Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,788,238	G→A	pseudogene (1842/2253 nt)	ygaQ →	uncharacterized protein, putative enzyme

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,788,238	0	G	A	100.0%	155.5 / NA	49	pseudogene (1842/2253 nt)	ygaQ	uncharacterized protein, putative enzyme
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (22/27);  total (22/27)

AGCAATGGCATATATAGCCGCTCTGCCGTTCAGCAGGCCTTTAGTTTACTGGGATGGCCAAGTATTAAAATCAACGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAGCTTAATAAAGGTTGCTCTACCTATCAGCAGCTCTACAATGAATTCCACGCATTATATATAGATAAAGCAGGAATATGGAGCGCATTTGAGGGTGTATCTGCAACTAAAAACGTTCTGGCCTTTAGT  >  NC_000913/2788112‑2788364                                                                                                                               |                                                                                                                               aGCAATGGCATATATAGCCGCTCTGCCGTTCAGCAGGCCTTTAGTTTACTGGGATGGCCAAGTATTAAAATCAACGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGt                                                                                                                    <  2:953949/139‑1 (MQ=255)          atatatAGCCGCTCTGCCGTTCAGCAGGCCTTTAGTTTACTGGGATGGCCAAGTATTAAAATCAACGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGTTGCTCTAcc                                                                                                           >  1:719389/1‑139 (MQ=255)                 gCCGCTCTGCCGTTCAGCAGGCCTTTAGTTTACTGGGATGGCCAAGTATTAAAATCAACGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGTTGCTCTACCTATcagc                                                                                                    <  1:1046012/139‑1 (MQ=255)                  ccGCTCTGCCGTTCAGCTGGCCTTTAGTTTACTGGGATGGCCAAGTATTAAAATCAACGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGTTGCTCTACCTATcagca                                                                                                   >  1:843470/1‑139 (MQ=255)                  ccGCTCTGCCGTTCAGCAGGCCTTTAGTTTACTGGGATGGCCAAGTATTAAAATCAAGGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGTTGCTCTACCTATcagca                                                                                                   >  1:144794/1‑139 (MQ=255)                  ccGCTCTGCCGTTCAGCAGGCCTTTAGTTTACTGGGATGGCCAAGTATTAAAATCAACGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGTTGctc                                                                                                               >  1:586985/1‑127 (MQ=255)                  ccGCTCTGCCGTTCAGCAGGCCTTTAGTTTACTGGGATGGCCAAGTATTAAAATCAACGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGTTGctc                                                                                                               <  2:586985/127‑1 (MQ=255)                  ccGCTCTGCCGTTCAGCAGGCCTTTAGTTTACTGGGATGGCCAAGTATTAAAATCAACGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGTTGCTCTACCTATcagca                                                                                                   >  1:817204/1‑139 (MQ=255)                       ctGCCGTTCAGCAGGCCTTTAGTTTACTGGGATGGCCAAGTATTAAAATCAACGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGTTg                                                                                                                  <  2:1271340/119‑1 (MQ=255)                       ctGCCGTTCAGCAGGCCTTTAGTTTACTGGGATGGCCAAGTATTAAAATCAACGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGTTg                                                                                                                  >  1:1271340/1‑119 (MQ=255)                       ctGCCGTTCAGCAGGCCTTTAGTTTACTGGGATGGCCAAGTATTAAAATCAACGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGTTGCTCTACCTATCAGCAGctct                                                                                              >  2:572995/1‑139 (MQ=255)                       ctGCCGTTCAGCAGGCCTTTAGTTTACTGGGATGGCCAAGTATTAAAATCAACGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGTTGCTCTACCTATCAGCAGctct                                                                                              >  2:439183/1‑139 (MQ=255)                        tGCCGTTCAGCAGGCCTTTAGTTTACTGGGATGGCCAAGTATTAAAATCAACGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGTTGCTCTACCTATCAGCAGCTCTa                                                                                             <  2:843470/139‑1 (MQ=255)                                   agGCCTTTAGTTTACTGGGATGGCCAAGTATTAAAATCAACGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGTTGCTCTACCTATCAGCAGCTCTACAATGAATTcc                                                                                  <  1:572995/139‑1 (MQ=255)                                    ggCCTTTAGTTTACTGGGATGGCCAAGTATTAAAATCAACGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGTTGCTCTACCTATCAGCAGCTCTACAATGAATTCCa                                                                                 <  1:439183/139‑1 (MQ=255)                                     gCCTTTAGTTTACTGGGATGGCCAAGTATTAAAATCAACGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGTTGCTCTACCTATCAGCAGCTCTACAATGAATTCCAc                                                                                <  2:691109/139‑1 (MQ=255)                                        tttAGTTTACTGGGATGGCCAAGTATTAAAATCAACGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGTTGCTCTACCTATCAGCAGCTCTACAATGAATTCCACGCa                                                                             <  2:719389/139‑1 (MQ=255)                                        tttAGTTTACTGGGATGGCCAAGTATTAAAATCAACGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGTTGCTCTACCTATCAGCAGCTCTACAATGAATTCCACGCa                                                                             <  2:905459/139‑1 (MQ=255)                                                aCTGGGATGGCCAAGTATTAAAATCAACGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATaaa                                                                                                                       >  1:1089038/1‑89 (MQ=255)                                                aCTGGGATGGCCAAGTATTAAAATCAACGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATaaa                                                                                                                       <  2:1089038/89‑1 (MQ=255)                                                 cTGGGATGGCCAAGTATTAAAATCAACGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAgg                                                                                                                     >  1:531779/1‑90 (MQ=255)                                                 cTGGGATGGCCAAGTATTAAAATCAACGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAgg                                                                                                                     <  2:531779/90‑1 (MQ=255)                                                      aTGGCCAAGTATTAAAATCAACGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGTTGCTCTACCt                                                                                                          >  1:148826/1‑96 (MQ=255)                                                      aTGGCCAAGTATTAAAATCAACGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGTTGCTCTACCt                                                                                                          <  2:148826/96‑1 (MQ=255)                                                        ggCCAAGTATTAAAATCAACGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGTTGCTCTACCTATCAGCAGCTCTACAATGAATTCCACGCATTATATATAGATAAAg                                                             <  2:817204/139‑1 (MQ=255)                                                        ggCCAAGTATTAAAATCAACGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGTTGCTCTACCTATCAGCAGCTCTACAATGAATTCCACGCATTATATATAGATAAAg                                                             <  2:14124/139‑1 (MQ=255)                                                                    aaaTCAACGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGTTGCTCTACCTATc                                                                                                       >  1:239693/1‑85 (MQ=255)                                                                    aaaTCAACGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGTTGCTCTACCTATc                                                                                                       <  2:239693/85‑1 (MQ=255)                                                                         aaCGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAgg                                                                                                                     <  2:994259/66‑1 (MQ=255)                                                                         aaCGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAgg                                                                                                                     >  1:994259/1‑66 (MQ=255)                                                                         aaCGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGTTGCTCTACCTATcagcag                                                                                                  <  1:854437/85‑1 (MQ=255)                                                                         aaCGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGTTGCTCTACCTATcagcag                                                                                                  >  2:854437/1‑85 (MQ=255)                                                                             aCTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGTTGTTCTACCTATCAGCAGCTCTACAATGAATTCCACGCATTATATATAGa                                                                  >  2:916822/1‑113 (MQ=255)                                                                             aCTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGTTGCTCTACCTATCAGCAGCTCTACAATGAATTCCACGCATTATATATAGa                                                                  <  1:916822/113‑1 (MQ=255)                                                                               tGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGTTGCTCTACCTATCAGCAGCTCTACAATGAATTCCACGCATTATATATAGATAAAGCAGGAATATGGAGCGCATTTGAg                                      <  2:144794/139‑1 (MQ=255)                                                                                                     tCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGTTGCTCTACCTATCAGCAGCTCTACAATGAATTCCACGCATTATATATAGAt                                                                 >  1:692659/1‑90 (MQ=255)                                                                                                     tCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGTTGCTCTACCTATCAGCAGCTCTACAATGAATTCCACGCATTATATATAGAt                                                                 <  2:692659/90‑1 (MQ=255)                                                                                                       cACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGTTGCTCTACCTATCAGCAGCTCTACAATGAATTCCACGCATTATATATAGATAAAGCAGGAATATGGAGCGCATTTGAGGGTGTATCTGCAACTAAAAACGtt              <  1:703101/139‑1 (MQ=255)                                                                                                            gtgtCGGCGGTGAGGCGTAACTTAATAAAGGTTGCTCTACCTATCAGCAGCTCTACAATGAATTCCACGCATtatat                                                                       <  2:630441/77‑1 (MQ=255)                                                                                                            gtgtCGGCGGTGAGGCGTAACTTAATAAAGGTTGCTCTACCTATCAGCAGCTCTACAATGAATTCCACGCATtatat                                                                       >  1:630441/1‑77 (MQ=255)                                                                                                               tCGGCGGTGAGGCGTAACTTAATAAAGGTTGCTCTACCTATcagcag                                                                                                  >  2:987112/1‑47 (MQ=255)                                                                                                               tCGGCGGTGAGGCGTAACTTAATAAAGGTTGCTCTACCTATcagcag                                                                                                  <  1:987112/47‑1 (MQ=255)                                                                                                               tCGGCGGTGAGGCGTAACTTAATAAAGGTTGCTCTACCTATCAGCAGCTCTACAATGAATTcc                                                                                  <  2:792443/63‑1 (MQ=255)                                                                                                               tCGGCGGTGAGGCGTAACTTAATAAAGGTTGCTCTACCTATCAGCAGCTCTACAATGAATTcc                                                                                  >  1:792443/1‑63 (MQ=255)                                                                                                               tCGGCGGTGAGGCGTAACTTAATAAAGGTTGCTCTACCTATCAGCAGCTCTACAATGAATTCCACGCa                                                                             <  1:53293/68‑1 (MQ=255)                                                                                                               tCGGCGGTGAGGCGTAACTTAATAAAGGTTGCTCTACCTATCAGCAGCTCTACAATGAATTCCACGCa                                                                             >  2:53293/1‑68 (MQ=255)                                                                                                                   cggTGAGGCGTAACTTAATAAAGGTTGCTCTACCTATCAGCAGCTCTACAATGAATTCCACGCATTATATATAGATAAAGCAGGAATATGGAGCGCATTTGAGGGTGTATCTGCAACTAAAAACGTTCTGGCCTTTAGt  >  2:720746/1‑139 (MQ=255)                                                                                                                        aGGCGTAACTTAATAAAGGTTGCTCTACCTATCAGCAGCTCTACAATGAATTCCACGCATTATATATAGATaa                                                               >  2:704674/1‑73 (MQ=255)                                                                                                                        aGGCGTAACTTAATAAAGGTTGCTCTACCTATCAGCAGCTCTACAATGAATTCCACGCATTATATATAGATaa                                                               <  1:704674/73‑1 (MQ=255)                                                                                                                               |                                                                                                                               AGCAATGGCATATATAGCCGCTCTGCCGTTCAGCAGGCCTTTAGTTTACTGGGATGGCCAAGTATTAAAATCAACGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAGCTTAATAAAGGTTGCTCTACCTATCAGCAGCTCTACAATGAATTCCACGCATTATATATAGATAAAGCAGGAATATGGAGCGCATTTGAGGGTGTATCTGCAACTAAAAACGTTCTGGCCTTTAGT  >  NC_000913/2788112‑2788364

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