Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,786,746	Δ1 bp	pseudogene (350/2253 nt)	ygaQ →	uncharacterized protein, putative enzyme

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,786,746	0	C	.	100.0%	292.5 / NA	66	pseudogene (350/2253 nt)	ygaQ	uncharacterized protein, putative enzyme
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base . (33/33);  total (33/33)

TCTGTTAAAAAACGATTATAAAATTTCCCTTTCTCCAGATACAACTTACCGAGAGTTGAATAAAGCAGCACAGCGTAGCATTACAGCGCCAGACAGGATAGGAGAAAGAAAAACATAGGTTTATCAACGAGATACAATGATTGAAAGAGGTGATAACAGCGGTGTTTATCAGTATGGTCGTGCTGAACATTTCACCCACATTATATCTGACAAACCTTCCCCAAAAGATAAATATGTTGCATATGC  >  NC_000913/2786612‑2786857                                                                                                                                       |                                                                                                                tCTGTTAAAAAACGATTATAAAATTTCCCTTTCTCCAGATACAACTTACCGAGAGTTGAATAAAGCAGCACAGCGTAGCATTACAGCGCCAGACAGGATAGGAGAAAGAAAAACATAAGTTTATCAACGAGATA‑AATGa                                                                                                            >  1:435121/1‑139 (MQ=255) tCTGTTAAAAAACGATTATAAAATTTCCCTTTCTCCAGATACAACTTACCGAGAGTTGAATAAAGCAGCACAGCGTAGCATTACAGCGCCAGACAGGATAGGAGAAAGAAAAACATAAGTTTATCAACGAGATA‑AATGa                                                                                                            >  2:644721/1‑139 (MQ=255)     ttAAAAAACGATTATAAAATTTCCCTTTCTCCAGATACAACTTACCGAGAGTTGAATAAAGCAGCACAGCGTAGCATTACAGCGCCAGACAGGATAGGAGAAAGAAAAACATAAGTTTATCAACGAGATA‑AATGATTGa                                                                                                        >  2:305385/1‑139 (MQ=255)             cGATTATAAAATTTCCCTTTCTCCAGATACAACTTACCGAGAGTTGAATAAAGCAGCACAGCGTAGCATTACAGCGCCAGACAGGATAGGAGAAAGAAAAACATAAGTTTATCAACGAGATA‑AATGATTGAAAGAGGTg                                                                                                >  2:628714/1‑139 (MQ=255)               aTTATAAAATTTCCCTTTCTCCAGATACAACTTACCGAGAGTTGAATAAAGCAGCACAGCGTAGCATTACAGCGCCAGACAGGATAGGAGAAAGAAAAACATAAGTTTATCAACGAGATA‑AATGATTGAAAGAGGTGAt                                                                                              >  1:145703/1‑139 (MQ=255)               aTTATAAAATTTCCCTTTCTCCAGATACAACTTACCGAGAGTTGAATAAAGCAGCACAGCGTAGCATTACAGCGCCAGACAGGATAGGAGAAAGAAAAACATAAGTTTATCAACGAGATA‑AATGATTGAAAGAGGTGAt                                                                                              >  1:876353/1‑139 (MQ=255)                    aaaaTTTCCCTTTCTCCAGATACAACTTACCGAGAGTTGAATAAAGCAGCACAGCGTAGCATTACAGCGCCAGACAGGATAGGAGAAAGAAAAACATAAGTTTATCAACGAGATA‑AATGATTGAAAGAGGTGATAACAg                                                                                         <  2:18414/139‑1 (MQ=255)                       aTTTCCCTTTCTCCAGATACAACTTACCGTGAGTTGAATAAAGCAGCACAGCGTAGCATTACAGCGCCAGACAGGATAGGAGAAAGTAAAACATAAGTTTATCAACGAGATA‑AATGATTGAAAGAGGTGATAACAGCgg                                                                                      <  1:628714/139‑1 (MQ=255)                         ttCCCTTTCTCCAGATACAACTTACCGAGAGTTGAATAAAGCAGCACAGCGTAGCATTACAGCGCCAGACAGGATAGGAGAAAGAAAAACATAAGTTTATCAACGAGATA‑AATGATTGAAAGAGGTGATAACAGCGgtg                                                                                    <  2:876353/139‑1 (MQ=255)                            ccTTTCTCCAGATACAACTTACCGAGAGTTGAATAAAGCAGCACAGCGTAGCATTACAGCGCCAGACAGGATAGGAGAAAGAAAAACATAAGTTTATCAACGAGATA‑AATGATTGAAAGAGGTGATAACAGCGGTGttt                                                                                 <  2:311924/139‑1 (MQ=255)                              tttCTCCAGATACAACTTACCGAGAGTTGAATAAAGCAGCACAGCGTAGCATTACAGCGCCAGACAGGATAGGAGAAAGAAAAACATAAGTTTATCAACGAGATA‑AATGATTGAAAGAGGTGATAACAGCGGTGTTTAt                                                                               <  2:415493/139‑1 (MQ=255)                                   ccAGATACAACTTACCGAGAGTTGAATAAAGCAGCACAGCGTAGCATTACAGCGCCAGACAGGATAGGAGAAAGAAAAACATAAGTTTATCAACGAGATA‑AATGATTGAAAGAGGTGATAACAGCGGTGTTTATCAGTa                                                                          <  1:839193/139‑1 (MQ=255)                                           aaCTTACCGAGAGTTGAATAAAGCAGCACAGCGTAGCATTACAGCGCCAGACAGGATAGGAGAAAGAAAAACATAAGTTTATCAACGAGATA‑AATGATTGAAAGAGGTGATAACAGCGGTGTTTATCAGTATGGTCGTg                                                                  <  1:127191/139‑1 (MQ=255)                                            aCTTACCGAGAGTTGAATAAAGCAGCACAGCGTAGCATTACAGCGCCAGACAGGATAGGAGAAAGAAAAACATAAGTTTATCAACGAGATA‑AATGATTGa                                                                                                        <  1:497509/100‑1 (MQ=255)                                            aCTTACCGAGAGTTGAATAAAGCAGCACAGCGTAGCATTACAGCGCCAGACAGGATAGGAGAAAGAAAAACATAAGTTTATCAACGAGATA‑AATGATTGa                                                                                                        >  2:497509/1‑100 (MQ=255)                                               tACCGAGAGTTGAATAAAGCAGCACAGCGTAGCATTACAGCGCCAGACAGGATAGGAGAAAGAAAAACATAAGTTTATCAACGAGATA‑AATGATTGAAAGAGGTGATAACAGCGGTGTTTATCAGTATGGTCGTGCTGa                                                              <  2:435121/139‑1 (MQ=255)                                               tACCGAGAGTTGAATAAAGCAGCACAGCGTAGCATTACAGCGCCAGACAGGATAGGAGAAAGAAAAACATAAGTTTATCAACGAGATA‑AATGATTGAAAGAGGTGATAACAGCGGTGTTTATCAGTATGGTCGTGCTGa                                                              <  1:644721/139‑1 (MQ=255)                                                aCCGAGAGTTGAATAAAGCAGCACAGCGTAGCATTACAGCGCCAGACAGGATAGGAGAAAGAAAAACATAAGTTTATCAACGAGATA‑AATGATTGAAAGAGGTGATAACAGCGGTGTTTATCAGTATGGTCGTGCTGaa                                                             >  1:593284/1‑139 (MQ=255)                                                        ttGAATAAAGCAGCACAGCGTAGCATTACAGCGCCAGACAGGATAGGAGAAAGAAAAACATAAGTTTATCAACGAGATA‑AATGATTGAAAGAGGTGATAACAGCGGTGTTTATCAGTATGGTCGTGCTGAACATTTCAc                                                     >  1:562905/1‑139 (MQ=255)                                                         tGAATAAAGCAGCACAGCGTAGCATTACAGCGCCAGACAGGATAGGAGAAAGAAAAACATAAGTTTATCAACGAGATA‑AATGATTGAAAGAGGTGATAACAGCGGTGTTTATCAGTATGGTCGTGCTGAACATTTCAcc                                                    <  2:503545/139‑1 (MQ=255)                                                         tGAATAAAGCAGCACAGCGTAGCATTACAGCGCCAGACAGGATAGGAGAAAGAAAAACATAAGTTTAACAACGAGATA‑AATGATTGAAAGAGGTGATAACAGCGGTGTTTATCAGTATGGTCGTGCTGAACATTTCAcc                                                    <  2:562905/139‑1 (MQ=255)                                                                     cacaGCGTAGCATTACAGCGCCAGACAGGATAGGAGAAAGAAAAACATAAGTTTATCAACGAGATA‑AATGATTGAAAGAGGTGATAACAGCg                                                                                       >  2:222482/1‑92 (MQ=255)                                                                     cacaGCGTAGCATTACAGCGCCAGACAGGATAGGAGAAAGAAAAACATAAGTTTATCAACGAGATA‑AATGATTGAAAGAGGTGATAACAGCg                                                                                       <  1:222482/92‑1 (MQ=255)                                                                     cacaGCGTAGCATTACAGCGCCAGACAGGATAGGAGAAAGAAAAACATAAGTTTATCAACGAGATA‑AATGATTGAAAGAGGTGATAACAGCGGTGTTTATCAGTATGGTCGTGCTGAACATTTCACCCACATTATATCt                                        >  2:62697/1‑139 (MQ=255)                                                                          cGTAGCATTACAGCGCCAGACAGGATAGGAGAAAGAAAAACATAAGTTTATCAACGAGATA‑AATGATTGAAAGAGGTGATAACAGCgg                                                                                      >  1:786431/1‑88 (MQ=255)                                                                          