Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 2,998,129 C→T pseudogene (700/1137 nt) ygeQ ← pseudogene, glycosyl hydrolase family 15, part of T3SS PAI ETT2 remnant

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,998,1290CT100.0% 196.9 / NA 59pseudogene (700/1137 nt)ygeQpseudogene, glycosyl hydrolase family 15, part of T3SS PAI ETT2 remnant
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (23/36);  total (23/36)

CTCAGGAATCTTCCATAACATAGAAATTGGCTTTATCCAGATAAGCAATCAGCAGCGCAACCGACTTTAATCGGTCACCTTTTTGCCAATCTTCAGCGTTAATAGTACCAGTGTTGATTGCTTGTATAAGGAGATCAAGGTAAAGACCTAAAGCATCATTTTGTTTATGGTTCCACAGCTGCGGCTTGCCTTC  >  NC_000913/2998033‑2998225
                                                                                                |                                                                                                
cTCAGGAATCTTCCATAACATAGAAATTGGCTTTATCCAGATAAGCAATCAGCAGCGCAACCGACTTTAATCGGTCACCTTTTTGCCAATCTTCAGTGtt                                                                                               <  1:1170448/100‑1 (MQ=255)
  gaGGAATCTTCCATAACATAGAAATTGGCTTTATCCAGATAAGCAATCAGCAGCGCAACCGACTTTAATCGGTCACCTTTTTGCCAATCTTCAGTGTTaa                                                                                             >  2:583203/2‑100 (MQ=255)
  cAGGAATCTTCCATAACATAGAAATTGGCTTTATCCAGATAAGCAATCAGCAGCGCAACCGACTTTAATCGGTCACCTTTTTGCCAATCTTCAGTGTTaa                                                                                             >  2:785306/1‑100 (MQ=255)
  cAGGAATCTTCCATAACATAGAAATTGGCTTTATCCAGATAAGCAATCAGCAGCGCAACCGACTTTAATCGGTCACCTTTTTGCCAATCTTCAGTGTTaa                                                                                             >  2:678283/1‑100 (MQ=255)
   aGGAATCTTCCATAACATAGAAATTGGCTTTATCCAGATAAGCAATCAGCAGCGCAACCGACTTTAATCGGTCACCTTTTTGCCAATCTTCAGTGTTAAt                                                                                            <  2:150941/100‑1 (MQ=255)
         cTTCCATAACATAGAAATTGGCTTTATCCAGATAAGCAATCAGCAGCGCAACCGACTTTAATCGGTCACCTTTTTGCCAATCTTCAGTGTTAATAGTAcc                                                                                      <  1:423692/100‑1 (MQ=255)
          ttCCATAACATAGAAATTGGCTTTATCCAGATAAGCAATCAGCAGCGCAACCGACTTTAATCGGTCACCTTTTTGCCAATCTTCAGTGTTATTAGTACCa                                                                                     >  2:1139635/1‑100 (MQ=255)
            ccATAACATAGAAATTGGCTTTATCCAGATAAGCAATCAGCAGCGCAACCGACTTTAATCGGTCACCTTTTTGCCAATCTTCAGTGTTAATAGTACCAgt                                                                                   >  1:1289472/1‑100 (MQ=255)
             cATAACATAGAAATTGGCTTTATCCAGATAAGCAATCAGCAGCGCAACCGACTTTAATCGGTCACCTTTTTGCCAATCTTCAGTGTTAATAGTACCAgtg                                                                                  >  1:147250/1‑100 (MQ=255)
                aaCATAGAAATTGGCTTTATCCAGATAAGCAATCAGCAGCGCAACCGACTTTAATCGGTCACCTTTTTGCCAATCTTCAGTGTTAATAGTACCAGTGtt                                                                                <  1:98244/99‑1 (MQ=255)
                   aTAGAAATTGGCTTTATCCAGATAAGCAATCAGCAGCGCAACCGACTTTAATCGGTCACCTTTTTGCCAATCTTCAGTGTTAATAGTACCAGTGTTGAtt                                                                            >  1:178059/1‑100 (MQ=255)
                        aaTTGGCTTTATCCAGATAAGCAATCAGCAGCGCAACCGACTTTAATCGGTCACCTTTTTGCCAATCTTCAGTGTTAATAGTACCAGTGTTGATTGCTTg                                                                       <  1:671835/100‑1 (MQ=255)
