255)                                                         gAACTGTAGGTCGGATAAGACGGATGGCGTCGCATCCGACAGCCGATGCCTGATGCGTCGCTGACGCGACTTATCAGGCCTACGGGGTGCACTGAACTGt                                >  1:1297937/1‑100 (MQ=11)                                                         gAACTGTAGGTCGGATAAGACGGATGGCGTCGCATCCGACAACCGATGCCTGATGCGCCGCTGACGTGACTTATCAGGCCTACGGGGTGCACtagatcgg                                >  1:989021/1‑93 (MQ=255)                                                                 ggTCGGATAAGACGGATGGCGTCGCATCCGACAGCCGATGCCTGATTCGGCGGTGACGCGACTTATCAAACCTACGGGGAGCACTGAACTgtcggtcg                          >  1:166085/1‑98 (MQ=11)                                                                 ggTCGGATAAGACGGATGGCGTCGCATCCGACAACCGATGCCTGATGCGCCGCTGACGTGACTTATCAGGCCTACAGGGTGCACTAAACAGTAAGTCGGa                        >  2:1652519/1‑100 (MQ=14)                                                                    cGGATAAGACGGATGGCGTCGCATCCGACAGCCGATGCCTGATGCGTCGCTGACGCGACTTATCAGGCCTACGGGGTGCACTGAACTGTAGGTCGGATaa                     <  1:1071019/100‑1 (MQ=11)                                                                      gATAAGACGGATGGCGTCGCATCCGACAGCCGATGCCTGATGCGTCGCTGACGCGACTTATCAGGCCTACGGGGTGCACTGAAGTGTAGGTCGGaagaga                   >  1:1062353/1‑95 (MQ=11)                                                                      gATAAGACGGATGGCGTCGCATCCGACAGCCGATGCCTGATGCGTCGCTGACGCGACTTATCAGGCCTACGGGGTGCACTGAACTGTAGGTCGGATAAGa                   <  2:1694419/100‑1 (MQ=11)                                                                          aGACGGATGGCGTCGCATCCGACAGCCGATGCCTGATGCGTCGCTGACGCGACTTATCAGGCCTACGGGGTGCACTGGACTGTAGGTCGGATAAGACGCa               >  2:1566399/1‑100 (MQ=11)                                                                          aGACGGATGGCGACGCATCCGACAGCCGATGCCTGATGCGTCGCTGACGCGACTTATCAGGCCTACGGGATGCACTGAACTGTAGGTCGGATAAGACGCa               >  2:1191873/1‑100 (MQ=11)                                                                           gACGGATGGCGTCGCATCCGACAGCCGATGCCTGATGCGTCGCTGACGCGACTTATCAGGCCTACGGGGTGCACTGAACTGTAGGTCGGATAAGACGCAt              <  1:35519/100‑1 (MQ=11)                                                                             cGGATGGCGTCGCATCCGACAGCCGATGCCTGATGCGTCGCTGACGCGACTTATCAGGCCTACGGGGTGCACTGAACTGTAGGTCGGATAAGACGCATAg            <  2:1352740/100‑1 (MQ=11)                                                                                       cGCATCCGACAACCGATGCCTGATGCGCCGCTGACGTGACTTATCAGGCCTACGGGGTGCACTGAACTGTAGGTCGGATAAGACGCATAGCGTCGCATcc  <  2:1683534/100‑1 (MQ=32)                                                                                                  |                                                                                         GACAGCCGATGCCTGATGCGTCGCTGACGCGACTTATCAGGCCTACGAGGTGCACTGAACTGTAGGTCGGATAAGACGGATGGCGTCGCATCCGACAACCGATGCCTGATGCGCCGCTGACGTGACTTATCAGGCCTACGGGGTGCACTGAACTGTAGGTCGGATAAGACGCATAGCGTCGCATCC  >  NC_000913/349595‑349780

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: ‑