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%	193.2 / NA	60	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 (31/29);  total (31/29)

ATATAATTAAAAATAAAATTTTTGCGT‑‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGCTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAACTAAATAATGTCTGGCTTGTTCGCAGATTTCGTTAACCTTGTCAGGGGAGAAACAATGATTAT  >  NC_000913/2995198‑2995447                                                                                                                       |                                                                                                                                      atatAATTAAAAATAAAATTTTTGCGTA‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGcc                                                                                                                  >  2:1079929/1‑139 (MQ=255)     aaTTAAAAATAAAATTTTTGCGTA‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCaaaa                                                                                                              <  1:1079929/139‑1 (MQ=255)     aaTTAAAAATAAAATTTTTGCGTA‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCaaaa                                                                                                              >  1:196660/1‑139 (MQ=255)         aaaaaTAAAATTTTTGCGTAAAAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAg                                                                                                           >  1:970929/1‑139 (MQ=255)                aaatTTTTGCGTAAAAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAattatt                                                                                                    <  2:970929/139‑1 (MQ=255)                 aatTTTTGCGTA‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCa                                                                                                  <  1:32375/139‑1 (MQ=255)                                               aTTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACAttttt                                                                     >  2:250226/1‑139 (MQ=255)                                                    aaaaTCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAAc                                                                <  1:250226/139‑1 (MQ=255)                                                                  atTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGc                                                                                                                   <  1:792810/74‑1 (MQ=255)                                                                  atTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGc                                                                                                                   >  2:792810/1‑74 (MQ=255)                                                                   ttAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATaa                                                                                                                                  <  1:1850032/58‑1 (MQ=255)                                                                   ttAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATaa                                                                                                                                  >  2:1850032/1‑58 (MQ=255)                                                                            tACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCaaaa                                                                                                              >  2:1427653/1‑69 (MQ=255)                                                                            tACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCaaaa                                                                                                              <  1:1427653/69‑1 (MQ=255)                                                                            tACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCa                                                                                                  >  1:1303480/1‑81 (MQ=255)                                                                            tACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCa                                                                                                  <  2:1303480/81‑1 (MQ=255)                                                                            tACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTCAAAACA‑TTTTTCAAATAAATAATTTTTTGCTTGGTTGCaa                                       >  1:1672909/1‑138 (MQ=255)                                                                            tACAATTAGATTATATTCAAATCATTAAACTTGAGCCA‑GGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAACTAAATAATGTCTGGCTTGTTCGCAg                                       >  1:355511/1‑139 (MQ=255)                                                                              cAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAACTAAATAATGTCTGGCTTGTTCGCAGa                                      <  2:196660/139‑1 (MQ=255)                                                                                    gATTATATTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAACTAAATAATGTCTGGCTTGTTCGCAGATTTCGt                                >  1:741604/1‑139 (MQ=255)                                                                                         tatTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAACTAAATAATGTCTGGCTTGTTCGCAGATTTCGtt                               <  1:857359/135‑1 (MQ=255)                                                                                         tatTCAAATCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAACTAAATAATGTCTGGCTTGTTCGCAGATTTCGtt                               >  2:857359/1‑135 (MQ=255)                                                                                               atccATTAAACTTGGGCAAGGGATTTATAATTCTCCAGGGTTTGCAAAACCAAATTTATCCTTACCCAAAGAAT‑TGTTTCAAACATTTTTTCAACTAAATAATGTCTGGCTTGTTCGCAGATTTCGTTAACCTTGTCAg                    <  2:1672909/136‑1 (MQ=255)                                                                                               aaTCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAattatt                                                                                                    >  2:739358/1‑60 (MQ=255)                                                                                               aaTCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAattatt                                                                                                    <  1:739358/60‑1 (MQ=255)                                                                                               aaTCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAACTAAATAATGTCTGGCTTGTTCGCAGATTTCGTTAACCTTGTCa                     >  1:1143963/1‑139 (MQ=255)                                                                                                aTCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCaaaa                                                                                                              <  1:188472/49‑1 (MQ=255)                                                                                                aTCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCaaaa                                                                                                              >  2:188472/1‑49 (MQ=255)                                                                                                aTCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGaa                                                                                                         >  1:1008315/1‑54 (MQ=255)                                                                                                aTCATTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGaa                                                                                                         <  2:1008315/54‑1 (MQ=255)                                                                                                   aTTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAACTAAATAATGTCTgg                                                  >  2:101573/1‑106 (MQ=255)                                                                                                   aTTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAACTAAATAATGTCTgg                                                  <  1:101573/106‑1 (MQ=255)                                                                                                   aTTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAACTAAATAATGTCTGGCTTGTTCGCAGATTTCGTTAACCTTGTCAgggg                 >  2:1402949/1‑139 (MQ=255)                                                                                                   aTTAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAACTAAATAATGTCTGGCTTGTTCGCAGATTTCGTTAACCTTGTCAgggg                 >  2:999178/1‑139 (MQ=255)                                                                                                    ttAAACTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAACTAAATAATGTCTGGCTTGTTCGCAGATTTCGTTAACCTTGTCAGGGga                >  1:1504560/1‑139 (MQ=255)                                                                                                       aaCTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAACTAAATAATGTCTGGCTTGTTCGCAGATTTCGTTAACCTTGTCAGGGGAGaa             <  1:999178/139‑1 (MQ=255)                                                                                                        aCTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAattatt                                                                                                    >  1:1374643/1‑51 (MQ=255)                                                                                                        aCTTGAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAattatt                                                                                                    <  2:1374643/51‑1 (MQ=255)                                                                                                            gAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAACTAaat                                                           >  1:1671752/1‑88 (MQ=255)                                                                                                            gAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAACTAaat                                                           <  2:1671752/88‑1 (MQ=255)                                                                                                            gAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAACTAAATAATGTCTGGCTTGTTCGCAGa                                      >  2:718331/1‑109 (MQ=255)                                                                                                            gAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAACTAAATAATGTCTGGCTTGTTCGCAGa                                      <  1:718331/109‑1 (MQ=255)                                                                                                            gAGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAACTAAATAATGTCTGGCTTGTTCGCAGATTTCGTTAACCTTGTCAGGGGAGAAACAAt        >  2:1159727/1‑139 (MQ=255)                                                                                                             aGCCAGGGAGTTATAAGTCCTTAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCaa                                                                 <  1:1240878/81‑1 (MQ=255)                                                                                                             aGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAat                                                                                                        <  2:137688/42‑1 (MQ=255)                                                                                                             aGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAat                                                                                                        >  1:137688/1‑42 (MQ=255)                                                                                                             aGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCaa                                                                 >  2:1240878/1‑81 (MQ=255)                                                                                                             aGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCaa                                                                 >  1:136997/1‑81 (MQ=255)                                                                                                             aGCCAGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCaa                                                                 <  2:136997/81‑1 (MQ=255)                                                                                                                 aGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGaa                                                                                                         <  2:837943/37‑1 (MQ=255)                                                                                                                 aGGGAGTTATAAGTCCTCAGGGCTTGCCAAAACAGaa                                                                                                         >  1:837943/1‑37 (MQ=255)                                                                                                                  gggAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAACTAAATAATGTCTGGCTTGTTCTCAGATTTCGTTAACCTTGTCAGGGGAGAAACAATGattat  <  2:1143963/139‑1 (MQ=255)                                                                                                                  gggAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAACTAAATAATGTCTGGCTTGTTCGCAGATTTCGTTAACCTTGTCAGGGGAGAAACAATGattat  <  2:741604/139‑1 (MQ=255)                                                                                                                  gggAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATGTTTTCAACTAAATAATGTCTGGCTTGTTCGCAGATTTCGTTAACCTTGTCAGGGTAGAAACAATGattat  <  1:1402949/139‑1 (MQ=255)                                                                                                                   ggAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACAtttt                                                                      <  2:1333722/70‑1 (MQ=255)                                                                                                                   ggAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCaa                                                                 <  1:830846/75‑1 (MQ=255)                                                                                                                   ggAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCaa                                                                 >  2:830846/1‑75 (MQ=255)                                                                                                                   ggAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAACTAAATAATGTCTGGCTTGTTCGCAGATTTCGTTAACCTTGTCAgggg                 <  1:1636463/123‑1 (MQ=255)                                                                                                                   ggAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAACTAAATAATGTCTGGCTTGTTCGCAGATTTCGTTAACCTTGTCAgggg                 >  2:1636463/1‑123 (MQ=255)                                                                                                                   ggAGTTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATAGCCAAAGAATGTGTTTCAAACAtttt                                                                      >  1:1333722/1‑70 (MQ=255)                                                                                                                       |                                                                                                                                      ATATAATTAAAAATAAAATTTTTGCGT‑‑AAAAAAATACCACAGGCATTAAAAAATCATGAGATGATTAAAATATTACAATTAGATTATATTCAAATCATTAAACTTGAGCCAGGGAGCTATAAGTCCTCAGGGCTTGCCAAAACAGAATTATTCATATCCAAAGAATGTGTTTCAAACATTTTTTCAACTAAATAATGTCTGGCTTGTTCGCAGATTTCGTTAACCTTGTCAGGGGAGAAACAATGATTAT  >  NC_000913/2995198‑2995447

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