                        aaTTGGCTTTATCCAGATAAGCAATCAGCAGCGCAACCGACTTTAATCGGTCACCTTTTTGCCAATCTTCAGTGTTAATAGTACCAGTGTTGATTGCTTg                                                                       <  1:581925/100‑1 (MQ=255)
                        aaTTGGCTTTATCCAGATAAGCAATCAGCAGCGCAACCGACTTTAATCGGTCACCTTTTTGCCAATCTTCAGTGTTAATAGTACCAGTGTTGATTGCTTg                                                                       >  2:146630/1‑100 (MQ=255)
                           tGGCTTTATCCAGCTAAGCAATCAGCAGCGTAACCGGTTTTAATCGGTTACCTTTTTGCGAATCTTCAGTGTTAATAGTACCAGTGTTGGTTGCTTGt                                                                      <  2:42405/98‑1 (MQ=255)
                           tGGCTTTATCCAGATAAGCAATCAGCAGCGCAACCGACTTTAATCGGTCACCTTTTTGCCAATCTTCATTGTTAATAGTACCAGTGTTGATTGCTTGta                                                                     <  2:414013/99‑1 (MQ=255)
                           tGGCTTTATCCAGATAAGCAATCAGCAGCGCAACCGACTTTAATCGGTCACCTTTTTGCCAATCTTCAGTGTTAATAGTACCAGTGTTGATTGCTTGtat                                                                    <  1:26812/100‑1 (MQ=255)
                            ggCTTTATCCAGATAAGCAATCAGCAGCGCAACCGACTTTAATCGGTCACCTTTTTGCCAATCTTCAGTGTTAATAGTACCAGTGTTGATTGCTTGtata                                                                   <  2:993690/100‑1 (MQ=255)
                            ggCTTTATCCAGATAAGCAATCAGCAGCGCAACCGACTTTAATCGGTCACCTTTTTGCCAATCTTCAGTGTTAATAGTACCAGTGTTGATTGCTTGtata                                                                   >  2:387311/1‑100 (MQ=255)
                             gCTTTATCCAGATAAGCAATCAGCAGCGCAACCGACTTTAATCGGTCACCTTTTTTTTTTTTTTCAGTGTTAATAGTACCAGTGTTGATTGCTTGtata                                                                   >  2:68648/1‑99 (MQ=255)
                                 tATCCAGATAAGCAATCAGCAGCGCAACCGACTTTAATCGGTCACCTTTTTGCCAATCTTCAGTGTTAATAGTACCAGTGTTGATTGCTTGTATAAGgag                                                              <  2:674326/100‑1 (MQ=255)
                                    ccAGATAAGCAATCAGCAGCGCAACCGACTTTAATCGGTCACCTTTTTGCCAATCTTCAGTGTTAATAGTACCAGTGTTGATTGCTTGTATAAGGAGATc                                                           <  2:1286319/100‑1 (MQ=255)
                                    ccAGATAAGCAATCAGCAGCGCAACCGACTTTAATCGGTCACCTTTTTGCCAATATTCAGTGTTAATAGTACCAGTGTTGATTGCTTGTATAAGgaga                                                             >  2:339269/1‑98 (MQ=255)
                                        aTAAGCAATCAGCAGCGCAACCGACTTTAATCGGTCACCTTTTTGCCAATCTTCAGTGTTAATAGTACCAGTGTTGATTGCTTGTATAAGGAGATCAAgg                                                       <  1:1128289/100‑1 (MQ=255)
                                         tAAGCAATCAGCAGCGCAACCGACTTTAATCGGTCACCTTTTTGCCAATCTTCAGTGTTAATAGTACCAGTGTTGATTGCTTGTATAAGGAGATCAAGGt                                                      >  2:1280752/1‑100 (MQ=255)
                                          aaGCAATCAGCAGCGCAACCGACTTTAATCGGTCACCTTTTTGCCAATCTTCAGTGTTAATAGTACCAGTGTTGATTGCTTGTATAAGGAGATCAAGGTa                                                     <  2:1196496/100‑1 (MQ=255)
                                           aGCAATCAGCAGCGCAACCGACTTTAATCGGTCACCTTTTTGCCAATCTTCAGTGTTAATAGTACCAGTGTTGATTGCTTGTATAAGGAGATCAAGGTaa                                                    >  2:965757/1‑100 (MQ=255)
                                           aGCAATCAGCAGCGCAACCGACTTTAATCGGTCACCTTTTTGCCAATCTTCAGTGTTAATAGTACCAGTGTTGAGTGCTTGTATAAGGAGATCAAGGTa                                                     <  2:151130/99‑1 (MQ=255)
                                            gCAATCAGCAGCGCAACCGACTTTAATCGGTCACCTTTTTGCCAATCTTCAGTGTTAATAGTACCAGTGTTGATTGCTTGTATAAGGAGATCAAGGTaaa                                                   <  1:413982/100‑1 (MQ=255)
