Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,997,876	G→A	pseudogene (953/1137 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_000913	2,997,876	0	G	A	100.0%	212.9 / NA	65	pseudogene (953/1137 nt)	ygeQ	pseudogene, glycosyl hydrolase family 15, part of T3SS PAI ETT2 remnant
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (36/29);  total (36/29)

AGTAAAGCCGCATCGGCTTCTCTGTAATGTTTATCTTTTTCCAGATAACCTGGGGATTCTCCCCCTAAATCAAGCTGTAACGTTATTCTTTCATAACCTTTATCTATGAGGTGGTTCAACCTCGTTGTTGAAAGAGTTTCATCCAGTTCATTGACTTTAGCTTCGCGTAGTAAATCAGAGACAAAAACAGAGTCTTT‑CTTCGAGAGTAGGTTTGACAAACGTTCCAGTCCAGAGGTCACCAGTGCAACGGAAG  >  NC_000913/2997750‑2998002                                                                                                                               |                                                                                                                                aGTAAAGCCGCATCGGCTTCTCTGTAATGTTTATCTTTTTCCAGATAACCTGGGGATTCTCCCCCTAAATCAAGCTGTAACGTTATTCTTTCATAACCTTTATCTATGAGGTGGTTCAACCTCGTTATTGaaa                                                                                                                           >  2:1325813/1‑133 (MQ=255) aGTAAAGCCGCATCGGCTTCTCTGTAATGTTTATCTTTTTCCAGATAACCTGGGGATTCTCCCCCTAAATCAAGCTGTAACGTTATTCTTTCATAACCTTTATCTATGAGGTGGTTCAACCTCGTTATTGaaa                                                                                                                           <  1:1325813/133‑1 (MQ=255) aGTAAAGCCGCATCGGCTTCTCTGTAATGTTTATCTTTTTCCAGATAACCTGGGGATTCTCCCCCTAAATCAAGCTGTAACGTTATTCTTTCATAACCTTTATCTATGAGGTGGTTCAACCTCGTTATTGAAAGAGttt                                                                                                                     >  2:608909/1‑139 (MQ=255)       gCCGCATCGGCTTCTCTGTAATGTTTATCTTTTTCCAGATAACCTGGGGATTCTCCCCCTAAATCAAGCTGTAACGTTATTCTTTCATAACCTTTATCTATGAGGTGGTTCAACCTCGTTATTGAAAGAGTTTCATCCa                                                                                                               >  1:175342/1‑139 (MQ=255)            aTCGGCTTCTCTGTAATGTTTATCTTTTTCCAGATAACCTGGGGATTCTCCCCCTAAATCAAGCTGTAACGTTATTCTTTCATAACCTTTATCTATGAGGTGGTTCAACCTCGTTATTGAAAGAGTTTCATCCAGTTCa                                                                                                          <  2:175342/139‑1 (MQ=255)                         tAATGTTTATCTTTTTCCAGATAACCTGGGGATTCTCCCCCTAAATCAAGCTGTAACGTTATTCTTTCATAACCTTTATCTATGAGGTGGTTCAACCTCGTTATTGAAAGAGTTTCATCCAGTTCATTGACTTTAGCtt                                                                                             >  2:1131189/1‑139 (MQ=255)                           aTGTTTATCTTTTTCCAGATAACCTGGGGATTCTCCCCCTAAATCAAGCTGTAACGTTATTCTTTCATAACCTTTATCTATGAGGTGGTTCAACCTCGTTATTGAAAGAGTTTCATCCAGTTCATTGACTTTAGCTTcg                                                                                           <  2:1693307/139‑1 (MQ=255)                                 aTCTTTTTCCAGATAACCTGGGGATTCTCCCCCTAAATCAAGCTGTAACGTTATTCTTTCATAACCTTTATCTATGAGGTGGTTCAACCTCGTTATTGAAAGAGTTTCATCCAGTTCATTGACTTTAGCTTcg                                                                                           <  2:1188248/133‑1 (MQ=255)                                 aTCTTTTTCCAGATAACCTGGGGATTCTCCCCCTAAATCAAGCTGTAACGTTATTCTTTCATAACCTTTATCTATGAGGTGGTTCAACCTCGTTATTGAAAGAGTTTCATCCAGTTCATTGACTTTAGCTTCGCgtagt                                                                                     >  1:1175749/1‑139 (MQ=255)                                 aTCTTTTTCCAGATAACCTGGGGATTCTCCCCCTAAATCAAGCTGTAACGTTATTCTTTCATAACCTTTATCTATGAGGTGGTTCAACCTCGTTATTGAAAGAGTTTCATCCAGTTCATTGACTTTAGCTTCGCgtagt                                                                                     >  1:1311342/1‑139 (MQ=255)                                 aTCTTTTTCCAGATAACCTGGGGATTCTCCCCCTAAATCAAGCTGTAACGTTATTCTTTCATAACCTTTATCTATGAGGTGGTTCAACCTCGTTATTGAAAGAGTTTCATCCAGTTCATTGACTTTAGCTTCGCgtagt                                                                                     <  1:520646/139‑1 (MQ=255)                                 aTCTTTTTCCAGATAACCTGGGGATTCTCCCCCTAAATCAAGCTGTAACGTTATTCTTTCATAACCTTTATCTATGACGTGGTTCAACCTCGTTATTGAAAGAGTTTCATCCAGTTCATTGACTTTAGCTTcg                                                                                           >  1:1188248/1‑133 (MQ=255)                                   cTTTTTCCAGATAACCTGGGGATTCTCCCCCTAAATCAAGCTGTAACGTTATTCTTTCATAACCTTTATCTATGAGGTGGTTCAACCTCGTTATTGaaa                                                                                                                           <  1:1138395/99‑1 (MQ=255)                                   cTTTTTCCAGATAACCTGGGGATTCTCCCCCTAAATCAAGCTGTAACGTTATTCTTTCATAACCTTTATCTATGAGGTGGTTCAACCTCGTTATTGaaa                                                                                                                           >  2:1138395/1‑99 (MQ=255)                                   cTTTTTCCAGATAACCTGGGGATTCTCCCCCTAAATCAAGCTGTAACGTTATTCTTTCATAACCTTTATCTATGAGGTGGTTCAACCTCGTTATTGAAAGAGTTTCATCCAGTTCATTGACTTTAGCTTCGCGTAGTaa                                                                                   >  2:782783/1‑139 (MQ=255)                                      tttCCAGATAACCTGGGGATTCTCCCCCTAAATCAAGCTGTAACGTTATTCTTTCATAACCTTTATCTATGAGGTGGTTCAACCTCGTTATTGAAAGAGTTTCATCCAGTTCATTGACTTTAGCTTCGCGTAGTAAATc                                                                                >  1:562695/1‑139 (MQ=255)                                       ttCCAGATAACCTGGGGATTCTCCCCCTAAATCAAGCTGTAACGTTATTCTTTCATAACCTTTATCTATGAGGTGGTTCAACCTCGTTATTGAAAGAGTTTCATCCAGTTCATTGACTTTAGCTTCGCGTAGTAAATCa                                                                               <  2:47112/139‑1 (MQ=255)                                                   tGGGGATTCTCCCCCTAAATCAAGCTGTAACGTTATTCTTTCATAACCTTTATCTATGAGGTGGTTCAACCTCGTTATTGAAAGAGTTTCATCCAGTTCATTGACTTTAGCTTCGCGTAGTAAATCAGAGACAAAAACa                                                                   <  1:1131189/139‑1 (MQ=255)                                                     gggATTCTCCCCCTAAATCAAGCTGTAACGTTATTCTTTCATAACCTTTATCTATGAGGTGGTTCAACCTCGTTATTGAAAGAGTTTCATCCAGTTCATTGACTTTAg                                                                                                <  2:1384260/108‑1 (MQ=255)                                                     gggATTCTCCCCCTAAATCAAGCTGTAACGTTATTCTTTCATAACCTTTATCTATGAGGTGGTTCAACCTCGTTATTGAAAGAGTTTCATCCAGTTCATTGACTTTAg                                                                                                >  1:1384260/1‑108 (MQ=255)                                                     gggATTCTCCCCCTAAATCAAGCTGTAACGTTATTCTTTCATAACCTTTATCTATGAGGTGGTTCAACCTCGTTATTGAAAGAGTTTCATCCAGTTCATTGACTTTAGCTTCGCGTAGTAAATCAGAGACAAAAACaga                                                                 >  2:1404086/1‑139 (MQ=255)                                                          tctcCCCCTAAATCAAGCTGTAACGTTATTCTTTCATAACCTTTATCTATGAGGTGGTTCAACCTCGTTATTGAAAGAGTTTCATCCAGTTCATTGACTTTAGCTTCGCGTAGTAAATCAGAGACAAAAACa                                                                   >  2:1494002/1‑132 (MQ=255)                                                          tctcCCCCTAAATCAAGCTGTAACGTTATTCTTTCATAACCTTTATCTATGAGGTGGTTCAACCTCGTTATTGAAAGAGTTTCATCCAGTTCATTGACTTTAGCTTCGCGTAGTAAATCAGAGACAAAAACa                                                                   <  1:1494002/132‑1 (MQ=255)                                                                        aaGCTGTAACGTTATTCTTTCATAACCTTTATCTATGAGGTGGTTCAACCTCGTTATTGAAAGAGTTTCATCCAGTTCATTGACTTTAGCTTCGCGTAGTAAATCAGAGACAAAAACAGAGTCTTT‑CTTCGAGAGTAgg                                             <  2:562695/139‑1 (MQ=255)                                                                          gCTGTAACGTTATTCTTTCATAACCTTTATCTATGAGGTGGTTCAACCTCGTTATTGAAAGAGTTTCATCCAg                                                                                                              <  2:31196/73‑1 (MQ=255)                                                                          gCTGTAACGTTATTCTTTCATAACCTTTATCTATGAGGTGGTTCAACCTCGTTATTGAAAGAGTTTCATCCAg                                                                                                              >  1:31196/1‑73 (MQ=255)                                                                              tAACGTTATTCTTTCATAACCTTTATCTATGAGGTGGTTCAACCTCGTTATTGAAAGAGTTTCATCCAGTTCATTGACTTTAGCTTCGCGTAGTAAATCAGAGACAAAAACAGAGTCTTT‑CTTCgaga                                                  >  1:165140/1‑128 (MQ=255)                                                                              tAACGTTATTCTTTCATAACCTTTATCTATGAGGTGGTTCAACCTCGTTATTGAAAGAGTTTCATCCAGTTCATTGACTTTAGCTTCGCGTAGTAAATCAGAGACAAAAACAGAGTCTTT‑CTTCgaga                                                  <  2:165140/128‑1 (MQ=255)                                                                                   ttATTCTTTCATAACCTTTATCTATGAGGTGGTTCAACCTCGTTATTGAAAGAGTTTCATCCAGTTCATTGACTTTAGCTTCGCGTAGTAAATCAGAGACAAAAACAGAGTCTTT‑CTTCGAGAGTAGGTTTGACAAACg                                  <  1:782783/139‑1 (MQ=255)                                                                                     aTTCTTTCATAACCTTTATCTATGAGGTGGTTCAACCTCGTTATTGAAAGAGTTTCATCCAGTTCATTGACTTTAGCTTCGCGTAGTAAATCAGAGACAAAAACAGAGTCTTT‑CTTCGAGAGTAGGTTTGACAAACGtt                                <  2:758133/139‑1 (MQ=255)                                                                                     aTTCTTTCATAACCTTTATCTATGAGGTGGTTCAACCTCGTTATTGAAAGAGTTTCATCCAGTTCATTGACTTTAGCTTCGCGTAGTAAATCAGAGACAAAAACAGAGTCTTT‑CTTCGAGAGTAGGTTTGACAAACGtt                                >  1:758133/1‑139 (MQ=255)                                                                                      ttCTTTCATAACCTTTATCTATGAGGTGGTTCAACCTCGTTATTGAAAGAGTTTCATCCAGTTCATTGACTTTAGCTTCGCGTAGTAAATCAGAGACAAAAACAGAGTCTTT‑CTTCGAGAGTAGGTTTGACAAACGTtc                               <  2:1248143/139‑1 (MQ=255)                                                                                      