Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,787,434	G→A	pseudogene (1038/2253 nt)	ygaQ →	uncharacterized protein, putative enzyme

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,787,434	0	G	A	100.0%	234.9 / NA	71	pseudogene (1038/2253 nt)	ygaQ	uncharacterized protein, putative enzyme
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (36/35);  total (36/35)

ATATCATTCCTGATTATACCTTTAACTTTATGGGAATTGGGGGTAGTGGTAAAAATGACCTGGATTATCCCTCTGCTGATATACGAGCGAAGATCAGTAAAGATATAGAAGGTGGTATCCCTGGCTATTAGCAAGGTCAGGTTTTGATTCCATTCATTAAAGATCCAGTAACAAAAGAACGTAAACAAATCCATCCAGAAGATATACATCTCACTGCAAAAGACTTCGAAGCAAGTAAAGATAACATCTCTAAGGATGAATGGG  >  NC_000913/2787304‑2787567                                                                                                                                   |                                                                                                                                      atatCATTCCTGATTATACCTTTAACTTTATGGGAATTGGGGGTAGTGGTAAAAATGACCTGGATTATCCCTCTGCTGATATACGAGCGAAGATCAGTAAAGATATAGAAGGTGGTATCCCTGGCTATTAACAAGGTCa                                                                                                                               >  1:659352/1‑139 (MQ=255) atatCATTCCTGATTATACCTTTAACTTTATGGGAATTGGGGGTAGTGGTAAAAATGACCTGGATTATCCCTCTGCTGATATACGAGCGAAGATCAGTAAAGATATAGAAGGTGGTATCCCTGGCTATTAACAAGGTCa                                                                                                                               <  1:4099/139‑1 (MQ=255)                     tttAACTTTATGGGAATTGGGGGTAGTGGTAAAAATGACCTGGATTATCCCTCTGCTGATATACGAGCGAAGATCAGTAAAGATATAGAAGGTGGTATCCCTGGCTATTAACAAGGTCAGGTTTTGATTCCATTCATTa                                                                                                           <  2:659352/139‑1 (MQ=255)                        aaCTTTATGGGAATTGGGGGTAGTGGTAAAAATGACCTGGATTATCCCTCTGCTGATATACGAGCGAAGATCAGTAAAGATATAGAAGGTGGTATCCCTGGCTATTAACAAGGTCAGGTTTTGATTCAATTCATTAAAg                                                                                                        >  2:14621/1‑139 (MQ=255)                              aTGGGAATTGGGGGTAGTGGTAAAAATGACCTGGATTATCCCTCTGCTGATATACGAGCGAAGATCAGTAAAGATATAGAAGGTGGTATCCCTGGCTATTAACAAGGTCAGGTTTTGATTCCATTCATTAAAGATCCAg                                                                                                  >  1:269632/1‑139 (MQ=255)                              aTGGGAATT‑GGGGTAGTGGTAAAAATGACCTGGATTATCCCTCTGCTGATATACGAGCGAAGATCAGTAAAGATATAGAAGGTGGTATCCCTGGCTATTAACAAGGTCAGGTTTTGAtt                                                                                                                     >  2:1734190/1‑119 (MQ=255)                              aTGGGAATT‑GGGGTAGTGGTAAAAATGACCTGGATTATCCCTCTGCTGATATACGAGCGAAGATCAGTAAAGATATAGAAGGTGGTATCCCTGGCTATTAACAAGGTCAGGTTTTGAtt                                                                                                                     <  1:1734190/119‑1 (MQ=255)                               tGGGAATTGGGGGTAGTGGTAAAAATGACCTGGATTATCCCTCTGCTGATATACGAGCGAAGATCAGTAAAGATATAGAAGGTGGTATCCCTGGCTATTAACAAGGTCAGGTTTTGATTCCATTCATTAAAGATCCAGt                                                                                                 <  1:14621/139‑1 (MQ=255)                                     ttGGGGGTAGTGGTAAAAATGACCTGGATTATCCCTCTGCTGATATACGAGCGAAGATCAGTAAAGATATAGAAGGTGGTATCCCTGGCTATTAACAAGGTCAGGTTTTGATTCCATTCATTAAAGATCCAGTAACaaa                                                                                           >  2:366405/1‑139 (MQ=255)                                       gggggTAGTGGTAAAAATGACCTGGATTATCCCTCTGCTGATATACGAGCGAAGATCAGTAAAGATATAGAAGGTGGTATCCCTGGCTATTAACAAGGTCAGGTTTTGATTCCATTCATTaa                                                                                                          >  2:1336989/1‑122 (MQ=255)                                       gggggTAGTGGTAAAAATGACCTGGATTATCCCTCTGCTGATATACGAGCGAAGATCAGTAAAGATATAGAAGGTGGTATCCCTGGCTATTAACAAGGTCAGGTTTTGATTCCATTCATTaa                                                                                                          <  1:1336989/122‑1 (MQ=255)                                             aGTGGTAAAAATGACCTGGATTATCCCTCTGCTGATATACGAGCGAAGATCAGTAAAGATATAGAAGGTGGTATCCCTGGCTATTAACAAGGTCAGGTTTTGATTCca                                                                                                                  <  1:941270/108‑1 (MQ=255)                                             aGTGGTAAAAATGACCTGGATTATCCCTCTGCTGATATACGAGCGAAGATCAGTAAAGATATAGAAGGTGGTATCCCTGGCTATTAACAAGGTCAGGTTTTGATTCca                                                                                                                  >  2:941270/1‑108 (MQ=255)                                                  tAAAAATGACCTGGATTATCCCTCTGCTGATATACGAGCGAAGATCAGTAAAGATATAGAAGGTGGTATCCCTGGCTATTAACAAGGTCAGGTTTTGATTCCATTCATTa                                                                                                           <  1:913625/110‑1 (MQ=255)                                                  tAAAAATGACCTGGATTATCCCTCTGCTGATATACGAGCGAAGATCAGTAAAGATATAGAAGGTGGTATCCCTGGCTATTAACAAGGTCAGGTTTTGATTCCATTCATTa                                                                                                           >  2:913625/1‑110 (MQ=255)                                                                    tCCCTCTGCTGATATACGAGCGAAGATCAGTAAAGATATAGAAGGTGGTATCCCTGGCTATTAACAAg                                                                                                                                   <  2:1070017/68‑1 (MQ=255)                                                                    tCCCTCTGCTGATATACGAGCGAAGATCAGTAAAGATATAGAAGGTGGTATCCCTGGCTATTAACAAg                                                                                                                                   >  1:1070017/1‑68 (MQ=255)                                                                    tCCCTCTGCTGATATACGAGCGAAGATCAGTAAAGATATAGAAGGTGGTATCCCTGGCTATTAACAAGGTCAGGTTTTGATTCCATTCATTAAAGATCCAGTAACAAAAGAACGTAAACAAATCCATCCagaag                                                                 >  2:522806/1‑134 (MQ=255)                                                                    tCCCTCTGCTGATATACGAGCGAAGATCAGTAAAGATATAGAAGGTGGTATCCCTGGCTATTAACAAGGTCAGGTTTTGATTCCATTCATTAAAGATCCAGTAACAAAAGAACGTAAACAAATCCATCCagaag                                                                 <  1:522806/134‑1 (MQ=255)                                                                         ctgctgATATACGAGCGAAGATCAGTAAAGATATAGAAGGTGGTATCCCTGGCTATTAACAAGGTCAGGTTTTGATTCCATTCATTAAAGATCCAGTAACAAAAGAACGTAAACAAATCCATCCAGAAGATATACAtct                                                       <  1:366405/139‑1 (MQ=255)                                                                          tgctgATATACGAGCGAAGATCAGTAAAGATATAGAAGGTGGTATCCCTGGCTATTAACAAGGTCAGGTTTTGATTCCATTCATTAAAGATCCAGTAACAAAAGAACGTAAACAAat                                                                            >  1:757300/1‑117 (MQ=255)                                                                          tgctgATATACGAGCGAAGATCAGTAAAGATATAGAAGGTGGTATCCCTGGCTATTAACAAGGTCAGGTTTTGATTCCATTCATTAAAGATCCAGTAACAAAAGAACGTAAACAAat                                                                            <  2:757300/117‑1 (MQ=255)                                                                              gATATACGAGCGAAGATCAGTAAAGATATAGAAGGTGGTATCCCTGGCTATTAACAAGGTCAGGTTTTGATTCCATTCATTAAAGATCCAGTAACAAAAGAACGTAAACAAATCCATCCAGAATATATACATCTCACTg                                                  >  2:374785/1‑139 (MQ=255)                                                                               atatACGAGCGAAGCTCAGTAAAGATATAGAAGGTGGTATCCCTGGCTATTAACAAGGTCAGGTTTTGATTCCATTCATTAAAGATCCAg                                                                                                  <  1:58798/90‑1 (MQ=255)                                                                               atatACGAGCGAAGATCAGTAAAGATATAGAAGGTGGTATCCCTGGCTATTAACAAGGTCAGGTTTTGATTCCATTCATTAAAGATCCAg                                                                                                  >  2:58798/1‑90 (MQ=255)                                                                                 ataCGAGCGAAGATCAGTAAAGATATAGAAGGTGGTATCCCTGGCTATTAACAAGGTCAGGTTTTGATTCCATTCATTAAAGATCCAGTAACAAAAGAACGTAAACAAATCCATCCAGAAGATATACATCTCACTGCaa                                               >  2:1158329/1‑139 (MQ=255)                                                                                      aGCGAAGATCAGTAAAGATATAGAAGGTGGTATCCCTGGCTATTAACAAGGTCAg                                                                                                                              <  2:730648/55‑1 (MQ=255)                                                                                      