                                            gCAATCAGCAGCGCAACCGACTTTAATCGGTCACCTTTTTGCCAATCTTCAGTGTTAATAGTACCAGTGTTGATTGCTTGTATAAGGAGATCAAGGTaaa                                                   >  1:306371/1‑100 (MQ=255)
                                               aTCAGCAGCGCAACCGACTTTAATCGGTCACCTTTTTGCCAATCTTCAGTGTTAATAGTACCAGTGTTGATTGCTTGTATAAGGAGATCAAGGTAAAGAc                                                <  2:31265/100‑1 (MQ=255)
                                                tCAGCAGCGCAACCGACTTTAATCGGTCACCTTTTTGCCAATCTTCAGTGTTAATAGTACCAGTGTTGATTGCTTGTATAAGGAGATCAAGGTAAAGAcc                                               <  2:1252987/100‑1 (MQ=255)
                                                  agcagcGCAACCGACTTTAATCGGTCACCTTTTTGCCAATCTTCAGTGTTAATAGTACCAGTGTTGATTGCTTGTATAAGGAGATCAAGGTAAAGACCTa                                             >  1:799090/1‑100 (MQ=255)
                                                     agcGCAACCGACTTTAATCGGTCACCTTTTTGCCAATCTTCAGTGTTAATGGTACCAGTGTTGATTGCTTGTATAAGGAGATCAAGGTAAAGACCTAAAg                                          <  1:712406/100‑1 (MQ=255)
                                                     agcGCAACCGACTTTAATCGGTCACCTTTTTGCCAATCTTCAGTGTTAATAGTACCAGTGTTGATTGCTTGTATAAGGAGATCAAGGTAAAGACCTAAAg                                          <  1:1001663/100‑1 (MQ=255)
                                                       cgcAACCGACTTTAATCGGTCACCTTTTTGCCAATCTTCAGTGTTAATAGTACCAGTGTTGATTGCTTGTATAAGGAGATCAAGGTAAAGACCTAAAGca                                        <  1:353183/100‑1 (MQ=255)
                                                       cgcAACCGACTTTAATCGGTCACCTTTTTGCCAATCTTCAGTGTTAATAGTACCAGTGTTGATTGCTTGTATAAGGAGATCAAGGTAAAGACCTAAAGca                                        >  1:321761/1‑100 (MQ=255)
                                                          aaCCGACTTTAATCGGTCACCTTTTTGCCAATCTTCAGTGTTAATAGTACCAGTGTTGATTGCTTGTATAAGGAGATCAAGGTAAAGACCTAAAGcatca                                     <  2:808133/100‑1 (MQ=255)
                                                             cGACTTTAATCGGTCACCTTTTTGCCAATCTTCAGTGTTAATAGTACCAGTGTTGATTGCTTGTATAAGGAGATCAAGGTAAAGACCTAAAGCATCAttt                                  <  2:446106/100‑1 (MQ=255)
                                                                cTTTAATCGGTCACCTTTTTGCCAATCTTCAGTGTTAATAGTACCAGTGTTGATTGCTTGTATAAGGAGATCAAGGTAAAGACCTAAAGCATCATTTTGt                               >  1:1210164/1‑100 (MQ=255)
                                                                  ttAATCGGTCACCTTTTTGCCAATCTTCAGTGTTAATAGTACCAGTGTTGATTGCTTGTCTAAGGAGATCAAGGTAAAGACCTAAAGAATCATTTTGtt                              >  2:1081333/1‑99 (MQ=255)
                                                                     aTCGGTCACCTTTTTGCCAATCTTCAGTGTTAATAGTACCAGTGTTGATTGCTTGTATAAGGAGATCAAGGTAAAGACCTAAAGCATCATTTTGTTTATg                          <  2:262569/100‑1 (MQ=255)
                                                                      tCGGTCACCTTTTTGCCAATCTTCAGTGTTAATAGTACCAGTGTTGATTGCTTGTATAAGGAGATCAAGGTAAAGACCTAAAGCATCATTTTGTTTATgg                         <  2:872631/100‑1 (MQ=255)
                                                                       cGGTCACCTTTTTGCCAATCTTCAGTGTTAATAGTACCAGTGTTGATTGCTTGTATAAGGAGATCAAGGTAAAGACCTAAAGCATCATTTTGTTTATGGt                        <  1:430921/100‑1 (MQ=255)
                                                                         gTCACCTTTTTGCCAATCTTCAGTGTTAATAGTACCAGTGTTGATTGCTTGTATAAGGAGATCAAGGTAAAGACCTAAAGCATCATTTTGTTTATGGTTc                      <  1:339272/100‑1 (MQ=255)