ttCTTTCATAACCTTTATCTATGAGGTGGTTCAACCTCGTTATTGAAAGAGTTTCATCCAGTTCATTGACTTTAGCTTCGCGTAGTAAATCAGAGACAAAAACAGAGTCTTT‑CTTCGAGAGTAGGTTTGACAAACGTtc                               <  1:608909/139‑1 (MQ=255)                                                                                      ttCTTTCATAACCTTTATCTATGAGGTGGTTCAACCTCGTTATTGAAAGAGTTTCATCCAGTTCATTGACTTTAGCTTCGCGTAGTAAATCAGAGACAAAAACAGAGTCTTT‑CTTCGAGAGTAGGTTTGACAAACGTtc                               >  1:963389/1‑139 (MQ=255)                                                                                        cTTTCATAACCTTTATCTATGAGGTGGTTCAACCTCGTTATTGAAAGAGTTTCATCCAGTTCATTGACTTTAGCTTCGCGTAGTAAATCAGAGACAAAAACAGAGTCTTT‑CTTCGAGAGTAGGTTTGACAAACGTtcca                             >  2:1762678/1‑139 (MQ=255)                                                                                                     tATCTATGAGGTGGTTCAACCTCGTTATTGAAAGAGTTTCATCCAGTTCATTGACTTTAGCTTCGCGTAGTAAATCAGAGACAAAAACAGAGTCTTT‑CTTCGAGAGTAGGTTTGACAAACGTTCCAGTCCAGAGGTCAc                >  1:149556/1‑139 (MQ=255)                                                                                                      aTCTATGAGGTGGTTCAACCTCGTTATTGAAAGAGTTTCATCCAGTTCATTGACTTTAGCTTcg                                                                                           <  1:905393/64‑1 (MQ=255)                                                                                                      aTCTATGAGGTGGTTCAACCTCGTTATTGAAAGAGTTTCATCCAGTTCATTGACTTTAGCTTcg                                                                                           >  2:905393/1‑64 (MQ=255)                                                                                                          aTGAGGTGGTTCAACCTCGTTATTGAAAGAGTTTCATCCAGTTCATTGACTTTAGCTTCGCGTAGTAAATCAGAGACAAAAACAGAGTCTTT‑CTTCGAGAGTAGGTTTGACAAACGTTCCAGTCCAGAGGTCACCAGTg           <  2:149556/139‑1 (MQ=255)                                                                                                           tGAGGTGGTTCAACCTCGTTATTGAAAGAGTTTCATCCAg                                                                                                              >  1:502985/1‑40 (MQ=255)                                                                                                           tGAGGTGGTTCAACCTCGTTATTGAAAGAGTTTCATCCAg                                                                                                              <  2:502985/40‑1 (MQ=255)                                                                                                           tGAGGTGGTTCAACCTCGTTATTGAAAGAGTTTCATCCAGTTCATTGACTTTAGCTTCGCGTAGTAAATCAGAGACAAAAACAGAGTCTTT‑CTTCGAGAGTAGGTTTGACAAACGTtc                               >  2:1055372/1‑118 (MQ=255)                                                                                                           tGAGGTGGTTCAACCTCGTTATTGAAAGAGTTTCATCCAGTTCATTGACTTTAGCTTCGCGTAGTAAATCAGAGACAAAAACAGAGTCTTT‑CTTCGAGAGTAGGTTTGACAAACGTtc                               <  1:1055372/118‑1 (MQ=255)                                                                                                           tGAGGTGGTTCAACCTCGTTATTGAAAGAGTTTCATCCAGTTCATTGACTTTAGCTTCGCGTAGTAAATCAGAGACAAAAACAGAGTCTTT‑CTTCGAGAGTAGGTTTGACAAACGTTCCAATCCAGAGGTCACCAGTGc          >  1:1527169/1‑139 (MQ=255)                                                                                                            