Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,994,896	G→C	pseudogene (197/633 nt)	ygeK ←	pseudogene, response regulator family, part of T3SS PAI ETT2 remnant; putative 2‑component transcriptional regulator

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,994,896	0	G	C	100.0%	155.0 / NA	44	pseudogene (197/633 nt)	ygeK	pseudogene, response regulator family, part of T3SS PAI ETT2 remnant; putative 2‑component transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base C (15/29);  total (15/29)

TTCGCCGGGTGACTGGTTTTCCATACGCATCCTTTCGCACCTGCTTCAAGCAATTTTATTGAATCAATATACGGCATCTTTGCTACAAATGTAATAATATGAGCATCTATCTTATGCGATTTAACCCATTTTACGAGTTCGGCCCCCATCATTCCACCTGCAAATTCTCCTAAAATAAATATTTAGGCTGTAGATTTGTTACACTCCGCTATAGCTTTCTTCAGATCTTTATAGCCCCCAACAACCTCATATAAATCAGGATAATGTCCGAGAAATCCAATTATCC  >  NC_000913/2994755‑2995040                                                                                                                                              |                                                                                                                                                 ttCGCCGGGTGACTGGTTTTCCATACGCATCCTTTCGCACCTGCTTCAAGCAATTTTATTGAATCAATATACGGCATCTTTGCTACAAATGTAATAATATGAGCATCTATCTTATGCGATTTAACCCATTTTACGAGTTCGCCCCCcatc                                                                                                                                          <  2:246768/150‑1 (MQ=255)    gCCGGGTGACTGGTTTTCCATACGCATCCTTTCGCACCTGCTTCAAGCAATTTTATTGAATCAATATACGGCATCTTTGCTACAAATGTAATAATATGAGCATCTATCTTATGCGATTTAACCCATTTTACGAGTTCGCCCCCCATCATTc                                                                                                                                      <  1:506282/151‑1 (MQ=255)        ggTGACTGGTTTTCCATACGCATCCTTTCGCACCTGCTTCAAGCAATTTTATTGAATCAATATACGGCATCTTTGCTACAAATGTAATAATATGAGCATCTATCTTATGCGATTTAACCCATTTTACGAGTTCGCCCCCCATCATTCCAcc                                                                                                                                  <  1:258817/151‑1 (MQ=255)               ggTTTTCCATACGCATCCTTTCGCACCTGCTTCAAGCAATTTTATTGAATCAATATACGGCATCTTTGCTACAAATGTAATAATATGAGCATCTATCTTATGCGATTTAACCCACTTTACGAGTTCGCCCCCCATCATTCCACCTGCAAAt                                                                                                                           <  1:264156/151‑1 (MQ=255)                  tttCCATACGCATCCTTTCGCACCTGCTTCAAGCAATTTTATTGAATCAATATACGGCATCTTTGCTACAAATGTAATAATATGAGCATCTATCTTATGCGATTTAACCCATTTTACGAGTTCGCCCCCCATCATTCCACCTGCaa                                                                                                                             <  1:181410/146‑1 (MQ=255)                  tttCCATACGCATCCTTTCGCACCTGCTTCAAGCAATTTTATTGAATCAATATACGGCATCTTTGCTACAAATGTAATAATATGAGCATCTATCTTATGCGATTTAACCCATTTTACGAGTTCGCCCCCCATCATTCCACCTGCaa                                                                                                                             >  2:181405/1‑146 (MQ=255)                          cGCATCCTTTCGCACCTGCTTCAAGCAATTTTATTGAATCAATATACGGCATCTTTGCTACAAATGTAATAATATGAGCATCTATCTTATGCGATTTAACCCATTTTACGAGTTCGCCCCCCATCATTCCACCTGCAAATTCTCCTAaaat                                                                                                                <  1:159174/151‑1 (MQ=255)                          cGCATCCTTTCGCACCTGCTTCAAGCAATTTTATTGAATCAATATACGGCATCTTTGCTACAAATGTAATAATATGAGCATCTATCTTATGCGATTTAACCCATTTTACGAGTTCGCCCCCCATCATTCCACCTGCAAATTCTCCTAaaat                                                                                                                <  1:458063/151‑1 (MQ=255)                            cATCCTTTCGCACCTGCTTCAAGCAATTTTATTGAATCAATATACGGCATCTTTGCTACAAATGTAATAATATGAGCATCTATCTTATGCGATTTAACCCATTTTACGAGTTCGCCCCCCATCATTCCACCTGCAAATTCTCCTAaaataa                                                                                                              <  1:373337/151‑1 (MQ=255)                                  ttCGCACCTGCTTCAAGCAATTTTATTGAATCAATATACGGCATCTTTGCTACAAATGTAATAATATGAGCATCTATCTTATGCGATTTAACCCATTTTACGAGTTCGCCCCCCATCATTCCACCTGCAAATTCTCCTAAAATAAATAtt                                                                                                         <  1:333254/150‑1 (MQ=255)                                      cACCTGCTTCAAGCAATTTTATTGAATCAATATACGGCATCTTTGCTACAAATGTAATAATATGAGCATCTATCTTATGCGATTTAACCCATTTTACGAGTTCGCCCCCCATCATTCCACCTGCAAATTCTCCTAAAATAAATATTTAGGc                                                                                                    >  2:209711/1‑151 (MQ=255)                                      cACCTGCTTCAAGCAATTTTATTGAATCAATATACGGCATCTTTGCTACAAATGTAATAATATGAGCATCTATCTTATGCGATTTAACCCATTTTACGAGTTCGCCCCCCATCATTCCACCTGCAAATTCTCCTAAAATAAATATTTAGGc                                                                                                    <  2:172053/151‑1 (MQ=255)                                       aCCTGCTTCAAGCAATTTTATTGAATCAATATACGGCATCTTTGCTACAAATGTAATAATATGAGCATCTATCTTATGCGATTTAACCCATTTTACGAGTTCGCCCCCCATCATTCCACCTGCAAATTCTCCTAAAATAAATATTTAGGCt                                                                                                   >  1:270395/1‑151 (MQ=255)                                          tGCTTCAAGCAATTTTATTGAATCAATATACGGCATCTTTGCTACAAATGTAATAATATGAGCATCTATCTTATGCGATTTAACCCATTTTACGAGTTCGCCCCCCATCATTCCACCTGCAAATTCTCCTAAAATAAATATTTAGGCTGt                                                                                                 >  2:137578/1‑150 (MQ=255)                                               cAAGCAATTTTATTGAATCAATATACGGCATCTTTGCTACAAATGTAATAATATGAGCATCTATCTTATGCGATTTAACCCATTTTACGAGTTCGCCCCCCATCATTCCACCTGCAAATTCTCCTAAAATAAATATTTAGGCTGTAGAttt                                                                                           <  2:86716/151‑1 (MQ=255)                                                aaGCAATTTTATTGAATCAATATACGGCATCTTTGCTACAAATGTAATAATATGAGCATCTATCTTATGCGATTTAACCCATTTTACGAGTTCGCCCCCCATCATTCCACCTGCAAATTCTCCTAAAATAAATATTTAGGCTGTAGATTTg                                                                                          <  2:74085/151‑1 (MQ=255)                                                   cAATTTTATTGAATCAATATACGGCCTCTTTGCTACAAATGTAATAATATGAGCATCTATCTTATGCGATTTAACCCATTTTACGAGTTCGCCCCCCATCATTCCACCTGCAAATTCTCCTAAAATAAATATTTAGGCTGTAGATTTGtt                                                                                        >  1:8404/1‑150 (MQ=255)                                                    aaTTTTATTGAATCAATATACGGCATCTTTGCTACAAATGTAATAATATGAGCATCTATCTTATGCGATTTAACCCATTTTACGAGTTCGCCCCCCATCATTCCACCTGCAAATTCTCCTAAAATAAATATTTAGGCTGTAGATTTGTTac                                                                                      <  2:42221/151‑1 (MQ=255)                                                         tATTGAATCAATATACGGCATCTTTGCTACAAATGTAATAATATGAGCATCTATCTTATGCGATTTAACCCATTTTACGAGTTCGCCCCCCATCATTCCACCTGCAAATTCTCCTAAAATAAATATTTAGGCTGTAGATTTGTTACACTcc                                                                                 >  2:249079/1‑151 (MQ=255)                                                         tATTGAATCAATATACGGCATCTTTGCTACAAATGTAATAATATGAGCATCTATCTTATGCGATTTAACCCATTTTACGAGTTCGCCCCCCATCATTCCACCTGCAAATTCTCCTAAAATAAATATTTAGGCTGTAGATTTGTTACACTc                                                                                  <  2:544223/150‑1 (MQ=255)                                                             gAATCAATATACGGCATCTTTGCTACAAATGTAATAATATGAGCATCTATCTTATGCGATTTAACCCATTTTACGAGTTCGCCCCCCATCATTCCACCTGCAAATTCTCCTAAAATAAATATTTAGGCTGTAGATTTGTTACACTCCGCt                                                                              >  2:138182/1‑150 (MQ=255)                                                                 