Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,169,693	C→T	pseudogene (475/475 nt)	gatR ←	pseudogene, repressor for gat operon, interrupted by IS3, split galactitol utilization operon repressor, fragment 2, split galactitol utilization operon repressor, interrupted

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,169,693	0	C	T	100.0%	220.9 / NA	67	pseudogene (475/475 nt)	gatR	pseudogene, repressor for gat operon, interrupted by IS3, split galactitol utilization operon repressor, fragment 2, split galactitol utilization operon repressor, interrupted
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (32/35);  total (32/35)

CTTCCGGCAGCGTTGCGTTGTCGATTACCACCAGATTGTCCACTGTTGCGTTAATCAAACTATTCTCTCTTGAACCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATACTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGACACAGCATCATCGGTAATAATAATGTCAATTTTTTCGATTGGTAGTACCTGATTAAAACCGCGACGGTTAAATTTCG  >  NC_000913/2169558‑2169826                                                                                                                                        |                                                                                                                                      cTTCCGGCAGCGTTGCGTTGTCGATTACCACCAGATTGTCCACTGTTGCGTTAATCAAACTATTCTCTCTTGAACCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAAtattac                                                                                                                                    >  2:1386673/1‑139 (MQ=255)  ttCCGGCAGCGTTGCGTTGTCGATTACCACCAGATTGTCCACTGTTGCGTTAATCAAACTATTCTCTCTTGAACCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTaca                                                                                                                                   >  1:1970920/1‑139 (MQ=255)  ttCCGGCAGCGTTGCGTTGTCGATTACCACCAGATTGTCCACTGTTGCGTTAATCAAACTATTCTCTCTTGAACCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTaca                                                                                                                                   <  1:1710590/139‑1 (MQ=255)    ccGGCAGCGTTGCGTTGTCGATTACCACCAGATTGTCCACTGTTGCGTTAATCAAACTATTCTCTCTTGAACCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACAcc                                                                                                                                 >  1:331596/1‑139 (MQ=255)        cAGCGTTGCGTTGTCGATTACCACCAGATTGTCCACTGTTGCGTTAATCAAACTATTCTCTCTTGAACCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGtaa                                                                                                                             <  1:1386673/139‑1 (MQ=255)                      cGATTACCACCAGATTGTCCACTGTTGCGTTAATCAAACTATTCTCTCTTGAACCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCcgc                                                                                                               <  2:832445/139‑1 (MQ=255)                              accaGATTGTCCACTGTTGCGTTAATCAAACTATTCTCTCTTGAACCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTg                                                                                                       <  2:1350096/139‑1 (MQ=255)                                   aTTGTCCACTGTTGCGTTAATCAAACTATTCTCTCTTGAACCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATg                                                                                                  <  2:2019770/139‑1 (MQ=255)                                       tCCACTGTTGCGTTAATCAAACTATTCTCTCTTGAACCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAg                                                                                              >  2:1810736/1‑139 (MQ=255)                                        ccACTGTTGCGTTAATCAAACTATTCTCTCTTGAACCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGt                                                                                             <  2:128564/139‑1 (MQ=255)                                          aCTGTTGCGTTAATCAAACTATTCTCTCTTGAACCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGttt                                                                                           >  2:1182004/1‑139 (MQ=255)                                              ttGCGTTAATCAAACTATTCTCTCTTGAACCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATc                                                                                        >  1:1920188/1‑138 (MQ=255)                                              ttGCGTTAATCAAACTATTCTCTCTTGAACCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATc                                                                                        <  2:1920188/138‑1 (MQ=255)                                                 cGTTAATCAAACTATTCTCTCTTGAACCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATcc                                                                                       >  1:1036499/1‑136 (MQ=255)                                                 cGTTAATCAAACTATTCTCTCTTGAACCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATcc                                                                                       <  2:1036499/136‑1 (MQ=255)                                                      aTCAAACTATTCTCTCTTGAACCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCa                                                                                               >  1:1955897/1‑123 (MQ=255)                                                      aTCAAACTATTCTCTCTTGAACCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCa                                                                                               <  2:1955897/123‑1 (MQ=255)                                                        cAAACTATTCTCTCTTGAACCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGaca                                                                             <  2:331596/139‑1 (MQ=255)                                                                tctctcTTGAACCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAAtac                                                                                                                                       <  1:1282831/73‑1 (MQ=255)                                                                tctctcTTGAACCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGACACAGcatca                                                                     <  1:1810736/139‑1 (MQ=255)                                                                tctctcTTGAACCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGACACAGcatca                                                                     <  2:1970920/139‑1 (MQ=255)                                                                         aaCCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTAccc                                                                                                                 >  2:1537112/1‑86 (MQ=255)                                                                         aaCCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTAccc                                                                                                                 <  1:1537112/86‑1 (MQ=255)                                                                         aaCCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCcgc                                                                                                               >  2:362608/1‑88 (MQ=255)                                                                         aaCCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCcgc                                                                                                               <  1:362608/88‑1 (MQ=255)                                                                         aaCCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATc                                                                                        >  1:1412809/1‑111 (MQ=255)                                                                         aaCCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATc                                                                                        <  2:1412809/111‑1 (MQ=255)                                                                              gggAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTAccc                                                                                                                 >  1:1543919/1‑81 (MQ=255)                                                                              gggAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTAccc                                                                                                                 <  2:1543919/81‑1 (MQ=255)                                                                              gggAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGtct                                                                                                           <  1:873358/87‑1 (MQ=255)                                                                              gggAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGtct                                                                                                           >  2:873358/1‑87 (MQ=255)                                                                              gggAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGACACAGcatcat                                                                    <  1:1351814/126‑1 (MQ=255)                                                                              gggAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGACACAGcatcat                                                                    >  2:1351814/1‑126 (MQ=255)                                                                              gggAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGACACAGcatca                                                                     <  1:278568/125‑1 (MQ=255)                                                                              gggAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGACACAGcatca                                                                     >  2:278568/1‑125 (MQ=255)                                                                                   aaTCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGACACAGcatca                                                                     <  2:1653919/120‑1 (MQ=255)                                                                                   aaTCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGACACAGcatca                                                                     >  1:1653919/1‑120 (MQ=255)                                                                                    aTCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTAccc                                                                                                                 >  1:1145021/1‑75 (MQ=255)                                                                                    aTCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTAccc                                                                                                                 <  2:1145021/75‑1 (MQ=255)                                                                                    aTCCGTAATGCCGGATGCG‑‑GTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATcc                                                                                       >  2:62672/1‑99 (MQ=255)                                                                                    aTCCGTAATGCCGGATGCG‑‑GTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATcc                                                                                       <  1:62672/99‑1 (MQ=255)                                                                                         tAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTa                                                                                                                    <  2:886318/67‑1 (MQ=255)                                                                                         tAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTa                                                                                                                    >  1:886318/1‑67 (MQ=255)                                                                                           aTGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTg                                                                                                       <  2:2034886/78‑1 (MQ=255)                                                                                           aTGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTg                                                                                                       >  1:2034886/1‑78 (MQ=255)                                                                                                 gATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGACACAGCATCATCGGTAATAATAATGTCAATTTTTTCGATTgg                                     <  2:979869/138‑1 (MQ=255)                                                                                                 gATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGACACAGCATCATCGGTAATAATAATGTCAATTTTTTCGATTgg                                     >  1:979869/1‑138 (MQ=255)                                                                                                          tAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGACACAGCATCATCGGTAATAATAATGTCAATTTTTTCGa                                         <  2:1430226/125‑1 (MQ=255)                                                                                                          tAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGACACAGCATCATCGGTAATAATAATGTCAATTTTTTCGa                                         >  1:1430226/1‑125 (MQ=255)                                                                                                                 cTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTAt                                                                                         <  1:2045352/70‑1 (MQ=255)                                                                                                                 cTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTAt                                                                                         >  2:2045352/1‑70 (MQ=255)                                                                                                                  ttATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGACACAGCATCATCGGTAATAATAATGTCAATTTTTTCGa                                         <  2:2024117/117‑1 (MQ=255)                                                                                                                  ttATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGACACAGCATCATCGGTAATAATAATGTCAATTTTTTCGa                                         >  1:2024117/1‑117 (MQ=255)                                                                                                                  ttATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCCCTGACACAGCATCATCGGTAATAATAATGTCAATTTTTTCGATTGgt                                    >  1:615776/1‑122 (MQ=255)                                                                                                                  ttATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCCCTGACACAGCATCATCGGTAATAATAATGTCAATTTTTTCGATTGgt                                    <  2:615776/122‑1 (MQ=255)                                                                                                                    aTCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGACACAGcatcat                                                                    <  1:584022/88‑1 (MQ=255)                                                                                                                    aTCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGACACAGcatcat                                                                    >  2:584022/1‑88 (MQ=255)                                                                                                                    aTCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGACACAGcatca                                                                     <  2:1172095/87‑1 (MQ=255)                                                                                                                    aTCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGACACAGcatca                                                                     >  1:1172095/1‑87 (MQ=255)                                                                                                                    aTCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGACACAGCATCATCGGTAATAATAATGTCAATTTTTTCGa                                         >  2:259396/1‑115 (MQ=255)                                                                                                                    aTCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGACACAGCATCATCGGTAATAATAATGTCAATTTTTTCGa                                         <  1:259396/115‑1 (MQ=255)                                                                                                                      ccGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCa                                                                                               >  2:1192107/1‑59 (MQ=255)                                                                                                                      ccGGCACACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGTCa                                                                                               <  1:1192107/59‑1 (MQ=255)                                                                                                                               aGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGacac                                                                            >  2:431461/1‑69 (MQ=255)                                                                                                                               aGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGacac                                                                            <  1:431461/69‑1 (MQ=255)                                                                                                                               aGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGACACAGCATCATCGGTAATAATAATGTCAATTTTTTCGATTGGTAGTACCTGATTAAAACCGCGACGGTTAAAt      >  2:1161493/1‑139 (MQ=255)                                                                                                                                   cAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGACACAGCATCATCGGTAATAATAATGTCAATTTTTTCGATTGGTAGTACCTGATTAAAACCGCGACGGTTAAATTTCg  >  1:90453/1‑139 (MQ=255)                                                                                                                                    aaTATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGACACAGca                                                                        >  1:1726513/1‑68 (MQ=255)                                                                                                                                    aaTATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGACACAGca                                                                        <  2:1726513/68‑1 (MQ=255)                                                                                                                                        |                                                                                                                                      CTTCCGGCAGCGTTGCGTTGTCGATTACCACCAGATTGTCCACTGTTGCGTTAATCAAACTATTCTCTCTTGAACCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATACTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGACACAGCATCATCGGTAATAATAATGTCAATTTTTTCGATTGGTAGTACCTGATTAAAACCGCGACGGTTAAATTTCG  >  NC_000913/2169558‑2169826

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