gAGGTGGTTCAACCTCGTTATTGAAAGAGTTTCATCCAGTTCATTGACTTTAGCTTCGCGTAGTAAATCAGAGACAAAAACAGAGTCTTT‑CTTCGAGAGTAGGTTTGACAAACGTTCCAGTCCAGAGGTCACCAGTGCa         >  1:1519956/1‑139 (MQ=255)                                                                                                            gAGGTGGTTCAACCTCGTTATTGAAAGAGTTTCATCCAGTTCATTGACTTTAGCTTCGCGTAGTAAATCAGAGACAAAAACAGAGTCTTT‑CTTCGAGAGTAGGTTTGACAAACGTTCCAGTCCAGAGGTCACCAGTGCa         >  2:379862/1‑139 (MQ=255)                                                                                                              ggtggtTCAACCTCGTTATTGAAAGAGTTTCATCCAGTTCATTGACTTTAGCTTCGCGTAGTAAATCAGAGACAAAAACAGAGTCTTT‑CTTCGAGAGTAGGTTTGACAAACGTTCCAGTCCAGAGGTCAc                >  1:231555/1‑130 (MQ=255)                                                                                                              ggtggtTCAACCTCGTTATTGAAAGAGTTTCATCCAGTTCATTGACTTTAGCTTCGCGTAGTAAATCAGAGACAAAAACAGAGTCTTT‑CTTCGAGAGTAGGTTTGACAAACGTTCCAGTCCAGAGGTCAc                <  2:231555/130‑1 (MQ=255)                                                                                                                 ggtTCAACCTCGTTATTGAAAGAGTTTCATCCAGTTCATTGACTTTAGCTTCGCGTAGTAAATCAGAGACa                                                                         >  2:1498504/1‑71 (MQ=255)                                                                                                                 ggtTCAACCTCGTTATTGAAAGAGTTTCATCCAGTTCATTGACTTTAGCTTCGCGTAGTAAATCAGAGACa                                                                         <  1:1498504/71‑1 (MQ=255)                                                                                                                  gtTCAACCTCGTTATTGAAAGAGTTTCATCCAGTTCATTGACTTTAGCTTcg                                                                                           >  2:630162/1‑52 (MQ=255)                                                                                                                  gtTCAACCTCGTTATTGAAAGAGTTTCATCCAGTTCATTGACTTTAGCTTcg                                                                                           <  1:630162/52‑1 (MQ=255)                                                                                                                  gtTCAACCTCGTTATTGAAAGAGTTTCATCCAGTTCATTGACTTTAGCTTCGCGTAGTAAATCAGAGACAAAAACAGAGTCTTT‑CTTCGAGAGTAGGTTTGACAAACGTTCCAGTCCAGAGGTCACCAGTGCAACGGaa   >  1:1335086/1‑139 (MQ=255)                                                                                                                   ttCATCCTCGTTATTGAAAGAGTTTCATCCAGTTCATTGACTTTAGCTTCGCGTAGTAAATCAGAGACAGAAACAGAGTCTTT‑CTTCGAGAGTAGGTTTGACAAACGTTCCAGTCCAGAGGTCACCAGTGCAACGGAAg  >  1:1093179/1‑139 (MQ=255)                                                                                                                   ttCAACCTCGTTATTGAAAGAGTTTCATCCAGTTCATTGACTTTAGCTTCGCGTAGTAAATCAGAGACAAAAACAGAGTCTTT‑CTTCGAGAGTAGGTTTGACAAACGTtc                               <  1:299434/110‑1 (MQ=255)                                                                                                                   ttCAACCTCGTTATTGAAAGAGTTTCATCCAGTTCATTGACTTTAGCTTCGCGTAGTAAATCAGAGACAAAAACAGAGTCTTT‑CTTCGAGAGTAGGTTTGACAAACGTtc                               >  2:299434/1‑110 (MQ=255)                                                                                                                   