Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	263,172	A→C	pseudogene (41/63 nt)	ykfN ←	pseudogene, YdiA family

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	263,172	0	A	C	98.7%	274.5 / ‑4.5	77	pseudogene (41/63 nt)	ykfN	pseudogene, YdiA family
Reads supporting (aligned to +/- strand):  ref base A (1/0);  major base C (43/32);  minor base T (1/0);  total (45/32)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.93e-01

CTTCGCTCACTATACATCCTTGGCTGCAGGTTTAGTTGTACACCACTCCTAAATTTAATGTGTTGGCAATGTGTTCAATAAAGCTCGAACAAATTAGCTCATTATGATCGGTTAATACTTCAACTTCTGGTTGCATGATTGTTTGTCCGTAAAAAGATAACGCGCCTGCCGGGTAGTAGCAGGCGCATTACG  >  NC_000913/263077‑263268                                                                                                |                                                                                                 cTTCGCTCACTATACATCCTTGGCTGCAGGTTTAGTTGTACACCACTCCTAAATTTAATGTGTTGGCAATGTGTTCAATAAAGCTCGAACAAATTCGCTc                                                                                              >  1:1439722/1‑100 (MQ=255)   tCGCTCACTATACATCCTTGGCTGCAGGTTTAGTTGTACACCACTCCTAAATTTAATGTGTTGGCAATGTGTTCAATAAAGCTCGAACAAATTCGCTCAt                                                                                            >  1:1438298/1‑100 (MQ=255)    cGCTCACTATACATCCTTGGCTGCAGGTTTAGTTGTACACCACTCCTAAATTTAATGTGTTGGCAATGTGTTCAATAAAGCTCGAACAAATTCGCTCAtt                                                                                           <  1:848873/100‑1 (MQ=255)        cACTATACATCCTTGGCTGCAGGTTTAGTTGTACACCACTCCTAAATTTAATGTGTTGGCAATGTGTTCAATAAAGCTCGAACAAATTCGCTCATTATGa                                                                                       >  2:1336865/1‑100 (MQ=255)           tataCATCCTTGGCTGCAGGTTTAGTTGTACACCACTCCTAAATTTAATGTGTTGGCAATGTGTTCAATAAAGCTCGAACAAATTCGCTCATTATGATCg                                                                                    <  2:144993/100‑1 (MQ=255)            ataCATCGTTGGCTTCGGGATTAGGTAAACACCACTCCTGATTTTAATGTGTTGACAAGGGATGCAATAAAACTCGAACAAATTAGCTCATTAGGATCgg                                                                                   >  1:992109/1‑100 (MQ=255)            ataCATCCTTGGCTGCAGGTTTAGTTGTACACGACTCCTAAATTTAATGTGTTGGCAATGTGTTCAATAAAGCTCGCACAAATTCGCTCATTATGATCg                                                                                    >  1:757520/1‑99 (MQ=255)            ataCATCCTTGGCTGCAGGTTTAGTTGTACACCACTCCTAAATTTAATGTGTTGGCAATGTGTTCAATAAAGCTCGAACAAATTCGCTCATTATGATCgg                                                                                   <  2:883362/100‑1 (MQ=255)              aCATCCTTGGCTGCATGTTTAGTTGTACACCACTCCTAAATTTAATGTGTTGGCAATGTGTTCAATAAAGCTCGAACAAATTCGCTCATTATGATCGGtt                                                                                 <  2:757522/100‑1 (MQ=255)              aCATCCTTGGCTGCAGGTTTAGTTGTACACCACTCCTAAATTTAATGTGTTGGCAATGTGTTCAATAAAGCTCGAACAAATTCGCTTATTATGATCGGtt                                                                                 <  1:1053899/100‑1 (MQ=255)              aCATCCTTGGCTGCAGGTTTAGTTGTACACCACTCCTAAATTTAATGTGTTGGCAATGTGTTCAATAAAGCTCGAACAAATTCGCTCATTATGATCGGtt                                                                                 <  2:245140/100‑1 (MQ=255)               cATCCTTGGCTGCAGGTTTAGTTGTACACCACTCCTAAATTTAATGTGTTGGCAATGTGTTCAATAAAGCTCGAACAAATTCGCTCATTATGATCGGTTa                                                                                <  1:445469/100‑1 (MQ=255)                aTCCTTGGCTGCAGGTTTAGTTGTACACCACTCCTAAATTTAATGTGTTGGCAATGTGTTCAATAAAGCTCGAACAAATTCGCTCATTATGATCGGTTaa                                                                               <  1:1542737/100‑1 (MQ=255)                aTCCTTGGCTGCAGGTTTAGTTGTACACCACTCCTAAATTTAATGTGTTGGCAATGTGTTCAATAAAGCTCGAACAAATTCGCTCATTATGATCGGTTaa                                                                               >  2:426324/1‑100 (MQ=255)                aTCCTTGGCTGCAGGTTTAGTTGTACACCACTCCTAAATTTAATGTGTTGGCAATGTGTTCAATAAAGCTCGAACAAATTCGCTCATTATGATCGGTTaa                                                                               >  2:1640399/1‑100 (MQ=255)                  ccTTGGCTGCAGGTTTAGTTGTACACCACTCCTAAATTTAATGTGTTGGCAATGTGTTCAATAAAGCTCGAACAAATTCGCTCATTATGATCGGTTAATa                                                                             >  2:1366944/1‑100 (MQ=255)                  ccTTGGCTGCAGGTTGAGTTGTACACCACTCCTAAATTTATTGTGTTGGCAATGTGTTCAATTAAGCTTGAACTACTTCGATCATTATGATCGGTTAATa                                                                             >  1:222600/1‑100 (MQ=255)                     tGGCTGCAGGTTTAGTTTTACACCACTCCTAAATTTAATGTGTTGGCAATGTGTTCAATAAAGCTCGAACAAATTCGCTCATTATGATCGGTTAATACtt                                                                          <  1:1263747/100‑1 (MQ=255)                      ggCTGCAGGTTTAGTTGTACACCACTCCTAAATTTAATGTGTTGGCAATGTGTTCAATAAAGCTCGAACAAATTCGCTCATTATGATCGGTTAATACTTc                                                                         >  1:750487/1‑100 (MQ=255)                       gCTGCAGGTTTAGTTGTACACCACTCCTAAATTTAATGTGTTGGCAATGTGTTCAATAAAGCTCGAACAAATTCGCTCATTATGATCGGTTAATACTTCa                                                                        >  1:935715/1‑100 (MQ=255)                        cTGCAGGTTTAGTTGTACACCACTCCTAAATTTAATGTGTTGGCAATGTGTTCAATAAAGCTCGAACAAATTCGCTCATTATGATCGGTTAATACTTCaa                                                                       >  2:1013955/1‑100 (MQ=255)                          gCAGGTTTAGTTGTACACCACTCCTAAATTTAATGTGTTGGCAATGTGTTCAATAAAGCTCGAACAAATTCGCTCATTATGATCGGTTAATACTTCAACt                                                                     >  1:576432/1‑100 (MQ=255)                            aGGTTTAGTTGTACACCGCTCCTAAATTTAATGTGTTGGCAATGTGTTCAATAAAGCTCGAACAAATTCGCTCATTATGATCGGTTAATACTTCAACTTc                                                                   <  2:803003/100‑1 (MQ=255)                              gTTTAGTTGTACACCACTCCTAAATTTAATGTGTTGGCAATGTGTTCAATAAAGCTCGAACAAATTCGCTCATTATGATCGGTTAATACTTCAACTTCTg                                                                 <  2:725239/100‑1 (MQ=255)                              gTTTAGTTGTACACCACTCCTAAATTTAATGTGTTGGCAATGTGTTCAATAAAGCTCGAACAAATTCGCTCATTATGATCGGTTAATACTTCAACTTCTg                                                                 <  2:356447/100‑1 (MQ=255)                               tttAGTTGTACACCACTCCTAAATTTAATGTGTTGGCAATGTGTTCAATAAAGCTCGAACAAATTCGCTCATTATGATCGGTTAATACTTCAACTTCTgg                                                                >  1:58155/1‑100 (MQ=255)                                ttAGTTGTACACCACTCCTAAATTTAATGTGTTGGCAATGTGTTCAATAAAGCTCGAACAAATTCGCTCATTATGATCGGTTAATACTTCAACTTCTGGt                                                               <  1:227889/100‑1 (MQ=255)                                  aGTTGTACACCACTCCTAAATTTAATGTGTTGGCAATGTGTTCAATAAAGCTCGAACAAATTCGCTCATTATGATCGGTTAATACTTCAACTTCTGGTTg                                                             <  1:1470288/100‑1 (MQ=255)                                  aGTTGTACACCACTCCTAAATTTAATGTGTTGGCAATGTGTTCAATAAAGCTCGAACAAATTCGCTCATTATGATCGGTTAATACTTCAACTTCTGGTTg                                                             <  1:840623/100‑1 (MQ=255)                                   gTTGTACACCACTACTAAATTTAATGTGTTGGCAATGTTTTCAATAAAGCTCGAACAAATTCGCTCATTATGATCGGTTAATACTTCAACTTCTGGTTGc                                                            >  1:1049735/1‑100 (MQ=255)                                     tGTACACCACTCCTAAATTTAATGTGTTGGCAATGTGTTCAATAAAGCTCGAACAAATTCGCTCATTATGATCGGTTAATACTTCAACTTCTGGTTGCAt                                                          >  1:1254093/1‑100 (MQ=255)                                     tGTACACCACTCCTAAATTTAATGTGTTGGCAATGTGTTCAATAAAGCTCGAACAAATTCGCTCATTATGATCGGTTAATACTTCAACTTCTGGTTGCAt                                                          >  2:1205928/1‑100 (MQ=255)                                         caccacTCCTAAATTTAATGTGTTGGCAATGTGTTCAATAAAGCTCGAACAAATTCGCTCATTATGATCGGTTAATACTTCAACTTCTGGTTGCATGAtt                                                      >  1:817343/1‑100 (MQ=255)                                         caccacTCCTAAATTTAATGTGTTGGCAATGTGTTCAATAAAGCTCGAACAAATTCGCTCATTATGATCGGTTAATACTTCAACTTCTGGTTGCATGAtt                                                      >  1:663590/1‑100 (MQ=255)                                           ccacTCCTAAATTTAATGTGTTGGCAATGTGTTCAATAAAGCTCGAACAAATTCGCTCATTATGATCGGTTAATACTTCAACTTCTGGTTGCATGAttgt                                                    >  2:132136/1‑100 (MQ=255)                                              cTCCTAAATTTAATGTGTTGGCAATGTGTTCAATAAAGCTCGAACAAATTCGCTCATTATGATCGGTTAATACTTCAACTTCTGGTTGCATGAttgtttg                                                 <  1:808751/100‑1 (MQ=255)                                               tCCTAAATTTAATGTGTTGGCAATGTGTTCAATAAAGCTCGAACAAATTCGCTCATTATGATCGGTTAATACTTCAACTTCTGGTTGCATGAttgtttgt                                                >  2:1069684/1‑100 (MQ=255)                                                ccTAAATTTAATGTGTTGGCAATGTGTTCAATAAAGCTCGAACAAATTCGCTCATTATGATCGGTTAATACTTCAACTTCTGGTTGCATGATTGTTTGTc                                               >  1:1571277/1‑100 (MQ=255)                                                ccTAAATTTAATGTGTTGGCAATGTGTTCAATAAAGCTCGAACAAATTCGCTCATTATGATCGGTTAATACTTCAACTTCTGGTTGCATGATTGTTTGTc                                               <  2:699407/100‑1 (MQ=255)                                                ccTAAATTTAATGTGTTGGCAATGTGTTCAATAAAGCTCGAACAAATTCGCTCATTATGATCGGTTAATACTTCAACTTCTGGTTGCATGATTGTTTGTc                                               >  1:1615678/1‑100 (MQ=255)                                                 cTAAATTTAATGTGTTGGCAATGTGTTCAATAAAGCTCGAACAAATTCGCTCATTATGATCGGTTAATACTTCAACTTCTGGTTGCATGATTGTTTGTcc                                              >  2:1680827/1‑100 (MQ=255)                                                 cTAAATTTAATGTGTTGGCAATGTGTTCAATAAAGCTCGAACAAATTCGCTCATTATGATCGGTTAATACTTCAACTTCTGGTTGCATGATTGTTTGTcc                                              >  2:733508/1‑100 (MQ=255)                                                   aaaTTTAATGTGTTGGCAATGTGTTCAATAAAGCTCGAACAAATTCGCTCATTATGATCGGTTAATACTTCAACTTCTGGTTGCATGATTGTTTGTCCGt                                            >  1:294025/1‑100 (MQ=255)                                                    aaTTTAATGTGTTGGCAATGTGTTCAATAAAGCTCGAACAAATTCGCTCATTATGATCGGTTAATACTTCAACTTCTGGTTGCATGATTGTTTGTCCGTa                                           >  1:531142/1‑100 (MQ=255)                                                         aaTGTGTTGGCAATGTGTTCAATAAAGCTCGAACACATTCGCTCATTATGATCGGTTAATACTTCAACTTCTGGTTGCATGATTGTTTGTCCGTAAAAAg                                      <  1:565299/100‑1 (MQ=255)                                                         aaTGTGTTGGCAATGTGTTCAATAAAGCTCGAACAAATTCGCTCATTATGATCGGTTAATACTTCAACTTCTGGTTGCATGATTGTTTGTCCGTAAAAAg                                      <  2:706274/100‑1 (MQ=255)                                                                 ggCAATGTGTTCAATAAAGCTCGAACAAATTCGCTCATTATGATCGGTTAATACTTCAACTTCTGGTTGCATGATTGTTTGTCCGTAAAAAGATAAcgcg                              >  2:360620/1‑100 (MQ=255)                                                                 ggCAATGTGTTCAATAAAGCTCGAACAAATTCGCTCATTATGATCGGTTAATACTTCAACTTCTGGTTGCATGATTGTTTGTCCGTAAAAAGATAAcgcg                              >  2:359910/1‑100 (MQ=255)                                                                 ggCAATGTGTTCAATAAAGCTCGAACAAATTCGCTCATTATGATCGGTTAATACTTCAACTTCTGGTTGCATGATTGTTTGTCCGTAAAAAGATAAcgcg                              <  2:1373931/100‑1 (MQ=255)                                                                 ggCAATGTGTTCAATAAAGCTCGAACAAATTCGCTCATTATGATCGGTTAATACTTCAACTTCTGGTTGCATGATTGTTTGTCCGTAAAAAGATAAcgcg                              >  2:1417650/1‑100 (MQ=255)                                                                 ggCAATGTGTTCAATAAAGCTCGAACAAATTCGCTCATTATGATCGGTTAATACTTCAACTTCTGGTTGCATGATTGTTTGTCCGTAAAAAGATAAcgcg                              >  2:579612/1‑100 (MQ=255)                                                                  