aGCGAAGATCAGTAAAGATATAGAAGGTGGTATCCCTGGCTATTAACAAGGTCAg                                                                                                                              >  1:730648/1‑55 (MQ=255)                                                                                      aGCGAAGATCAGTAAAGATATAGAAGGTGGTATCCCTGGCTATTAACAAGGTCAGGTTTTGa                                                                                                                       <  1:612295/62‑1 (MQ=255)                                                                                      aGCGAAGATCAGTAAAGATATAGAAGGTGGTATCCCTGGCTATTAACAAGGTCAGGTTTTGa                                                                                                                       >  2:612295/1‑62 (MQ=255)                                                                                      aGCGAAGATCAGTAAAGATATAGAAGGTGGTATCCCTGGCTATTAACAAGGTCAGGTTTTGATTCCATTCATTaaa                                                                                                         >  1:643244/1‑76 (MQ=255)                                                                                      aGCGAAGATCAGTAAAGATATAGAAGGTGGTATCCCTGGCTATTAACAAGGTCAGGTTTTGATTCCATTCATTaaa                                                                                                         <  2:643244/76‑1 (MQ=255)                                                                                        cGAAGATCAGTAAAGATATAGAAGGTGGTATCCCTGGCTATTAACAAGGTCAGGTTTTGATTCCATTCATTAAAGATCCAGTAACAAAAGAACGTAAACAAATCCATCCAGAAGATATACATCTCACTGCAAAAGACtt                                        >  1:1372640/1‑139 (MQ=255)                                                                                         gAAGATCAGTAAAGATATAGAAGGTGGTATCCCTGGCTATTAACAAGGt                                                                                                                                 >  1:1117406/1‑49 (MQ=255)                                                                                         gAAGATCAGTAAAGATATAGAAGGTGGTATCCCTGGCTATTAACAAGGt                                                                                                                                 <  2:1117406/49‑1 (MQ=255)                                                                                         gAAGATCAGTAAAGATATAGAAGGTGGTATCCCTGGCTATTAACAAGGTCAGGTTTTGATTCCATTCATTAAAGATCCAGTAACAAAAGa                                                                                        <  2:948680/90‑1 (MQ=255)                                                                                         gAAGATCAGTAAAGATATAGAAGGTGGTATCCCTGGCTATTAACAAGGTCAGGTTTTGATTCCATTCATTAAAGATCCAGTAACAAAAGa                                                                                        >  1:948680/1‑90 (MQ=255)                                                                                         gAAGATCAGTAAAGATATAGAAGGTGGTATCCCTGGCTATTAACAAGGTCAGGTTTTGATTCCATTCATTAAAGATCCAGTAACAAAAGAACGTAAACAAATCCATCCAGAAGATATACATCTCACTGCAAAAGACTTc                                       >  2:546792/1‑139 (MQ=255)                                                                                            gATCAGTAAAGATATAGAAGGTGGTATCCCTGGCTATTAACAAGGTCAGGTTTTGATTCCATTCATTAAAGATcc                                                                                                    <  1:1119800/75‑1 (MQ=255)                                                                                            gATCAGTAAAGATATAGAAGGTGGTATCCCTGGCTATTAACAAGGTCAGGTTTTGATTCCATTCATTAAAGATcc                                                                                                    >  2:1119800/1‑75 (MQ=255)                                                                                            gATCAGTAAAGATATAGAAGGTGGTATCCCTGGCTATTAACAAGGTCAGGTTTTGATTCCATTCATTAAAGATCCAGTAACAAAAGAAc                                                                                      >  2:104941/1‑89 (MQ=255)                                                                                            gATCAGTAAAGATATAGAAGGTGGTATCCCTGGCTATTAACAAGGTCAGGTTTTGATTCCATTCATTAAAGATCCAGTAACAAAAGAAc                                                                                      <  1:104941/89‑1 (MQ=255)                                                                                             