ttCAACCTCGTTATTGAAAGAGTTTCATCCAGTTCATTGACTTTAGCTTCGCGTAGTAAATCAGAGACAAAAACAGAGTCTTT‑CTTCGAGAGTAGGTTTGACAAACGTTCCAGTCCAGAGGTCACCAGTGCAACGGAAg  >  2:618515/1‑139 (MQ=255)                                                                                                                     cAACCTCGTTATTGAAAGAGTTTCATCCAGTTCATTGACTTTAGCTTCGCGTAGTAAATCAGAGACAAAAACAGAGTCTTTCCTTCGAGAGTAGGTTTGACAAACGTTCCAGTCCAGAGGTCACCAGTGCAACGGAAg  >  1:225546/1‑138 (MQ=255)                                                                                                                     cAACCTCGTTATTGAAAGAGTTTCATCCAGTTCATTGACTTTAGCTTCGCGTAGTAAATCAGAGACAAAAACAGAGTCTTTCCTTCGAGAGTAGGTTTGACAAACGTTCCAGTCCAGAGGTCACCAGTGCAACGGAAg  <  2:225546/138‑1 (MQ=255)                                                                                                                       aCCTCGTTATTGAAAGAGTTTCATCCAGTTCATTGACTTTAGCTTCGCGTAGTAAATCAGAGACAAAAACAGAGTCTTT‑CTTCGAGAGTAGGTTTGACaaa                                    <  2:341756/101‑1 (MQ=255)                                                                                                                       aCCTCGTTATTGAAAGAGTTTCATCCAGTTCATTGACTTTAGCTTCGCGTAGTAAATCAGAGACAAAAACAGAGTCTTT‑CTTCGAGAGTAGGTTTGACaaa                                    >  1:341756/1‑101 (MQ=255)                                                                                                                       aCCTCGTTATTGAAAGAGTTTCATCCAGTTCATTGACTTTAGCTTCGCGTAGTAAATCAGAGACAAAAACAGAGTCTTT‑CTTCGAGAGTAGGTTTGACAAACGTtc                               <  1:117739/106‑1 (MQ=255)                                                                                                                       aCCTCGTTATTGAAAGAGTTTCATCCAGTTCATTGACTTTAGCTTCGCGTAGTAAATCAGAGACAAAAACAGAGTCTTT‑CTTCGAGAGTAGGTTTGACAAACGTtc                               >  2:117739/1‑106 (MQ=255)                                                                                                                        ccTCGTTATTGAAAGAGTTTCATCCAGTTCATTGACTTTAGCTTCGCGTAGTAAATCAGAGACAAAAACAGAGTCTTT‑CTTCGAGAGTAGGTTTGACaaa                                    <  2:1241699/100‑1 (MQ=255)                                                                                                                        ccTCGTTATTGAAAGAGTTTCATCCAGTTCATTGACTTTAGCTTCGCGTAGTAAATCAGAGACAAAAACAGAGTCTTT‑CTTCGAGAGTAGGTTTGACaaa                                    >  1:1241699/1‑100 (MQ=255)                                                                                                                            gttattGAAAGAGTTTCATCCAGTTCATTGACTTTAGCTTCGCGTAGTAAATCAGAGACAAAAACAGAGTCTTT‑CTTCGAGAGTAGGTTTGACAAACGTTCCAGTCCagag                     <  2:1534919/111‑1 (MQ=255)                                                                                                                               |                                                                                                                                AGTAAAGCCGCATCGGCTTCTCTGTAATGTTTATCTTTTTCCAGATAACCTGGGGATTCTCCCCCTAAATCAAGCTGTAACGTTATTCTTTCATAACCTTTATCTATGAGGTGGTTCAACCTCGTTGTTGAAAGAGTTTCATCCAGTTCATTGACTTTAGCTTCGCGTAGTAAATCAGAGACAAAAACAGAGTCTTT‑CTTCGAGAGTAGGTTTGACAAACGTTCCAGTCCAGAGGTCACCAGTGCAACGGAAG  >  NC_000913/2997750‑2998002

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