gCAATGTGTTCAATAAAGCTCGAACAAATTCGCTCATTATGATCGGTTAATACTTCAACTTCTGGTTGCATGATTGTTTGTCCGTAAAAAGATAACgcgc                             >  1:1242384/1‑100 (MQ=255)                                                                  gCAATGTGTTCAATAAAGCTCGAACAAATTCGCTCATTATGATCGGTTAATACTTCAACTTCTGGTTGCATGATTGTTTGTCCGTAAAAAGATAACgcgc                             >  1:73982/1‑100 (MQ=255)                                                                   cAATGTGTTCAATAAAGCTCGAACAAATTCGCTCATTATGATCGGTTAATACTTCAACTTCTGGTTGCATGATTGTTTGTCCGTAAAAAGATAACGCGcc                            <  2:156372/100‑1 (MQ=255)                                                                     aTGTGTTCAATAAAGCTCGAACAAATTCGCTCATTATGATCGGTTAATACTTCAACTTCTGGTTGCATGATTGTTTGTCCGTAAAAAGATAACGCGCCTg                          >  2:1507878/1‑100 (MQ=255)                                                                      tgtgTTCAATAAAGCTCGAACAAATTCGCTCATTATGATCGGTTAATACTTCAACTTCTGGTTGCATGATTGTTTGTCCGTAAAAAGATAACGCGCCTGc                         <  2:712732/100‑1 (MQ=255)                                                                      tgtgTTCAATAAAGCTCGAACAAATTCGCTCATTATGATCGGTTAATACTTCAACTTCTGGTTGCATGATTGTTTGTCCGTAAAAAGATAACGCGCCTGc                         <  2:348111/100‑1 (MQ=255)                                                                        tgtTCAATAAAGCTCGAACAAATTCGCTCATTATGATCGGTTAATACTTCAACTTCTGGTTGCATGATTGTTTGTCCGTAAAAAGATAACGCGCCTGCCg                       >  2:677613/1‑100 (MQ=255)                                                                         tatCAATAAAGCTCGAACAAATTCGCTCATTATGATCGGTTAATACTTCAACTTCTGGTTGCATGATTGTTTGTCCGTAAAAAGATAACGCGCCTGCCgg                      <  1:831272/98‑1 (MQ=255)                                                                         gtTCAATAAAGCTCGAACAAATTCGCTCATTATGATCGGTTAATACTTCAACTTCTGGTTGCATGATTGTTTGTCCGTAAAAAGATAACGCGCCTGCCgg                      >  1:856600/1‑100 (MQ=255)                                                                         gtTCAATAAAGCTCGAACAAATTCGCTCATTATGATCGGTTAATACTTCAACTTCTGGTTGCATGATTGTTTGTCCGTAAAAAGATAACGCGCCTGCCgg                      >  2:1362978/1‑100 (MQ=255)                                                                         gtTCAATAAAGCTCGAACAAATTCGCTCATTATGATCGGTTAATACTTCAACTTCTGGTTGCATGATTGTTTGTCCGTAAAAAGATAACGCGCCTGCCg                       >  1:538386/1‑99 (MQ=255)                                                                           tCAATAAAGCTCGAACAAATTCGCTCATTATGATCGGTTAATACTTCAACTTCTGGTTGCATGATTGTTTGTCCGTAAAAAGATAACGCGCCTGCCggtt                    <  2:1152217/100‑3 (MQ=255)                                                                            cAATAAAGCTCGAACAAATTCGCTCATTATGATCGGTTAATACTTCAACTTCTGGTTGCATGATTGTTTGTCCGTAAAAAGATAACGCGCCTGCCGGgta                   >  2:1488400/1‑100 (MQ=255)                                                                            cAATAAAGCTCGAACAAATTCGCTCATTATGATCGGTTAATACTTCAACTTCTGGTTGCATGATTGTTTGTCCGTAAAAAGATAACGCGCCTGCCGGgta                   >  1:1572195/1‑100 (MQ=255)                                                                             