cAATATACGGCATCTTTGCTACAAATGTAATAATATGAGCATCTATCTTATGCGATTTAACCCATTTTACGAGTTCGCCCCCCATCATTCCACCTGCAAATTCTCCTAAAATAAATATTTAGGCTGTAGATTTGTTACACTCCGCTATAg                                                                          <  1:414712/150‑1 (MQ=255)                                                                   atatACGGCATCTTTGCTACAAATGTAATAATATGAGCATCTATCTTATGCGATTTAACCCATTTTACGAGTTCGCCCCCCATCATTCCACCTGCAAATTCTCCTAAAATAAATATTTAGGCTGTAGATTTGTTACACTCCGCTATAGCtt                                                                       >  2:390922/1‑151 (MQ=255)                                                                         ggCATCTTTGCTACAAATGTAATAATATGAGCATCTATCTTATGCGATTTAACCCATTTTACGAGTTCGCCCCCCATCATTCCACCTGCAAATTCTCCTAAAATAAATATTTAGGCTGTAGATTTGTTACACTCCGCTATAGCTttcttc                                                                  >  1:573687/1‑150 (MQ=255)                                                                            aTCTTTGCTACAAATGTAATAATATGAGCATCTATCTTATGCGATTTAACCCATTTTACGAGTTCGCCCCCCATCATTCCACCTGCAAATTCTCCTAAAATAAATATTTAGGCTGTAGATTTGTTACACTCCGCTATAGCTttcttc                                                                  >  1:481339/1‑147 (MQ=255)                                                                             tCTTTGCTACAAATGTAATAATATGAGCATCTATCTTATGCGATTTAACCCATTTTACGAGTTCGCCCCCCATCATTCCACCTGCAAATTCTCCTAAAATAAATATTTAGGCTGTAGATTTGTTACACTCCGCTATAGCTttcttc                                                                  >  2:62189/1‑146 (MQ=255)                                                                                ttGCTACAAATGTAATAATATGAGCATCTATCTTATGCGATTTAACCCATTTTACGAGTTCGCCCCCCATCATTCCACCTGCAAATTCTCCTAAAATAAATATTTAGGCTGTAGATTTGTTACACTCCGCTATAGCTTTCTTCAGATCtt                                                           <  2:284483/150‑1 (MQ=255)                                                                                           gTAATAATATGAGCATCTATCTTATGCGATTTAACCCATTTTACGAGTTCGCCCCCCATCATTCCACCTGCAAATTCTCCTAAAATAAATATTTAGGCTGTAGATTTGTTACACTCCGCTATAGCTTTCTTCAGATCTTTATAGCCCCcaa                                               <  1:242770/151‑1 (MQ=255)                                                                                            taataaTATGAGCATCTATCTTATGCGATTTAACCCATTTTACGAGTTCGCCCCCCATCATTCCACCTGCAAATTCTCCTAAAATAAATATTTAGGCTGTAGATTTGTTACACTCCGCTATAGCTTTCTTCAGATCTTTATAGCCCCcaac                                              >  1:319224/1‑151 (MQ=255)                                                                                             aataatATGAGCATCTATCTTATGCGATTTAACCCATTTTACGAGTTCGCCCCCCATCATTCCACCTGCAAATTCTCCTAAAATAAATATTTAGGCTGTAGATTTGTTACACTCCGCTATAGCTTTCTTCAGATCTTTATAGCCCCcaaca                                             <  2:513724/151‑1 (MQ=255)                                                                                                     gAGCATCTATCTTATGCGATTTAACCCATTTTACGAGTTCGCCCCCCATCATTCCACCTGCAAATTCTCCTAAAATAAATATTTAGGCTGTAGATTTGTTACACTCCGCTATAGCTTTCTTCAGATCTTTATAGCCCCCAACAACCTCata                                     <  2:181045/151‑1 (MQ=255)                                                                                                             atctTATGCGATTTAACCCATTTTACGAGTTCGCCCCCCATCATTCCACCTGCAAATTCTCCTAAAATAAATATTTAGGCTGTAGATTTGTTACACTCCGCTATAGCTTTCTTCAGATCTTTATAGCCCCCAACAACCTCATATAAAt                                <  2:567718/148‑1 (MQ=255)                                                                                                             atctTATGCGATTTAACCCATTTTACGAGTTCGCCCCCCATCATTCCACCTGCAAATTCTCCTAAAATAAATATTTAGGCTGTAGATTTGTTACACTCCGCTATAGCTTTCTTCAGATCTTTATAG‑CCCCAACAACCTCATATAAATCAg                             <  1:330035/150‑1 (MQ=255)                                                                                                                 tATGCGATTTAACCCATTTTACGAGTTCGCCCCCCATCATTCCACCTGCAAATTCTCCTAAAATAAATATTTAGGCTGTAGATTTGTTACACTCCGCTATAGCTTTCTTCAGATCTTTATAGCCCCCAACAACCTCATATAAATCAgg                            <  2:440715/148‑1 (MQ=255)                                                                                                                 tATGCGATTTAACCCATTTTACGAGTTCGCCCCCCATCATTCCACCTGCAAATTCTCCTAAAATAAATATTTAGGCTGTAGATTTGTTACACTCCGCTATAGCTTTCTTCAGATCTTTATAGCCCCCAACAACCTCATATAAATCAg                             <  1:252701/147‑1 (MQ=255)                                                                                                                 tATGCGATTTAACCCATTTTACGAGTTCGCCCCCCATCATTCCACCTGCAAATTCTCCTAAAATAAATATTTAGGCTGTAGATTTGTTACACTCCGCTATAGCTTTCTTCAGATCTTTATAGCCCCCAACAACCTCATATAAATCAGGa                           <  1:62189/149‑1 (MQ=255)                                                                                                                  aTGCGATTTAACCCATTTTACGAGTTCGCCCCCCATCATTCCACCTGCAAATTCTCCTAAAATAAATATTTAGGCTGTAGATTTGTTACACTCCGCTATAGCTTTCTTCAGATCTTTATAGCCCCCAACAACCTCATATAAATCAGGATaa                        <  1:510802/151‑1 (MQ=255)                                                                                                                  aTGCGATTTAACCCATTTTACGAGTTCGCCCCCCATCATTCCACCTGCAAATTCTCCTAAAATAAATATTTAGGCTGTAGATTTGTTACACTCCGCTATAGCTTTCTTCAGATCTTTATAGCCCCCAACAACCTCATATAAATCAGGATa                         >  2:28736/1‑150 (MQ=255)                                                                                                                    gCGATTTAACCCATTTTACGAGTTCGCCCCCCATCATTCCACCTGCAAATTCTCCTAAAATAAATATTTAGGCTGTAGATTTGTTACACTCCGCTATAGCTTTCTTCAGATCTTTATAGCCCCCAACAACCTCATATAAATCAGGATAAt                       <  2:345144/150‑1 (MQ=255)                                                                                                                         ttAACCCATTTTACGAGTTCGCCCCCCATCATTCCACCTGCAAATTCTCCTAAAATAAATATTTAGGCTGTAGATTTGTTACACTCCGCTATAGCTTTCTTCAGATCTTTATAGCCCCCAACAACCTCATATAAATCAGGATAATGTCCg                  >  2:107110/1‑150 (MQ=255)                                                                                                                          tAACCCATTTTACGAGTTCGCCCCCCATCATTCCACCTGCAAATTCTCCTAAAGTAAATATTTAGGCTGTAGATTTGTTACACTCCGCTATAGCTTTCTTCAGATCTTTATAGCCCCCAACAACCTCATATAAATCAGGATAATGTCCga                 <  1:33821/150‑1 (MQ=255)                                                                                                                               cATTTTACGAGTTCGCCCCCCATCATTCCACCTGCAAATTCTCCTAAAATAAATATTTAGGCTGTAGATTTGTTACACTCCGCTATAGCTTTCTTCAGATCTTTATAGCCCCCAACAACCTCATATAAATCAGGATAATGTCCGAGAAATc           >  2:163285/1‑151 (MQ=255)                                                                                                                                       gAGTTCGCCCCCCATCATTCCACCTGCAAATTCTCCTAAAATAAATATTTAGGCTGTAGATTTGTTACACTCCGCTATAGCTTTCTTCAGATCTTTATAGCCCCCAACAACCTCATATAAATCAGGATAATGTCCGAGAAATCCAATTATc   <  1:125772/151‑1 (MQ=255)                                                                                                                                        aGTTCGCCCCCCATCATTCCACCTGCAAATTCTCCTAAAATAAATATTTAGGCTGTAGATTTGTTACACTCCGCTATAGCTTTCTTCAGATCTTTATAGCCCCCAACAACCTCATATAAATCAGGATAATGTCCGAGAAATCCAATTATcc  <  2:521021/151‑1 (MQ=255)                                                                                                                                              |                                                                                                                                                 TTCGCCGGGTGACTGGTTTTCCATACGCATCCTTTCGCACCTGCTTCAAGCAATTTTATTGAATCAATATACGGCATCTTTGCTACAAATGTAATAATATGAGCATCTATCTTATGCGATTTAACCCATTTTACGAGTTCGGCCCCCATCATTCCACCTGCAAATTCTCCTAAAATAAATATTTAGGCTGTAGATTTGTTACACTCCGCTATAGCTTTCTTCAGATCTTTATAGCCCCCAACAACCTCATATAAATCAGGATAATGTCCGAGAAATCCAATTATCC  >  NC_000913/2994755‑2995040

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