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%	164.4 / NA	52	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 (24/28);  total (24/28)

CCGGCAGCGTTGCGTTGTCGATTACCACCAGATTGTCCACTGTTGCGTTAATCAAACTATTCTCTCTTGAACCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATACTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGACACAGCATCATCGGTAATAATAATGTCAATTTTTTCGATTGGTAGTACCTGATTAAAACCGCGACGGTTAAATTT  >  NC_000913/2169561‑2169824                                                                                                                                     |                                                                                                                                    ccGGCAGCGTTGCGTTGTCGATTACCACCAGATTGTCCACTGTTGCGTTAATCAAACTATTCTCTCTTGAACCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACAcc                                                                                                                               >  2:1510755/1‑139 (MQ=255)           tgcgttgTCGATTACCACCAGATTGTCCACTGTTGCGTTAATCAAACTATTCTCTCTTGAACCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTaattaatt                                                                                                                     <  1:684087/139‑1 (MQ=255)               ttgTCGATTACCACCAGATTGTCCACTGTTGCGTTAATCAAACTATTCTCTCTTGAACCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATT‑‑ACCGTAATTAATTTTAccc                                                                                                               <  1:1017937/139‑1 (MQ=255)                 gTCGATTACCACCAGATTGTCCACTGTTGCGTTAATCAAACTATTCTCTCTTGAACCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTAccc                                                                                                               <  1:1690186/139‑1 (MQ=255)                      ttACCACCAGATTGTCCACTGTTGCGTTAATCAAACTATTCTCTCTTGAACCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGtc                                                                                                          <  2:983310/139‑1 (MQ=255)                            ccaGATTGTCCACTGTTGCGTTAATCAAACTATTCTCTCTTGAACCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGc                                                                                                    >  2:183717/1‑139 (MQ=255)                               gATTGTCCACTGTTGCGTTAATCAAACTATTCTCTCTTGAACCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAAt                                                                                                 >  2:996819/1‑139 (MQ=255)                                   gTCCACTGTTGCGTTAATCAAACTATTCTCTCTTGAACCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCa                                                                                             <  1:282739/139‑1 (MQ=255)                                           ttGCGTTAATCAAACTATTCTCTCTTGAACCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATcc                                                                                     <  1:996819/139‑1 (MQ=255)                                           ttGCGTTAATCAAACTATTCTCTCATGACCCAGGCAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTAACCGGCATACAGAACAATCTTCCACCGAAAGTAATATTACCCGCGTCTTCTGCAATGCCAGTTTATcc                                                                                     <  1:273456/139‑1 (MQ=255)                                              cGTTAATCAAACTATTCTCTCTTGAACCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATcc                                                                                     >  2:875631/1‑136 (MQ=255)                                              cGTTAATCAAACTATTCTCTCTTGAACCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATcc                                                                                     <  1:875631/136‑1 (MQ=255)                                                     cAAACTATTCTCTCTTGAACCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATcc                                                                                     <  2:1449152/129‑1 (MQ=255)                                                     cAAACTATTCTCTCTTGAACCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATcc                                                                                     >  1:1449152/1‑129 (MQ=255)                                                             tctctcTTGAACCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGACACAGcatca                                                                   <  2:1782519/139‑1 (MQ=255)                                                              ctctctTGAACCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGACACAGcatcat                                                                  <  2:437182/139‑1 (MQ=255)                                                                  ctTGAACCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGACACAGCATCATCGGt                                                              <  2:1613396/139‑1 (MQ=255)                                                                      aaCCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGACACAGCatcatc                                                                 >  2:1517996/1‑132 (MQ=255)                                                                      aaCCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGACACAGCatcatc                                                                 <  1:1517996/132‑1 (MQ=255)                                                                      aaCCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGACACAGCATCATCGGt                                                              <  2:87632/135‑1 (MQ=255)                                                                      aaCCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGACACAGCATCATCGGt                                                              >  1:87632/1‑135 (MQ=255)                                                                        ccAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGcc                                                                                              >  1:1654130/1‑101 (MQ=255)                                                                        ccAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGcc                                                                                              <  2:1654130/101‑1 (MQ=255)                                                                           gggAGAATCCGTAATGCCTGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGcc                                                                                              <  1:1087846/98‑1 (MQ=255)                                                                           gggAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGtaa                                                                                                                           >  2:521012/1‑69 (MQ=255)                                                                           gggAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGtaa                                                                                                                           <  1:521012/69‑1 (MQ=255)                                                                           gggAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGcc                                                                                              >  2:1087846/1‑98 (MQ=255)                                                                           gggAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGa                                                                             <  2:1389856/115‑1 (MQ=255)                                                                           gggAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGACACAGcatcat                                                                  >  1:179796/1‑126 (MQ=255)                                                                           gggAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGACACAGcatcat                                                                  <  2:179796/126‑1 (MQ=255)                                                                           gggAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGACACAGcatca                                                                   <  2:435208/125‑1 (MQ=255)                                                                           gggAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGACACAGcatca                                                                   >  1:435208/1‑125 (MQ=255)                                                                           gggAGAAACCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACctctta                                                                             >  1:1389856/1‑113 (MQ=255)                                                                                caTCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATcc                                                                                     >  1:1123221/2‑102 (MQ=255)                                                                                aaTCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGACACAGCATCATCGGTAATAATAATGTCaa                                                >  1:721947/1‑139 (MQ=255)                                                                                aaTCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCGGCAATGCCAGTTTATcc                                                                                     <  2:1123221/102‑1 (MQ=255)                                                                                         tGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGACACAGCATCATCGGTAATAATAATGTCAATTTTTTCGa                                       <  2:721947/139‑1 (MQ=255)                                                                                           ccGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGACACAGcatc                                                                    >  1:514995/1‑108 (MQ=255)                                                                                           ccGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGACACAGcatc                                                                    <  2:514995/108‑1 (MQ=255)                                                                                            cGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGtaa                                                                                                                           <  1:796234/52‑1 (MQ=255)                                                                                            cGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGtaa                                                                                                                           >  2:796234/1‑52 (MQ=255)                                                                                                              cTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGACACAGCATCATCGGTAATAATAATGTCAATTTTTTCGATTGGTAGTACCTGATTAAAAc                  >  1:1647102/1‑139 (MQ=255)                                                                                                               ttATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGACACAGCATCATCGGt                                                              <  1:649372/94‑1 (MQ=255)                                                                                                               ttATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGACACAGCATCATCGGt                                                              >  2:649372/1‑94 (MQ=255)                                                                                                                 aTCCGGCATACAGAACAATATTACACCGTAATTAATTTTAccc                                                                                                               <  1:92054/43‑1 (MQ=255)                                                                                                                 aTCCGGCATACAGAACAATATTACACCGTAATTAATTTTAccc                                                                                                               >  2:92054/1‑43 (MQ=255)                                                                                                                 aTCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGt                                                                                           >  2:581910/1‑63 (MQ=255)                                                                                                                 aTCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGt                                                                                           <  1:581910/63‑1 (MQ=255)                                                                                                                 aTCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGACACAGCATCATCGGTAATAATAATGTCAATTTTTTCGATTGGTAGTACCTGATTAAAACcgc               >  2:842909/1‑139 (MQ=255)                                                                                                                       cATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGACACAGCATCATCGGTAATAATAATGTCAATTTTTTCGATTGGTAGTACCTGATTAAAACCGCGACGGt         <  1:1510755/139‑1 (MQ=255)                                                                                                                        aTACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGACACAGCATCATCGGTAATAATAATGTCAATTTTTTCGATTGGTAGTACCTGATTAAAACCGCGACGGtt        >  2:292854/1‑139 (MQ=255)                                                                                                                              aaCAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGACACAGCATCATCGGTAATAATAATGTCAATTTTTTCGATTGGTAGTACCTGATTAAAACCGCGACGGTTAAAttt  >  1:229636/1‑139 (MQ=255)                                                                                                                                     |                                                                                                                                    CCGGCAGCGTTGCGTTGTCGATTACCACCAGATTGTCCACTGTTGCGTTAATCAAACTATTCTCTCTTGAACCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATACTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGACACAGCATCATCGGTAATAATAATGTCAATTTTTTCGATTGGTAGTACCTGATTAAAACCGCGACGGTTAAATTT  >  NC_000913/2169561‑2169824

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