cGTAGCATTACAGCGCCAGACAGGATAGGAGAAAGAAAAACATAAGTTTATCAACGAGATA‑AATGATTGAAAGAGGTGATAACAGCgg                                                                                      <  2:786431/88‑1 (MQ=255)                                                                          cGTAGCATTACAGCGCCAGACAGGATAGGAGAAAGAAAAACATAAGTTTATCAACGAGATA‑AATGATTGAAAGAGGTGATAACAGCGGTGTTTATCAGTATGGTCGTGCTGAACATTTCACCCACATtat                                            <  2:576580/130‑1 (MQ=255)                                                                          cGTAGCATTACAGCGCCAGACAGGATAGAAGAAAGAAAAACATAAGTTTATCAACGAGATA‑AATGATTCAAAGAGGTGATAACAGCGGTGTTTATCAGTATGGTCGTGCTGAACATTTCACCCACATtat                                            >  1:576580/1‑130 (MQ=255)                                                                                    cAGCGCCAGACAGGATAGGAGAAAGAAAAACATAAGTTTATCAACGAGATA‑AATGATTGAAAGAGGTGATAACAGCGGTGTTTATCAGTa                                                                          >  1:175273/1‑90 (MQ=255)                                                                                    cAGCGCCAGACAGGATAGGAGAAAGAAAAACATAAGTTTATCAACGAGATA‑AATGATTGAAAGAGGTGATAACAGCGGTGTTTATCAGTa                                                                          <  2:175273/90‑1 (MQ=255)                                                                                    cAGCGCCAGACAGGATAGGAGAAAGAAAAACATAAGTTTATCAACGAGATA‑AATGATTGAAAGAGGTGATAACAGCGGTGTTTATCAGTATGGTCGTGCTGAACATTTCACCCACATTATATCTGACAAACCTTCCCCa                         >  2:201263/1‑139 (MQ=255)                                                                                    cAGCGCCAGACAGGATAGGAGAAAGAAAAACATAAGTTTATCAACGAGATA‑AATGATTGAAAGAGGTGATAACAGCGGTGTTTATCAGTATGGTCGTGCTGAACATTTCACCCACATTATATCTGACAAACCTTCCCCa                         >  1:879458/1‑139 (MQ=255)                                                                                    cAGCGCCAGACAGGATAGGAGAAAGAAAAACATAAGTTTATCAACGAGATA‑AATGATTGAAAGAGGTGATAACAGCGGTGTTTATCAGTATGGTCGTGCTGAACATTTCACCCACATTATATCTGACAAACCTTCCCCa                         >  1:746878/1‑139 (MQ=255)                                                                                    cAGCGCCAGACAGGATAGGAGAAAGAAAAACATAAGTTTATCAACGAGATA‑AATGATTGAAAGAGGTGATAACAGCGGTGTTTATCAGTATGGTCGTGCTGAACATTTCACCCACATTATATCTGACAAACCTTCCCCa                         <  1:388241/139‑1 (MQ=255)                                                                                     aGCGCCAGACAGGATAGGAGAAAGAAAAACATAAGTTTATCAACGAGATA‑AATGATTGAAAGAGGTGATAACAGCGGTGTTTATCAGTATGGTCGTGCTGAACATTTCACCCACATTATATCTGACAAACCTTCCCCaa                        <  2:108191/139‑1 (MQ=255)                                                                                      gcgcCAGACAGGATAGGAGAAAGAAAAACATAAGTTTATCAACGAGATA‑AATGATTGAAAGAGGTGATAACAGCGGTGTTTATCAGTATGGTCGTGCTGAACATTTCACCCACATTATATCTGACAAACCTTCCCCaaa                       >  2:434866/1‑139 (MQ=255)                                                                                         ccAGACAGGATAGGAGAAAGAAAAACATAAGTTTATCAACGAGATA‑AATGATTGAAAGAGGTGATAACAGCg                                                                                       >  2:573750/1‑72 (MQ=255)                                                                                         ccAGACAGGATAGGAGAAAGAAAAACATAAGTTTATCAACGAGATA‑AATGATTGAAAGAGGTGATAACAGCg                                                                                       <  1:573750/72‑1 (MQ=255)                                                                                         ccAGACAGGATAGGAGAAAGAAAAACATAAGTTTATCAACGAGATA‑AATGATTGAAAGAGGTGATAACAGCGGTGTTTATCAGTATGGTCGTGCTGAACATTTCACCCACATTATATCTGACAAACCTTCCCCAAAAGa                    <  2:746878/139‑1 (MQ=255)                                                                                           