aaTAAAGCTCGAACAAATTCGCTCATTATGATCGGTTAATACTTCAACTTCTGGTTGCATGATTGTTTGTCCGTAAAAAGATAACGCGCCTGCCGGgtag                  <  1:437531/100‑1 (MQ=255)                                                                              aTAAAGCTCGAACAAATTTGCTCATTATGATCGGTTAATACTTCAACTTCTGGTTGCATGATTGTTTGTCCGTAAAAAGATAACGCGCCTGCCGGgtagt                 >  1:148684/1‑100 (MQ=255)                                                                                    cTCGAACAAATTCGCTCATTATGATCGGTTAATACTTCAACTTCTGGTTGCATGATTGTTTGTCCGTAAAAAGATAACGCGCCTGCCGGGTAGTAGCAgg           <  2:190155/100‑1 (MQ=255)                                                                                    cTCGAACAAATTCGCTCATTATGATCGGTTAATACTTCAACTTCTGGTTGCATGATTGTTTGTCCGTAAAAAGATAACGCGCCTGCCGGGTAGTAGCAgg           >  1:1374923/1‑100 (MQ=255)                                                                                     tCGAACAAATTCGCTCATTATGATCGGTTAATACTTCAACTTCTGGTTGCATGATTGTTTGTCCGTAAAAAGATAACGCGCCTGCCGGGTAGTAGCAGgc          <  1:24959/100‑1 (MQ=255)                                                                                      cGAACAAATTCGCTCATTATGATCGGTTAATACTTCAACTTCTGGTTGCATGATTGTTTGTCCGTAAAAAGATAACGCGCCTGCCGGGTAGTAGCAGgcg         >  1:1260066/1‑100 (MQ=255)                                                                                      cGAACAAATTCGCTCATTATGATCGGTTAATACCTCAACTTCTGGTTGCATGATTGTTTGTCCGTAAAAAGATAACGCGCCTGCCGGGTAGTAGCAGgcg         >  2:882354/1‑100 (MQ=255)                                                                                        aaCAAATTCGCTCATTATGATCGGTTAATACTTCAACTTCTGGTTGCATGATTGTTTGTCCGTAAAAAGATAACGCGCCTGCCGGGTAGTAGCAGGCGCa       <  2:398273/100‑1 (MQ=255)                                                                                        aaCAAATTCGCTCATTATGATCGGTTAATACTTCAACTTCTGGTTGCATGATTGTTTGTCCGTAAAAAGATAACGCGCCTGCCGGGTAGTAGCAGGCGCa       <  1:1680820/100‑1 (MQ=255)                                                                                         aCAAATTCGCTCATTATGATCGGTTAATACTTCAACTTCTGGTTGCATGATTGTTTGTCCGTAAAAAGATAACGCGCCTGCCGGGTAGTAGCAGGCGCAt      <  1:733506/100‑1 (MQ=255)                                                                                          cAAATTCGCTCATTATGATCGGTTAATACTTCAACTTCTGGTTGCATGATTGTTTGTCCGTAAAAAGATAACGCGCCTGCCGGGTAGTAGCAGGCGCAtt     >  2:543381/1‑100 (MQ=255)                                                                                             aTTCGCTCATTATGATCGGTTAATACTTCAACTTCTGGTTGCATGATTGTTTGTCCGTAAAAAGATAACGCGCCTGCCGGGTAGTAGCAGGCGCATTACg  <  1:108909/100‑1 (MQ=255)                                                                                                |                                                                                                 CTTCGCTCACTATACATCCTTGGCTGCAGGTTTAGTTGTACACCACTCCTAAATTTAATGTGTTGGCAATGTGTTCAATAAAGCTCGAACAAATTAGCTCATTATGATCGGTTAATACTTCAACTTCTGGTTGCATGATTGTTTGTCCGTAAAAAGATAACGCGCCTGCCGGGTAGTAGCAGGCGCATTACG  >  NC_000913/263077‑263268

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