                                                                             ccTTTTTGCCAATCTTCAGTGTTAATAGTACCAGTGTTGATTGCTTGTATAAGGAGATCAAGGTAAAGACCTAAAGCATCATTTTGTTTATGGTTCcaca                  <  1:1117986/100‑1 (MQ=255)
                                                                             ccTTTTTGCCAATCTTCAGTGTTAATAGTACCAGTGTTGATTGCTTGTATAAGGAGATCAAGGTAAAGACCTAAAGCATCATTTTGTTTATGGTTCcaca                  <  2:466855/100‑1 (MQ=255)
                                                                             ccTTTTTGCCAATCTTCAGTGTTAATAGTACCAGTGTTGATTGCTTGTATAAGGAGATCAAGGTAAAGACCTAAAGCATCATTTTGTTTATGGTTCcaca                  <  2:38445/100‑1 (MQ=255)
                                                                               tttttGCCAATCTTCAGTGTTAATAGTACCAGTGTTGATTGCTTGTATAAGGAGATCAAGGTAAAGACCTAAAGCATCATTTTGTTTATGGTTCCACAGc                <  2:614597/100‑1 (MQ=255)
                                                                                ttttGCCAATCTTCAGTGTTAATAGTACCAGTGTTGATTGCTTGTATAAGGAGATCAAGGTAAAGACCTAAAGCATCATTTTGTTTATGGTTCCACAGCt               <  1:1280763/100‑1 (MQ=255)
                                                                                   tGCCAATCTTCAGTGTTAATAGTACCAGTGTTGATTGCTTGTATAAGGAGATCAAGGTAAAGACCTAAAGCATCATTTTGTTTATGGTTCCACAGCTGCg            >  1:117013/1‑100 (MQ=255)
                                                                                    gCCAATCTTCAGTGTTAATAGTACCAGTGTTGATTGCTTGTATAAGGAGATCAAGGTAAAGACCTAAAGCATCATTTTGTTTATGGTTCCACAGCTGCgg           <  2:985467/100‑1 (MQ=255)
                                                                                     ccAATCTTCAGTGTTAATAGTACCAGTGTTGATTGCTTGTATAAGGAGATCAAGGTAAAGCCCTAAAACATCATTTTGTTTATGGTTCCACAGCTGCGGc          >  2:916374/1‑100 (MQ=255)
                                                                                     ccAATCTTCAGTGTTAATAGTACCAGTGTTGATTGCTTGTATAAGGAGATCAAGGTAAAGACCTAAAGCATCATTTTGTTTATGGTTCCACAGCTGCGGc          >  1:186875/1‑100 (MQ=255)
                                                                                     ccAATCTTCAGTGTTAATAGTACCAGTGTTGATTGCTTGTATAAGGAGATCAAGGTAAAGACCTAAAGCATCATTTTGTTTATGGTTCCACAGCTGCGGc          >  1:1156266/1‑100 (MQ=255)
                                                                                        aTCTTCAGTGTTAATAGTGCCAGTGTTGATTGCTTGTATAAGGAGATCAAGGTAAAGACCTAAAGCATCATTTTGTTTATGGTTCCACAGCTGCGGCt         <  2:321758/98‑1 (MQ=255)
                                                                                          cTTCAGTGTTAATAGTACCAGTGTTGATTGCTTGTATAAGGAGATCAAGGTAAAGACCTAAAGCATCATTTTGTTTATGGTTCCACAGCTGCGGCTTGcc     <  1:1060960/100‑1 (MQ=255)
                                                                                          cTTCAGTGTTAATAGTACCAGTGTTGATTGCTTGTATAAGGAGATCAAGGTAAAGACCTAAAGCATCATTTTGTTTATGGTTCCACAGCTGCGGCTTGcc     <  2:553526/100‑1 (MQ=255)
                                                                                             cAGTGTTAATAGTACCAGTGTTGATTGCTTGTATAAGGAGATCAAGGTAAAGACCTAAAGCATCATTTTGTTTATGGTTCCACAGCTGCGGCTTGCcttc  >  2:953757/1‑100 (MQ=255)
                                                                                                |                                                                                                
CTCAGGAATCTTCCATAACATAGAAATTGGCTTTATCCAGATAAGCAATCAGCAGCGCAACCGACTTTAATCGGTCACCTTTTTGCCAATCTTCAGCGTTAATAGTACCAGTGTTGATTGCTTGTATAAGGAGATCAAGGTAAAGACCTAAAGCATCATTTTGTTTATGGTTCCACAGCTGCGGCTTGCCTTC  >  NC_000913/2998033‑2998225

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap:     Deleted base: