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%	200.4 / NA	62	pseudogene (1842/2253 nt)	ygaQ	uncharacterized protein, putative enzyme
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (32/30);  total (32/30)

AACAATTAGCAATGGCATATATAGCCGCTCTGCCGTTCAGCAGGCCTTTAGTTTACTGGGATGGCCAAGTATTAAAATCAACGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAGCTTAATAAAGGTTGCTCTACCTATCAGCAGCTCTACAATGAATTCCACGCATTATATATAGATAAAGCAGGAATATGGAGCGCATTTGAGGGTGTATCTGCAACTAAAAACGTTCTGGCCTTTAGTCGTGG  >  NC_000913/2788105‑2788369                                                                                                                                      |                                                                                                                                    aaCAATTAGCAATGGCATATATAGCCGCTCTGCCGTTCAGCAGGCCTTTAGTTTACTGGGATGGCCAAGTATTAAAATCAACGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTtaa                                                                                                                                >  1:48413/1‑139 (MQ=255)      ttAGCAATGGCATATATAGCCGCTCTGCCGTTCAGCAGGCCTTTAGTTTACTGGGATGGCCAAGTATTAAAATCAACGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAg                                                                                                                           <  2:31548/139‑1 (MQ=255)        aGCAATGACATATATAGCCGCTCTGCCGTTCAGCAGGCCTTTAGTTTACTGGGATGGCCAAGCATTAAAATCAACGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGt                                                                                                                         >  1:526551/1‑139 (MQ=255)              ggCATATATAGCCGCTCTGCCGTTCAGCAGGCCTTTAGTTTACTGGGATGGCCAAGTATTAAAATCAACGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGTTGctc                                                                                                                    <  1:644310/138‑1 (MQ=255)              ggCATATATAGCCGCTCTGCCGTTCAGCAGGCCTTTAGTTTACTGGGATGGCCAAGTATTAAAATCAACGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGTTGctc                                                                                                                    >  2:644310/1‑138 (MQ=255)                cATATATAGCCGCTCTGCCGTTCAGCAGGCCTTTAGTTTACTGGGATGGCCAAGTATTAAAATCAACGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGTTGCTCTAc                                                                                                                 >  1:37315/1‑139 (MQ=255)                     ataGCCGCTCTGCCGTTCAGCAGGCCTTTAGTTTACTGGGATGGCCAAGTATTAAAATCAACGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGTTGCTCTACCTATc                                                                                                            <  2:153858/139‑1 (MQ=255)                         ccGCTCTGCCGTTCAGCAGGCCTTTAGTTTACTGGGATGGCCAAGTATTAAAATCAACGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGTTGCTCTACCTATcagca                                                                                                        >  1:701565/1‑139 (MQ=255)                         ccGCTCTGCCGTTCAGCAGGCCTTTAGTTTACTGGGATGGCCAAGTATTAAAATCAACGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGTTGCTCTACCTATcagca                                                                                                        >  1:691855/1‑139 (MQ=255)                         ccGCTCTGCCGTTCAGCAGGCCTTTAGTTTACTGGGATGGCCAAGTATTAAAATCAACGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGTTGCTCTACCTATcagca                                                                                                        >  1:525876/1‑139 (MQ=255)                         ccGCTCTGCCGTTCAGCAGGCCTTTAGTTTACTGGGATGGCCAAGTATTAAAATCAACGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGTTGCTCTACCTATcagca                                                                                                        >  1:361847/1‑139 (MQ=255)                         ccGCTCTGCCGTTCAGCAGGCCTTTAGTTTACTGGGATGGCCAAGTATTAAAATCAACGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGTTGCTCTACCTATcagca                                                                                                        >  2:523980/1‑139 (MQ=255)                         ccGCTCTGCCGTTCAGCAGGCCTTTAGTTTACTGGGATGGCCAAGTATTAAAATCAACGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGTTGCTCTACCTATcagca                                                                                                        >  2:305888/1‑139 (MQ=255)                         ccGCTCTGCCGTTCAGCAGGCCTTTAGTTTACTGGGATGGCCAAGTATTAAAATCAACGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGTTGCTCTACCTATcagca                                                                                                        >  2:263947/1‑139 (MQ=255)                          