aTCAGTAAAGATATAGAAGGTGGTATCCCTGGCTATTAACAAGGTCAGGTTTTGATTCCATTCATTaaa                                                                                                         >  1:327290/1‑69 (MQ=255)                                                                                             aTCAGTAAAGATATAGAAGGTGGTATCCCTGGCTATTAACAAGGTCAGGTTTTGATTCCATTCATTaaa                                                                                                         <  2:327290/69‑1 (MQ=255)                                                                                             aTCAGTAAAGATATAGAAGGTGGTATCCCTGGCTATTAACAAGGTCAGGTTTTGATTCCATTCATTAAAGATCCAGTAACAAAAGAACGTAAACAAATCCATCCAGAATATATACATCTCACTGCAAAAGACTTCGAAg                                   <  1:374785/139‑1 (MQ=255)                                                                                              tCAGTAAAGATATAGAAGGTGGTATCCCTGGCTATTAACAAGGTCAGGTTTTGATTCCATTCATTAAAGATCCAGTAACAAAAGAACGTAAACAAATCCATCCAGAAGATATACATCTCACTGCAAAAGACTTCGAAGc                                  <  2:269632/139‑1 (MQ=255)                                                                                                      gATATAGAAGGTGGTATCCCTGGCTATTAACAAGGTCAGGTTTTGATTcc                                                                                                                   <  1:1366680/50‑1 (MQ=255)                                                                                                      gATATAGAAGGTGGTATCCCTGGCTATTAACAAGGTCAGGTTTTGATTcc                                                                                                                   >  2:1366680/1‑50 (MQ=255)                                                                                                        tataGAAGGTGGTATCCCTGGCTATTAACAAGGTCAGGTTGTGATTCCATTCATTAAAGATCCAGTAACAAAAGAACGTAAACAAATCCATCCAGTAGATAGACATCTCACTGCAAAAGACTTCGAAGCAAGTAAAGAt                        <  1:1158329/139‑1 (MQ=255)                                                                                                         ataGAAGGTGGTATCCCTGGCTATTAACAAGGTCAGGTTTTGATTcc                                                                                                                   <  1:823192/47‑1 (MQ=255)                                                                                                         ataGAAGGTGGTATCCCTGGCTATTAACAAGGTCAGGTTTTGATTcc                                                                                                                   >  2:823192/1‑47 (MQ=255)                                                                                                          taGAAGGTGGTATCCCTGGCTATTAACAAGGTCAGGTTTTGATTCCATTCATTAAAGATCCAGTAACAAAAGAACGTAAACAAATCCATCCAGAAGATATACATCTCACTGCaaa                                              >  1:717685/1‑115 (MQ=255)                                                                                                          taGAAGGTGGTATCCCTGGCTATTAACAAGGTCAGGTTTTGATTCCATTCATTAAAGATCCAGTAACAAAAGAACGTAAACAAATCCATCCAGAAGATATACATCTCACTGCaaa                                              <  2:717685/115‑1 (MQ=255)                                                                                                           aGAAGGTGGTATCCCTGGCTATTAACAAGGTCAGGTTTTGATTCCATTCATTAAAGATCCAGTAACAAAAGAACGTAAACAAATCCATCCAGAAGATATACATCTCACTGCAAAAGACTTCGAAGCAAGTAAAGATAAc                     <  1:546792/139‑1 (MQ=255)                                                                                                                 tggtATCCCTGGCTATTAACAAGGTCAGGTTTTGATTCCATTCATTAAAGATCCAGTAACAAAAGAACGTAAACAAATCCATCCAGAAGATATACATCTCACTGCAAAAGACTTCGAAGCAAGTAAAGATAACATctct               >  1:1520338/1‑139 (MQ=255)                                                                                                                  ggtATCCCTGGCTAGTAACAAGGTCAGGTTTTGATTCCATTCATTAAAGATCCAGTAACAAAAGAACGTAAAGAAATCCATCCAGAAGATATACATCTCGCTGCAAAAGACTTCGAAGCAAGTAAAGATAACATCTCTa              >  1:1051603/1‑139 (MQ=255)                                                                                                                      tCCCTGGCTATTAACAAGGTCAGGTTTTGATTCCATTCATTAAAGATCCAGTAACAAAAGAACGTaaa                                                                                 <  1:725493/68‑1 (MQ=255)                                                                                                                      tCCCTGGCTATTAACAAGGTCAGGTTTTGATTCCATTCATTAAAGATCCAGTAACAAAAGAACGTaaa                                                                                 >  2:725493/1‑68 (MQ=255)                                                                                                                           ggCTATTAACAAGGTCAGGTTTTGATTCCATTCATTAAAGATCCa                                                                                                   <  1:714090/45‑1 (MQ=255)                                                                                                                           ggCTATTAACAAGGTCAGGTTTTGATTCCATTCATTAAAGATCCa                                                                                                   >  2:714090/1‑45 (MQ=255)                                                                                                                           ggCTATTAACAAGGTCAGGTTTTGATTCCATTCATTAAAGATCCAGTAACAAAAGAACGTAAACAAATCCATCCAGAAGATATACATCTCACTGCAAAAGACTTCGAAGCAAGTAAAGATaa                      >  1:1220709/1‑122 (MQ=255)                                                                                                                           ggCTATTAACAAGGTCAGGTTTTGATTCCATTCATTAAAGATCCAGTAACAAAAGAACGTAAACAAATCCATCCAGAAGATATACATCTCACTGCAAAAGACTTCGAAGCAAGTAAAGATaa                      <  2:1220709/122‑1 (MQ=255)                                                                                                                           ggCTATTAACAAGGTCAGGTTTTGATTCCATTCATTAAAGATCCAGTAACAAAAGAACGTAAACAAATCCATCCAGAAGATATACATCTCACTGCAAAAGACTTCGAAGCAAGTAAAGATAAc                     >  1:1670244/1‑123 (MQ=255)                                                                                                                           ggCTATTAACAAGGTCAGGTTTTGATTCCATTCATTAAAGATCCAGTAACAAAAGAACGTAAACAAATCCATCCAGAAGATATACATCTCACTGCAAAAGACTTCGAAGCAAGTAAAGATAAc                     >  1:321781/1‑123 (MQ=255)                                                                                                                           ggCTATTAACAAGGTCAGGTTTTGATTCCATTCATTAAAGATCCAGTAACAAAAGAACGTAAACAAATCCATCCAGAAGATATACATCTCACTGCAAAAGACTTCGAAGCAAGTAAAGATAAc                     <  2:321781/123‑1 (MQ=255)                                                                                                                           ggCTATTAACAAGGTCAGGTTTTGATTCCATTCATTAAAGATCCAGTAACAAAAGAACGTAAACAAATCCATCCAGAAGATATACATCTCACTGCAAAAGACTTCGAAGCAAGTAAAGATAAc                     <  2:1670244/123‑1 (MQ=255)                                                                                                                           ggCTATTAACAAGGTCAGGTTTTGATTCCATTCATTAAAGATCCAGTAACAAAAGAACGTAAACAAATCCATCCAGAAGATATACATCTCACTGCAAAAGACTTCGAAGCAAGTAAAGATAACATctct               >  1:1279257/1‑129 (MQ=255)                                                                                                                           ggCTATTAACAAGGTCAGGTTTTGATTCCATTCATTAAAGATCCAGTAACAAAAGAACGTAAACAAATCCATCCAGAAGATATACATCTCACTGCAAAAGACTTCGAAGCAAGTAAAGATAACATctct               <  2:1279257/129‑1 (MQ=255)                                                                                                                              tATTAACAAGGTCAGGTTTTGATTCCATTCATTAAAGATCCAGTAACAAAAGAACGTAAACAAATCCATCCAGAAGATATACATCTCACTGCAAAAGACTTCGAAGCAAGTAAAGATAACATCTCTAAGGATGAATggg  <  2:1372640/139‑1 (MQ=255)                                                                                                                                ttAACAAGGTCAGGTTTTGATTCCATTCATTAAAGATCCAGTAACAAAAGAACGTAAACAAat                                                                            <  1:1466469/63‑1 (MQ=255)                                                                                                                                ttAACAAGGTCAGGTTTTGATTCCATTCATTAAAGATCCAGTAACAAAAGAACGTAAACAAat                                                                            >  2:1466469/1‑63 (MQ=255)                                                                                                                                   |                                                                                                                                      ATATCATTCCTGATTATACCTTTAACTTTATGGGAATTGGGGGTAGTGGTAAAAATGACCTGGATTATCCCTCTGCTGATATACGAGCGAAGATCAGTAAAGATATAGAAGGTGGTATCCCTGGCTATTAGCAAGGTCAGGTTTTGATTCCATTCATTAAAGATCCAGTAACAAAAGAACGTAAACAAATCCATCCAGAAGATATACATCTCACTGCAAAAGACTTCGAAGCAAGTAAAGATAACATCTCTAAGGATGAATGGG  >  NC_000913/2787304‑2787567

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