aGACAGGATAGGAGAAAGAAAAACATAAGTTTATCAACGAGATA‑AATGATTGAAAGAGGTGATAACAGCGGTGTTTATCAGTATGGTCGTGCTGAACATTTCACCCACATTATATCTGACAAACCTTCCCCAAAAGATa                  <  2:879458/139‑1 (MQ=255)                                                                                           aGACAGGATAGGAGAAAGAAAAACATAAGTTTATCAACGAGATA‑AATGATTGAAAGAGGTGATAACAGCGGTGTTTATCAGTATGGTCGTGCTGAACATTTCACCCACATTATATCTGACAAACCTTCCCCAAAAGATa                  >  2:838566/1‑139 (MQ=255)                                                                                            gACAGGATAGGAGAAAGAAAAACATAAGTTTATCAACGAGATA‑AATGATTGAAAGAGGTGATAACAg                                                                                         >  1:888157/1‑67 (MQ=255)                                                                                            gACAGGATAGGAGAAAGAAAAACATAAGTTTATCAACGAGATA‑AATGATTGAAAGAGGTGATAACAg                                                                                         <  2:888157/67‑1 (MQ=255)                                                                                            gACAGGATAGGAGAAAGAAAAACATAAGTTTATCAACGAGATA‑AATGATTGAAAGAGGTGATAACAGCGGTGTTTATCAGTATGGTCGTGCTGAACATTTCACCCACATTATATCTGACAAACCTTCCCCAAAAGATaa                 >  2:605827/1‑139 (MQ=255)                                                                                               aGGATAGGAGAAAGAAAAACATAAGTTTATCAACGAGATA‑AATGATTGAAAGAGGTGATAACAGCGGTGTTTATCAGTATGGTCGTGCTGAACATTTCACCCACATTATATCTGACAAACCTTCCCCAAAAGATAAata              <  2:593284/139‑1 (MQ=255)                                                                                                 gATAGGAGAAAGAAAAACATAAGTTTATCAACGAGATA‑AATGATTGAAAGAGGTGATAACAGCGGTGTTTATCAGTATGGTCGTg                                                                  >  1:68721/1‑85 (MQ=255)                                                                                                 gATAGGAGAAAGAAAAACATAAGTTTATCAACGAGATA‑AATGATTGAAAGAGGTGATAACAGCGGTGTTTATCAGTATGGTCGTg                                                                  <  2:68721/85‑1 (MQ=255)                                                                                                 gATAGGAGAAAGAAAAACATAAGTTTATCAACGAGATA‑AATGATTGAAAGAGGTGATAACAGCGGTGTTTATCAGTATGGTCGTGCTGAACATTTCACCCACATTATATCTGACAAACCTTCCCCAAAAGATAAATATg            >  2:444842/1‑139 (MQ=255)                                                                                                 gATAGGAGAAAGAAAAACATAAGTTTATCAACGAGATA‑AATGATTGAAAGAGGTGATAACAGCGGTGTTTATCAGTATGGTCGTGCTGAACATTTCACCCACATTATATCTGACAAACCTTCCCCAAAAGATAAATATg            <  1:434866/139‑1 (MQ=255)                                                                                                 gATAGGAGAAAGAAAAACATAAGTTTATCAACGAGATA‑AATGATTGAAAGAGGTGATAACAGCGGTGTTTATCAGTATGGTCGTGCTGAACATTTCACCCACATTATATCTGACAAACCTTCCCCAAAAGATAAATATg            <  1:201263/139‑1 (MQ=255)                                                                                                   tAGGAGAAAGAAAAACATAAGTTTATCAACGAGATA‑AATGATTGAAAGAGGTGATAACAGCGGTGTTTATCAGTATGGTCGTGCTGAACATTTCACCCACATtat                                            <  1:610439/105‑1 (MQ=255)                                                                                                   tAGGAGAAAGAAAAACATAAGTTTATCAACGAGATA‑AATGATTGAAAGAGGTGATAACAGCGGTGTTTATCAGTATGGTCGTGCTGAACATTTCACCCACATtat                                            >  2:610439/1‑105 (MQ=255)                                                                                                      gagaAAGAAAAACATAAGTTTATCAACGAGATA‑AATGATAGAAAGAGGTGATAACAGCGGTGTTTATCAGTATGGTCGTGCTGAACATTTCACCCACATTATATCTGACAAACCTTCCCCAAAAGTTAAATATGTTGCa       >  2:614160/1‑139 (MQ=255)                                                                                                           agaaaAACATAAGTTTATCAACGAGATA‑AATGATTGAAAGAGGTGATAACAg                                                                                         >  1:690725/1‑52 (MQ=255)                                                                                                           agaaaAACATAAGTTTATCAACGAGATA‑AATGATTGAAAGAGGTGATAACAg                                                                                         <  1:730543/52‑1 (MQ=255)                                                                                                           agaaaAACATAAGTTTATCAACGAGATA‑AATGATTGAAAGAGGTGATAACAg                                                                                         >  2:730543/1‑52 (MQ=255)                                                                                                           agaaaAACATAAGTTTATCAACGAGATA‑AATGATTGAAAGAGGTGATAACAg                                                                                         <  2:690725/52‑1 (MQ=255)                                                                                                           agaaaAACATAAGTTTATCAACGAGATA‑AATGATTGAAAGAGGTGATAACAGTGGTGTTTATCAGTATGGTCGTGCTGAACATTTCACCCACATTATATCTGACAAACCTTCCCCAAAAGATAAATATGTTGCata     >  1:656404/1‑136 (MQ=255)                                                                                                           agaaaAACATAAGTTTATCAACGAGATA‑AATGATTGAAAGAGGTGATAACAGTGGTGTTTATCAGTATGGTCGTGCTGAACATTTCACCCACATTATATCTGACAAACCTTCCCCAAAAGATAAATATGTTGCata     <  2:656404/136‑1 (MQ=255)                                                                                                           agaaaAACATAAGTTTATCAACGAGATA‑AATGATTGAAAGAGGTGATAACAGCGGTGttt                                                                                 >  2:205360/1‑60 (MQ=255)                                                                                                           agaaaAACATAAGTTTATCAACGAGATA‑AATGATTGAAAGAGGTGATAACAGCGGTGttt                                                                                 <  1:205360/60‑1 (MQ=255)                                                                                                           agaaaAACATAAGTTTATCAACGAGATA‑AATGATTGAAAGAGGTGATAACAGCGGTGTTTATCAGTATGGTCGTGCTg                                                               >  2:755426/1‑78 (MQ=255)                                                                                                           agaaaAACATAAGTTTATCAACGAGATA‑AATGATTGAAAGAGGTGATAACAGCGGTGTTTATCAGTATGGTCGTGCTg                                                               <  1:755426/78‑1 (MQ=255)                                                                                                           agaaaAACATAAGTTTATCAACGAGATA‑AATGATTGAAAGAGGTGATAACAGCGGTGTTTATCAGTATGGTCGTGCTGAACATTTCAcc                                                    <  2:418143/89‑1 (MQ=255)                                                                                                           agaaaAACATAAGTTTATCAACGAGATA‑AATGATTGAAAGAGGTGATAACAGCGGTGTTTATCAGTATGGTCGTGCTGAACATTTCAcc                                                    >  1:418143/1‑89 (MQ=255)                                                                                                           agaaaAACATAAGTTTATCAACGAGATA‑AATGATTGAAAGAGGTGATAACAGCGGTGTTTATCAGTATGGTCGTGCTGAACATTTCACCCACATTATATCTGACAAACCTTCCCCAAAAGATAAATATGTTGCATATGc  >  1:422635/1‑139 (MQ=255)                                                                                                                                       |                                                                                                                TCTGTTAAAAAACGATTATAAAATTTCCCTTTCTCCAGATACAACTTACCGAGAGTTGAATAAAGCAGCACAGCGTAGCATTACAGCGCCAGACAGGATAGGAGAAAGAAAAACATAGGTTTATCAACGAGATACAATGATTGAAAGAGGTGATAACAGCGGTGTTTATCAGTATGGTCGTGCTGAACATTTCACCCACATTATATCTGACAAACCTTCCCCAAAAGATAAATATGTTGCATATGC  >  NC_000913/2786612‑2786857

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