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%	193.9 / NA	60	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 (28/32);  total (28/32)

TTCCGGCAGCGTTGCGTTGTCGATTACCACCAGATTGTCCACTGTTGCGTTAATCAAACTATTCTCTCTTGAACCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATACTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGACACAGCATCATCGGTAATAATAATGTCAATTTTTTCGATTGGTAGTACCTGATTAAAACCGCGACGGTTAAATTTCGA  >  NC_000913/2169559‑2169827                                                                                                                                       |                                                                                                                                       ttCCGGCAGCGTTGCGTTGTCGATTACCACCAGATTGTCCACTGTTGCGTTAATCAAACTATTCTCTCTTGAACCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTaca                                                                                                                                    <  2:1493768/139‑1 (MQ=255)   ccGGCAGCGTTGCGTTGTCGATTACCACCAGATTGTCCACTGTTGCGTTAATCAAACTATTCTCTCTTGAACCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACAcc                                                                                                                                  >  1:825796/1‑139 (MQ=255)   ccGGCAGCGTTGCGTTGTCGATTACCACAAGATTGTCCACTGTTGGGTTAAGCAAACTATTGTTTCTTGAACCAGGGAGCATCCGTAATGCCAGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACAcc                                                                                                                                  >  2:156008/1‑139 (MQ=255)       cAGCGTTGCGTTGTCGATTACCACCAGATTGTCCACTGTTGCGTTAATCAAACTATTCTCTCTTGAACCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGtaa                                                                                                                              <  2:190921/139‑1 (MQ=255)             tgcgttgTCGATTACCACCAGATTGTCCACTGTTGCGTTAATCAAACTATTCTCTCTTGAACCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTaattaatt                                                                                                                        >  1:1536582/1‑139 (MQ=255)               cgttgTCGATTACCACCAGATTGTCCACTGTTGCGTTAATCAAACTATTCTCTCTTGAACCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAAtttt                                                                                                                      >  2:263035/1‑139 (MQ=255)                             accaGATTGTCCACTGTTGCGTTAATCAAACTATTCTCTCTTGAACCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTg                                                                                                        <  1:1096957/139‑1 (MQ=255)                              ccaGATTGTCCACTGTTGCGTTAATCAAACTATTCTCTCTTGAACCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTAccc                                                                                                                  >  2:585326/1‑128 (MQ=255)                              ccaGATTGTCCACTGTTGCGTTAATCAAACTATTCTCTCTTGAACCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTAccc                                                                                                                  <  1:585326/128‑1 (MQ=255)                                aGATTGTCCACTGTTGCGTTAATCAAACTATTCTCTCTTGAACCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTacac                                                                                                                                   >  2:493385/1‑109 (MQ=255)                                aGATTGTCCACTGTTGCGTTAATCAAACTATTCTCTCTTGAACCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTacac                                                                                                                                   <  1:493385/109‑1 (MQ=255)                                  aTTGTCCACTGTTGCGTTAATCAAACTATTCTCTCTTGAACCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTaca                                                                                                                                    >  1:1477718/1‑106 (MQ=255)                                  aTTGTCCACTGTTGCGTTAATCAAACTATTCTCTCTTGAACCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTaca                                                                                                                                    <  2:1477718/106‑1 (MQ=255)                                      tCCACTGTTGCGTTAATCAAACTATTCTCTCTTGAACCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTaca                                                                                                                                    <  2:1285986/102‑1 (MQ=255)                                      tCCACTGTTGCGTTAATCAAACTATTCTCTCTTGAACCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTaca                                                                                                                                    >  1:1285986/1‑102 (MQ=255)                                      tCCACTGTTGCGTTAATCAAACTATTCTCTCTTGAACCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTg                                                                                                        >  2:525333/1‑130 (MQ=255)                                      tCCACTGTTGCGTTAATCAAACTATTCTCTCTTGAACCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTg                                                                                                        <  1:525333/130‑1 (MQ=255)                                      tCCACTGTTGCGTTAATCAAACTATTCTCTCTTGAACCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAg                                                                                               >  2:1282938/1‑139 (MQ=255)                                             ttGCGTTGATCAAACTATTCTCTCTTGAACCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATcc                                                                                        <  1:1317216/139‑1 (MQ=255)                                             ttGCGTTAATCAAACTATTCTCTCTTGAACCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATcc                                                                                        <  2:1536582/139‑1 (MQ=255)                                             ttGCGTTAATCAAACTATTCTCTCTTGAACCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATcc                                                                                        <  1:1282938/139‑1 (MQ=255)                                                cGTTAATCAAACTATTCTCTCTTGAACCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCAcc                                                                                     <  2:825796/139‑1 (MQ=255)                                                     aTCAAACTATTCTCTCTTGAACCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGACATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGa                                                                                >  2:712708/1‑139 (MQ=255)                                                     aTCAAACTATTCTCTCTTGAACCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGACATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGa                                                                                <  1:712708/139‑1 (MQ=255)                                                       cAAACTATTCTCTCTTGAACCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATc                                                                                         <  2:1151875/128‑1 (MQ=255)                                                       cAAACTATTCTCTCTTGAACCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATc                                                                                         >  1:1151875/1‑128 (MQ=255)                                                               tctctcTTGAACCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGACATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGACACAGcatca                                                                      >  2:361741/1‑139 (MQ=255)                                                                   tctTGAACCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGAcaca                                                                            >  1:21717/1‑129 (MQ=255)                                                                   tctTGAACCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGAcaca                                                                            <  2:21717/129‑1 (MQ=255)                                                                   tctTGAACCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACATCTGACACAGCATCATCgg                                                                  >  1:898062/1‑139 (MQ=255)                                                                        aaCCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGACACAGcatca                                                                      >  1:155086/1‑130 (MQ=255)                                                                        aaCCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGACACAGcatca                                                                      <  2:155086/130‑1 (MQ=255)                                                                             gggAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAAtatta                                                                                                                                      >  1:281907/1‑61 (MQ=255)                                                                             gggAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATcc                                                                                        >  1:314719/1‑107 (MQ=255)                                                                             gggAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATcc                                                                                        <  2:314719/107‑1 (MQ=255)                                                                                  aaTCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCAc                                                                                      >  1:1500179/1‑104 (MQ=255)                                                                                  aaTCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCAc                                                                                      <  2:1500179/104‑1 (MQ=255)                                                                                           tGCCGGATGCGGTGTAAACCCCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGACACAGCATCATCGGTAATAATAATGTCAATTTTTTCGa                                          <  1:1088961/139‑1 (MQ=255)                                                                                           tGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGACACAGCATCATCGGTAATAATAATGTCAATTTTTTCGa                                          <  1:134938/139‑1 (MQ=255)                                                                                            gCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGACACAGCATCATCGGTAATAATAATGTCAATTTTTTCGa                                          >  2:235686/1‑138 (MQ=255)                                                                                            gCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGACACAGCATCATCGGTAATAATAATGTCAATTTTTTCGa                                          <  1:235686/138‑1 (MQ=255)                                                                                            gCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGACACAGCATCATCGGTAATAATAATGTCAATTTTTTCGAt                                         <  1:758951/139‑1 (MQ=255)                                                                                              cGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGtc                                                                                                             <  1:488446/69‑1 (MQ=255)                                                                                              cGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGtc                                                                                                             >  2:488446/1‑69 (MQ=255)                                                                                                       tgtAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGaca                                                                              <  2:1101586/91‑1 (MQ=255)                                                                                                       tgtAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGaca                                                                              >  1:1101586/1‑91 (MQ=255)                                                                                                         tAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATcc                                                                                        <  1:184748/79‑1 (MQ=255)                                                                                                         tAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATcc                                                                                        >  2:184748/1‑79 (MQ=255)                                                                                                                cTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGAcaca                                                                            >  1:318008/1‑84 (MQ=255)                                                                                                                cTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGAcaca                                                                            <  2:318008/84‑1 (MQ=255)                                                                                                                 ttATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGACACAGCATCATCGGTAATAATAATGTCAATTTTTTCGATTGGTAGTACCTGATTAAAAcc                    >  2:584417/1‑139 (MQ=255)                                                                                                                     ccGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGACACAGCATCATCGGTAATAATAATGTCAATTTTTTCGATTGGTAGTACCTGATTAAAACCGCGa                <  1:263035/139‑1 (MQ=255)                                                                                                                        gCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGaca                                                                              <  2:416828/74‑1 (MQ=255)                                                                                                                        gCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGaca                                                                              >  1:416828/1‑74 (MQ=255)                                                                                                                          aTACAGAACTATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGACACAGCATCATCGGTAATAATAATGTCAATTTTTTCGATTGGTAGTACCTGATTAAAACCGCGACGGtt           <  1:982448/139‑1 (MQ=255)                                                                                                                                aaCAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACct                                                                                    >  1:626157/1‑60 (MQ=255)                                                                                                                                aaCAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACct                                                                                    <  2:626157/60‑1 (MQ=255)                                                                                                                                  cAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGACACAGCATCATCGGTAATAATAATGTCAAttttt                                              >  2:371577/1‑96 (MQ=255)                                                                                                                                  cAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGACACAGCATCATCGGTAATAATAATGTCAAttttt                                              <  1:371577/96‑1 (MQ=255)                                                                                                                                   aaTATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGACACAGCATCATCGGTAATAATAATGTCAATTTTTTCGATTGGTAGTACCTGATTAAAACCGCGACGGTTAAATTTCGa  >  1:1489841/1‑139 (MQ=255)                                                                                                                                   aaTATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGACACAGCATCATCGGTAATAATAATGTCAATTTTTTCGATTGGTAGTACCTGATTAAAACCGCGACGGTTAAATTTCGa  <  1:44657/139‑1 (MQ=255)                                                                                                                                       |                                                                                                                                       TTCCGGCAGCGTTGCGTTGTCGATTACCACCAGATTGTCCACTGTTGCGTTAATCAAACTATTCTCTCTTGAACCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATACTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGACACAGCATCATCGGTAATAATAATGTCAATTTTTTCGATTGGTAGTACCTGATTAAAACCGCGACGGTTAAATTTCGA  >  NC_000913/2169559‑2169827

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