cGCTCTGCCGTTCAGCGGGCCTTTAGTTTACTGGGATGGCCAAGTATTAAAATCAACGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGTTGCTCTACCTATcagcag                                                                                                       >  1:635479/1‑139 (MQ=255)                             tctGCCGTTCAGCAGGCCTTTAGTTTACTGGGATGGCCAAGTATTAAAATCAACGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATaaa                                                                                                                            >  2:173636/1‑115 (MQ=255)                             tctGCCGTTCAGCAGGCCTTTAGTTTACTGGGATGGCCAAGTATTAAAATCAACGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATaaa                                                                                                                            <  1:173636/115‑1 (MQ=255)                              ctGCCGTTCAGCAGGCCTTTAATTTACTGGGATGGCCAAGTATTAAAATCAACGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGTGGTGAGGCGTAACTTAATAAAGGTTGCTCTACCTATCAGCAGctct                                                                                                   >  1:204789/1‑139 (MQ=255)                                   gTTCAGCAGGCCTTTAGTTTACTGGGATGGCCAAGTATTAAAATCAACGACTGAAATTAAAAATTATGATGGGTCTACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGTTGCTCTACCTATCAGCAGCTCTACAAt                                                                                              <  1:523980/139‑1 (MQ=255)                                           ggCCTTTAGTTTACTGGGATGGCCAAGTATTAAAATCAACGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGTTGctc                                                                                                                    <  2:647969/109‑1 (MQ=255)                                           ggCCTTTAGTTTACTGGGATGGCCAAGTATTAAAATCAACGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGTTGctc                                                                                                                    >  1:647969/1‑109 (MQ=255)                                           ggCCTTTAGTTTACTGGGATGGCCAAGTATTAAAATCAACGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGTTGCTCTACCTATCAGCAGCTCTACAATGAATTCCa                                                                                      <  1:706164/139‑1 (MQ=255)                                           ggCCTTTAGTTTACTGGGATGGCCAAGTATTAAAATCAACGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGTTGCTCTACCTATCAGCAGCTCTACAATGAATTCCa                                                                                      <  2:37315/139‑1 (MQ=255)                                            gCCTTTAGTTTACTGGGATGGCCAAGTATTAAAATCAACGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGTTGCTCTACCTATCAGCAGCTCTACAATGAATTCCAc                                                                                     <  2:701565/139‑1 (MQ=255)                                            gCCTTTAGTTTACTGGGATGGCCAAGTATTAAAATCAACGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGTTGCTCTACCTATCAGCAGCTCTACAATGAATTCCAc                                                                                     <  2:526551/139‑1 (MQ=255)                                               tttAGTTTACTGGGATGGCCAAGTATTAAAATCAACGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGTTGCTCTACCTATCAGCAGCTCTACAATGAATTCCACGCa                                                                                  <  2:48413/139‑1 (MQ=255)                                                ttAGTTTACTGGGATGGCCAAGTATTAAAATCAACGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAATGTTGCTCTACCTATCAGCAGCTCTACAATGAATTCCACGCAt                                                                                 <  2:525876/139‑1 (MQ=255)                                                ttAGTTTACTGGGATGGCCAAGTATTAAAATCAACGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGTTGCTCTACCTATCAGCAGCTCTACAATGAATTCCACGCAt                                                                                 <  2:691855/139‑1 (MQ=255)                                                ttAGTTTACTGGGATGGCCAAGTATTAAAATCAACGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGTTGCTCTACCTATCAGCAGCTCTACAATGAATTCCACGCAt                                                                                 <  2:361847/139‑1 (MQ=255)                                                 tAGTTTACTGGGATGGCCAAGTATTAAAATCAACGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGTTg                                                                                                                       <  2:772611/100‑1 (MQ=255)                                                 tAGTTTACTGGGATGGCCAAGTATTAAAATCAACGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGTTg                                                                                                                       >  1:772611/1‑100 (MQ=255)                                                        cTGGGATGGCCAAGTATTAAAATCAACGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGTTGCTCTACCTATCAGCAGCTCTACAATGAATTcc                                                                                       >  2:268746/1‑125 (MQ=255)                                                        cTGGGATGGCCAAGTATTAAAATCAACGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGTTGCTCTACCTATCAGCAGCTCTACAATGAATTcc                                                                                       <  1:268746/125‑1 (MQ=255)                                                        cTGGGATGGCCAAGTATTAAAATCAACGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGTTGCTCTACCTATCAGCAGCTCTACAATGAATTCCACGCATtatatata                                                                         >  1:653095/1‑139 (MQ=255)                                                         tGGGATGGCCAAGTATTAAAATCAACGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGTTGCTCTACCTATCAGCAGCTCTACAATGAATTCCACGCATTATATATAg                                                                        >  2:50661/1‑139 (MQ=255)                                                          gggATGGCCAAGTATTAAAATCAACGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGTTGCTCTACCTATCAGCAGCTCTACAATGAATTCCACGCATTATATATAGa                                                                       <  1:63856/139‑1 (MQ=255)                                                          gggATGGCCAAGTATTAAAATCAACGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGTTGCTCTACCTATCAGCAGCTCTACAATGAATTCCACGCATTATATATAGa                                                                       <  1:262585/139‑1 (MQ=255)                                                             aTGGCCAAGTATTAAAATCAACGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGTTGCTCTACCTATCAGCAGCTCTACAATGAATTCCa                                                                                      <  1:770873/121‑1 (MQ=255)                                                             aTGGCCAAGTATTAAAATCAACGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGTTGCTCTACCTATCAGCAGCTCTACAATGAATTCCa                                                                                      >  2:770873/1‑121 (MQ=255)                                                                gCCAAGTATTAAAATCAACGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGTTGCTCTACCTATCAGCAGCTCTACAATGAATTCCACGCATTATATATAGATAAAGc                                                                 >  2:241056/1‑139 (MQ=255)                                                                                aaCGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGTTGCTCTACCTATCAGCAGCTCTACAATGAATTCCa                                                                                      >  1:138684/1‑102 (MQ=255)                                                                                aaCGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGTTGCTCTACCTATCAGCAGCTCTACAATGAATTCCa                                                                                      <  2:156480/102‑1 (MQ=255)                                                                                aaCGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGTTGCTCTACCTATCAGCAGCTCTACAATGAATTCCa                                                                                      <  2:138684/102‑1 (MQ=255)                                                                                aaCGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGTTGCTCTACCTATCAGCAGCTCTACAATGAATTCCa                                                                                      >  1:156480/1‑102 (MQ=255)                                                                                aaCGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGTTGCTCTACCTATCAGCAGCTCTACAATGAATTCCACGCATTATATATAGATAAAGCAGGAATATGGAGCGCa                                                 >  2:362616/1‑139 (MQ=255)                                                                                  cGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGTTGCTCTACCTATCAGCAGCTCTACAATGAATTCCACGCATTATATATAGATAAAGCAGGAATATGGAGCGCAtt                                               <  2:653095/139‑1 (MQ=255)                                                                                          aTTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGTTGCTCTACCTATCAGCAGCTCTACAATGAATTCCACGCATTATATATAGATAAAGCAGGAATATGGAGCGCATTTGAGGgtg                                       <  1:305888/139‑1 (MQ=255)                                                                                                    atgatgGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGTTGCTCTACCTATCAGCAGCTCTACAATGAATTCCACGCATTATATATAGATAAAGCAGGAATATGGa                                                      >  2:728412/1‑114 (MQ=255)                                                                                                    atgatgGGTCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGTTGCTCTACCTATCAGCAGCTCTACAATGAATTCCACGCATTATATATAGATAAAGCAGGAATATGGa                                                      <  1:728412/114‑1 (MQ=255)                                                                                                            tCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGTTGCTCTACCTATcagcag                                                                                                       >  2:314530/1‑57 (MQ=255)                                                                                                            tCCACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGTTGCTCTACCTATcagcag                                                                                                       <  1:314530/57‑1 (MQ=255)                                                                                                             ccACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGTTGct                                                                                                                     >  2:363040/1‑42 (MQ=255)                                                                                                             ccACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGTTGct                                                                                                                     <  1:363040/42‑1 (MQ=255)                                                                                                              cACGCGTGTCGGCGGTGAGGCGTAACTTAATAAAGGTTGCTCTACCTATCAGCAGCTCTACAATGAATTCCACGCATTATATATAGATAAAGCAGGAATATGGAGCGCATTTGAGGGTGTATCTGCAACTAAAAACGtt                   <  1:50661/139‑1 (MQ=255)                                                                                                                    tgtCGGCGGTGAGGCGTAACTTAATAAAGGTTGct                                                                                                                     >  1:136852/1‑35 (MQ=255)                                                                                                                    tgtCGGCGGTGAGGCGTAACTTAATAAAGGTTGct                                                                                                                     <  2:136852/35‑1 (MQ=255)                                                                                                                      tCGGCGGTGAGGCGTAACTTAATAAAGGTTGCTCTACCTATCAGCAGct                                                                                                     >  2:56351/1‑49 (MQ=255)                                                                                                                      tCGGCGGTGAGGCGTAACTTAATAAAGGTTGCTCTACCTATCAGCAGct                                                                                                     <  1:56351/49‑1 (MQ=255)                                                                                                                      tCGGCGGTGAGGCGTAACTTAATAAAGGTTGCTCTACCTATCAGCAGCTCTACAATGAATTCCACGCATTATATATAGATAAAGCAGGAATATGGAGCGCATTTGAGGGTGTATCTGCAACTAAAAACGTTCTGGCCtt           >  1:734341/1‑139 (MQ=255)                                                                                                                      tCGGCGGTGAGGCGTAACTTAATAAAGGTTGCTCTACCTATCAGCAGCTCTACAATGAATTCCACGCATTATATATAGATAAAGCAGGAATATGGAGCGCATTTGAGGGTGTATCTGCAACTAAAAACGTTCTGGCCtt           >  1:800413/1‑139 (MQ=255)                                                                                                                      tCGGCGGTGAGGCGTAACTTAATAAAGGTTGCTCTACCTATCAGCAGCTCTACAATGAATTCCACGCATTATATATAGATAAAGCAGGAATATGGAGCGCATTTGAGGGTGTATCTGCAACTAAAAACGTTCTGGCCtt           >  2:211797/1‑139 (MQ=255)                                                                                                                               aGGCGTAACTTAATAAAGGTTGCTCTACCTATCAGCAGCTCTACAATGAATTCCACGCATTATATATAGATAAAGCAGGAATATGGAGCGCATTTGAGGGTGTATCTGCAACTAAAAACGTTCTGGCCTTTAGTCGTgg  <  1:430940/139‑1 (MQ=255)                                                                                                                                      |                                                                                                                                    AACAATTAGCAATGGCATATATAGCCGCTCTGCCGTTCAGCAGGCCTTTAGTTTACTGGGATGGCCAAGTATTAAAATCAACGACTGAAATTAAAAATTATGATGGGTCCACGCGTGTCGGCGGTGAGGCGTAGCTTAATAAAGGTTGCTCTACCTATCAGCAGCTCTACAATGAATTCCACGCATTATATATAGATAAAGCAGGAATATGGAGCGCATTTGAGGGTGTATCTGCAACTAAAAACGTTCTGGCCTTTAGTCGTGG  >  NC_000913/2788105‑2788369

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