Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,995,314	C→T	pseudogene (447/447 nt)	ygeN ←	pseudogene, orgB family, part of T3SS PAI ETT2 remnant

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,995,314	0	C	T	100.0%	213.0 / NA	65	pseudogene (447/447 nt)	ygeN	pseudogene, orgB family, part of T3SS PAI ETT2 remnant
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (35/30);  total (35/30)

AATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGCTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAACTAAATAATGTCTGGCTTGTTCGCAGATTTCGTTAACCTTGTCAGGGGAGAAACAATGATTATT  >  NC_000913/2995192‑2995448                                                                                                                            |                                                                                                                                       aatGAAATATAATTAAAAATAAAATTTTTGCGTAAAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAggg                                                                                                                         >  1:1636897/1‑139 (MQ=255)         ataATTAAAAAGAAAATTTTTGCGTAAAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGTCTTACCaa                                                                                                                 <  1:1074301/139‑1 (MQ=255)           aaTTAAAAATAAAATTTTTGCGTAAAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCaaaa                                                                                                               >  2:676986/1‑139 (MQ=255)           aaTTAAAAATAAAATTTTTGCGTAAAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCaaaa                                                                                                               >  2:1165605/1‑139 (MQ=255)               aaaaaTAAAATTTTTGCGTAAAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGa                                                                                                           >  2:1437034/1‑139 (MQ=255)                     aaaatTTTTGCGTAAAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAattatt                                                                                                     <  1:866345/139‑1 (MQ=255)                       aatTTTTGCGTAAAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCa                                                                                                   <  1:1437034/139‑1 (MQ=255)                                           aCCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAattatt                                                                                                     <  2:1339926/117‑1 (MQ=255)                                           aCCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAattatt                                                                                                     >  1:1339926/1‑117 (MQ=255)                                           aCCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCa                                                                               <  1:676986/139‑1 (MQ=255)                                              acaGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAAc                                                                            >  1:301680/1‑139 (MQ=255)                                               caGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGaa                                                                                                          >  2:539161/1‑108 (MQ=255)                                               caGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGaa                                                                                                          <  1:539161/108‑1 (MQ=255)                                               caGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACa                                                                           >  2:1209874/1‑139 (MQ=255)                                                       aaaaaaTCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCa                                                                   >  1:1123209/1‑139 (MQ=255)                                                            aTCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAACTaa                                                              >  2:523458/1‑139 (MQ=255)                                                              cATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTTTTTCAAACATTTTTTCAACTAaat                                                            <  2:1123209/139‑1 (MQ=255)                                                                       atTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACAtttttt                                                                     >  2:570677/1‑121 (MQ=255)                                                                       atTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACAtttttt                                                                     <  1:570677/121‑1 (MQ=255)                                                                                 tACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACAtttttt                                                                     <  2:984972/111‑1 (MQ=255)                                                                                 tACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACAtttttt                                                                     >  1:984972/1‑111 (MQ=255)                                                                                 tACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAACTAAATAATGt                                                       <  2:225775/125‑1 (MQ=255)                                                                                 tACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAACTAAATAATGt                                                       >  1:225775/1‑125 (MQ=255)                                                                                   cAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAACTAAATAATGTCTGGCTTGTTCGCAGa                                       <  2:301680/139‑1 (MQ=255)                                                                                   cAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAACTAAATAATGTCTGGCTTGTTCGCAGa                                       <  1:1165605/139‑1 (MQ=255)                                                                                        aGATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAACTAAATAATGTCTGGCTTGTTCGCAGa                                       >  1:1324163/1‑134 (MQ=255)                                                                                        aGATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAACTAAATAATGTCTGGCTTGTTCGCAGa                                       <  2:1324163/134‑1 (MQ=255)                                                                                        aGATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAACTAAATAATGTCTGGCTTGTTCGCAGATTTCg                                  <  2:1591664/139‑1 (MQ=255)                                                                                          aTTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAatta                                                                                                       <  1:235971/68‑1 (MQ=255)                                                                                          aTTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAatta                                                                                                       >  2:235971/1‑68 (MQ=255)                                                                                             atatTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAACTAAATAATGTCTGGCTTGTTCGCAGATTTCGTTAAc                             <  1:564739/139‑1 (MQ=255)                                                                                              tatTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAggg                                                                                                                         <  2:480672/46‑1 (MQ=255)                                                                                              tatTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAggg                                                                                                                         >  1:480672/1‑46 (MQ=255)                                                                                              tatTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAACTAAATAATGTCTGGCTTGTTCGCAGATTTCGTTAAcc                            >  1:978460/1‑139 (MQ=255)                                                                                                ttCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAACTAAATAATGTCTGGCTTGTTCGCAGATTTCGTTAACCtt                          >  1:952447/1‑139 (MQ=255)                                                                                                    aaTCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAACTAAATAATGTCTGGCTTGTTCGCAGATTTCGTTAACCTTGTCa                      >  1:224682/1‑139 (MQ=255)                                                                                                     aTCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCaaaa                                                                                                               >  2:600968/1‑49 (MQ=255)                                                                                                     aTCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCaaaa                                                                                                               <  1:600968/49‑1 (MQ=255)                                                                                                     aTCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAACTAAATAATGTCTGGCTTGTTCGCAGATTTCg                                  >  1:117045/1‑126 (MQ=255)                                                                                                     aTCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAACTAAATAATGTCTGGCTTGTTCGCAGATTTCg                                  <  2:117045/126‑1 (MQ=255)                                                                                                     aTCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAACTAAATAATGTCTGGCTTGTTCGCAGATTTCGTTAACCTTGTCAg                     >  1:335592/1‑139 (MQ=255)                                                                                                        aTTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCaaaa                                                                                                               <  1:934315/46‑1 (MQ=255)                                                                                                        aTTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCaaaa                                                                                                               >  2:934315/1‑46 (MQ=255)                                                                                                        aTTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAAtg                                                                                      >  2:426177/1‑71 (MQ=255)                                                                                                        aTTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAAtg                                                                                      <  1:426177/71‑1 (MQ=255)                                                                                                        aTTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAAc                                                                 <  1:148557/92‑1 (MQ=255)                                                                                                        aTTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAAc                                                                 >  2:148557/1‑92 (MQ=255)                                                                                                         ttAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAACTAAATAATGTCTGGCTTGTTCGCAGATTTCGTTAACCTTGTCAGGGga                 <  2:224682/139‑1 (MQ=255)                                                                                                          tAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAACTAAATAATGTCTGGCTTGTTCGCAGATTTCGTTAAc                             <  1:583847/126‑1 (MQ=255)                                                                                                          tAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAACTAAATAATGTCTGGCTTGTTCGCAGATTTCGTTAAc                             >  2:583847/1‑126 (MQ=255)                                                                                                          tAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAACTAAATAATGTCTGGCTTGTTCGCAGATTTCGTTAACCTTGTCAgggg                  <  2:108441/137‑1 (MQ=255)                                                                                                          tAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAACTAAATAATGTCTGGCTTGTTCGCAGATTTCGTTAACCTTGTCAgggg                  >  1:108441/1‑137 (MQ=255)                                                                                                          tAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAACTAAATAATGTCTGGCTTGTTCGCAGATTTCGTTAACCTTGTCAGGGgag                <  2:952447/139‑1 (MQ=255)                                                                                                                 gAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAAt                                                                                       <  1:558318/61‑1 (MQ=255)                                                                                                                 gAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAAt                                                                                       >  2:558318/1‑61 (MQ=255)                                                                                                                 gAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAACTAAATAATGTCTGGCTTGTTCGCAGATTTCGTTAACCTTGTCAGGGGAGAAACAAt         >  2:1476021/1‑139 (MQ=255)                                                                                                                  aGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAACTAaataa                                                          >  2:1081734/1‑89 (MQ=255)                                                                                                                  aGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAACTAaataa                                                          <  1:1081734/89‑1 (MQ=255)                                                                                                                  aGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAACTAAATAATGTCTGGCTTGTTCGCAGATTTCGTTAACCTTGTCAGGGGAGAAACAATg        >  1:1657681/1‑139 (MQ=255)                                                                                                                  aGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAACTAAATAATGTCTGGCTTGTTCGCAGATTTCGTTAACCTTGTCAGGGGAGAAACAATg        >  1:705206/1‑139 (MQ=255)                                                                                                                       gggAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAACTAAATAATGTCTGGCTTGTTCGCAGATTTCGTTAACCTTGTCAGGGGAGAAACAATGattat   <  2:1657681/139‑1 (MQ=255)                                                                                                                        ggAGTTATAAGTCCTCAGGGCTTGCCAAAACAGac                                                                                                          <  1:1017392/35‑2 (MQ=255)                                                                                                                        ggAGTTATAAGTCCTCAGGGCTTGCCAAAACAGaa                                                                                                          >  2:1017392/1‑35 (MQ=255)                                                                                                                        ggAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAACTAAATAATGTCTGGCTTGTTCGCAGATTTCGTTAACCTTGTCAGGGGAGAAACAATGattatt  >  1:928758/1‑139 (MQ=255)                                                                                                                        ggAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAACTAAATAATGTCTGGCTTGTTCGCAGATTTCGTTAACCTTGTCAGGGGAGAAACAATGattatt  >  2:1114812/1‑139 (MQ=255)                                                                                                                            |                                                                                                                                       AATGAAATATAATTAAAAATAAAATTTTTGCGT‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGCTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAACTAAATAATGTCTGGCTTGTTCGCAGATTTCGTTAACCTTGTCAGGGGAGAAACAATGATTATT  >  NC_000913/2995192‑2995448

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