Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	2,089,854	A→T	10.0%	intergenic (‑141/‑142)	yefM ← / → hisL	YefM antitoxin of the YoeB‑YefM toxin‑antitoxin pair and DNA binding transcriptional repressor/his operon leader peptide

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,089,854	0	A	T	10.0%	128.5 / 8.1	51	intergenic (‑141/‑142)	yefM/hisL	YefM antitoxin of the YoeB‑YefM toxin‑antitoxin pair and DNA binding transcriptional repressor/his operon leader peptide
Reads supporting (aligned to +/- strand):  ref base A (25/20);  new base T (2/3);  total (27/24)
Fisher's exact test for biased strand distribution p-value = 6.51e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.96e-02

ATGTCAATCTCCTCTTTTGTACAGTTCATTGTACAATGATGAGCGTTAATTAACTATTTATTAATTAGTTTGTAGATCAAGGTATTGTCAGTGAGACGAAAATCCAGGCTTCGCTATTTTTGGTGCCATCAGCTAAGAGGACAGTCCTCTTAGCCCCCTCCTTTCCCCGCTCATTCATTAAACAAATCCATTGCCATAAAATATATAAAAAAGCCCTTGCTTTCTAACGTGAAAGTGGTTTAGGTTAAAAGACATCAGTTGAATAAACATTCACAGAGACTTTTA  >  NC_000913/2089712‑2089996                                                                                                                                               |                                                                                                                                               aTGTCAATCTCCTCTTTTGTACAGTTCATTGTACAATGATGAGCGTTAATTAACTATTTATTAATTAGTTTGTAGATCAAGGTATTGTCAGTGAGACGAAAATCCAGGCTTCGCTATTTTTGGTGCCATCAGCTAAGAGGACa                                                                                                                                                <  2:672209/143‑1 (MQ=255)    tCAATCTCCTCTTTTGTACAGTTCATTGTACAATGATGAGCGTTAATTAACTATTTATTAATTAGTTTGTAGATCAAGGTATTGTCAGTGAGACGAAAATCCAGGCTTCGCTATTTTTGGTGCCATCAGCTAAGAGGACAGTc                                                                                                                                             >  1:411159/1‑143 (MQ=255)        tctcCTCTTTTGTACAGTTCATTGTACAATGATGAGCGTTAATTAACTATTTATTAATTAGTTTGTAGATCAAGGTATTGTCAGTGAGACGAAAATCCAGGCTTCGCTATTTTTGGTGCCATCAGCTAAGAGGACAGTCctct                                                                                                                                         >  2:68387/1‑143 (MQ=255)        tctcCTCTTTTGTACAGTTCATTGTACAATGATGAGCGTTAATTAACTATTTATTAATTAGTTTGTAGATCAAGGTATTGTCAGTGAGACGAAAATCCAGGCTTCACTATTTTTGGTGCCATCAGCTAAGAGGACAGTCctct                                                                                                                                         >  2:690151/1‑143 (MQ=255)          tcctcTTTTGTACAGTTCATTGTACAATGATGAGCGTTAATTAACTATTTATTAATTAGTTTGTAGATCAAGGTATTGTCAGTGAGACGAAAATCCAGGCTTCGCTATTTTTGGTGCCATCAGCTATGAGGACAGTCCTCTTa                                                                                                                                       >  1:370032/1‑143 (MQ=255)          tcctcTTTTGTACAGTTCATTGTACAATGATGAGCGTTAATTAACTATTTATTAATTAGTTTGTAGATCAAGGTATTGTCAGTGAGACGAAAATCCAGGCTTCGCTATTTTTGGTGCCATCAGCTAAGAGGACTGTCCTCTTa                                                                                                                                       <  1:244448/143‑1 (MQ=255)          tcctcTTTTGTACAGTTCAGTGTACAATGATGAGCGTTAATTAACTATTTATTAATTAGTTTGTAGATCAAGGTATTGTCAGTGAGACGAAAATCCAGGCTTCGCTATTTTTGGTGCCATCAGCTAAGAGGACTGTCCTCTTa                                                                                                                                       <  1:6658/143‑1 (MQ=255)            ctctTTTGTACAGATCATTGTACAATGATGAGCGTTAATTGACTATATACTAATGAGCTTGTAGATCAAGGTATTGTCAGTGAGCCGAAAATCCCGGATTCGCTATTTTTGGTGCAATCAGCTAAGAGGACAGTCCTCTTaac                                                                                                                                     >  2:232284/1‑141 (MQ=255)               ttttGTACAGTTCATTGTACAATGATGAGCGTTAATTAACTATTTATTAATTAGTTTGTAGATCAAGGTATTGTCAGTGAGACGAAAATCCAGGCTTCGCTATTTTTGGTGCCATCAGCTAAGAGGACAGTCCTCTTAGcccc                                                                                                                                  >  1:889772/1‑143 (MQ=255)                tttGTACAGTTCATTGTACAATGATGAGCGTTAATTAACTATTTATTAATTAGTTTGTAGATCAAGGTATTGTCAGTGAGACGAAAATCCAGGCTTCGCTATTTTTGGTGCCATCAGCTAAGAGGACTGTCCTCTTAGctgat                                                                                                                                 <  1:189646/143‑5 (MQ=255)                  tgttccgTTCATTGTACAATGATGAGCGTTAATTAACTATTTATTAATTAGTTTGTAGATCAAGGTATTGTCAGTGAGACGAAAATCCAGGCTTCGCTATTTTTGGTGCCATCAGCTAAGAGGACAGTCCTCTTAGCCCcctc                                                                                                                               <  2:292522/137‑1 (MQ=255)                    tACAGTTCATTGTACAATGATGAGCGTTAATTAACTATTTATTAATTAGTTTGTAGATCAAGGTATTGTCAGTGAGACGAAAATCCAGGCTTCGCTATTTTTGGTGCCATCAGCTAAGAGGCCAGTCCTCTTAGCCCccccct                                                                                                                             >  1:900553/1‑143 (MQ=255)                        gTTCATTGTACAATGATGAGCGTTAATTAACTATTTATTAATTAGTTTGTAGATCAAGGGATTGTCACCGCGACGATATTCCAGGCTTCGCTATTTTTGGTGCCATCAGCTAAGAGGACAGTCCTCTTAGCCCCCTCCTTTcc                                                                                                                         >  1:768509/1‑143 (MQ=255)                         ttCATTGTACAATGATGAGCGTTAATTAACTATTTATTAATTAGTTTGTAGATCAAGGTATTGTCAGTGAGACGAAAATCCAGGCTTCGCTATTTTTGGTGCCATCAGCTAAGAGGACAGTCCTCTTAGCCCCCTCCTTTccc                                                                                                                        >  1:53396/1‑143 (MQ=255)                         ttCATTGTACAATGATGAGCGTTAATTAACTATTTATTAATTAGTTTGTAGATCAAGGTATTGTCAGTGAGACGAAAATCCAGGCTTCGCTATTTTTGGTGCCATCAGCTAAGAGGACAGTCCTCTTAGCCCCCTCCTTTccc                                                                                                                        <  1:585652/143‑1 (MQ=255)                         ttCATTGTACAATGATGAGCGTTAATTAAATATTTATTAATTAGTTTGTAGATCAAGGTATTGTCAGTGCGAAGAAAATCCAGGCTTCGATATTTTTGGTGTCATCAGATAATAGGACAATCATCTTAGCCCtctcctctacc                                                                                                                        >  2:136549/1‑138 (MQ=255)                           cATTGTACAATGATGAGCGTTAATTAACTATTTATTAATTAGTTTGTAGATCAAGGTATTGTCAGTGAGACGAAAATCCAGGCTTCGCTATTTTTGGTGCCATCAGCTAAGAGGACAGTCCTCTTAGCCCCCTCCTTTCCCCg                                                                                                                      >  2:915687/1‑143 (MQ=255)                             ttGTACAATGATGAGCGTTAATTAACTATTTATTAATTAGTTTGTAGATCAAGGTATTGTCAGTGAGACGAAAATCCAGGCTTCGCTATTTTTGGTGCCATCAGCTAAGAGGACAGTCCTCTTAGCCCCCTCCTTTCCCCGCt                                                                                                                    <  1:470957/143‑1 (MQ=255)                                      gatgaGCGTTAATTAACTATTTATTAATTAGTTTGTAGATCAAGGTATTGTCAGGGAGACGAAAATCCAGGCTTCGCTATTTTTGGTGCCATCAGCTAAGAGGACAGTCCTCTTAGCCCCCTCCTTTCCCCGCTCATTCATTa                                                                                                           <  1:154493/143‑1 (MQ=255)                                        tgaGCGTTAACTAACTATTTATTAATTAGTTTGTAGATCAAGGTATTGTCAGTGAGACGAAAATCCAGGCTTCGCTATTTTTGGTGCCATCAGCTAAGAGGACAGTCCTCTTAGCCCCCTCCTTTCCCCGCTCATTCATTaaa                                                                                                         <  1:581348/143‑1 (MQ=255)                                                aattaaCTATTTATTAATTAGTTTGTAGATCAAGGTATTGTCAGTGAGACGAAAATCCAGGCTTCACTATTTTTGGTGCCATCAGCTAAGAGGACAGTCCTCTTAGCCCCCTCCTTTCCCCGCTCATTCATTAAACAAATCCa                                                                                                 <  1:690151/143‑1 (MQ=255)                                                   taaCTATTTATTAATTAGTTTGTAGATCAAGGTATTGTCAGTGAGACGAAAATCCAGGCTTCGCTATTTTTGGTGCCATCAGCTAAGAGGACAGTCCTCTTAGCCCCCTCCTTTCCCCGCTCATTCATTAAACAAATCCATTg                                                                                              <  1:323113/143‑1 (MQ=255)                                                   taaCTATTTATTAATTAGTTTGTAGATCAAGGTATTGTCAGTGAGACGAAAATCCAGGCTTCGCTATTTTTGGTGCCATCAGCTAAGAGGACAGTCCTCTTAGCCCCCTCCTTTCCCCGCTCATTCATTAAACAAATCCATTg                                                                                              <  1:609181/143‑1 (MQ=255)                                                            attaattaGTTTGTAGATCAAGGTATTGTCAGTGAGACGAAAATCCAGGCTTCGCTATTTTTGGTGCCATCAGCTAAGAGGACAGTCCTCTTAGCCCCCTCCTTTCCCCGCTCATTCATTAAACAAATCCATTGCCATAAAat                                                                                     >  1:743648/1‑143 (MQ=255)                                                             ttaattaGTTTGTAGATCAAGGTATTGTCAGTGAGACGAAAATCCAGGCTTCGCTATTTTTGGTGCCATCAGCTAAGAGGACAGTCCTCTTAGCCCCCTCCTTTCCCCGCTCATTCATTAAACAAATCCATTGCCATAAAata                                                                                    >  1:245890/1‑143 (MQ=255)                                                                attaGTTTGTAGATCAAGGTATTGTCAGTGAGACGAAAATCCAGGCTTCGCTATTTTTGGTGCCATCAGCTAAGAGGACAGTCCTCTTAGCCCCCTCCTTTCCCCGCTCATTCATTAAACAAATCCATTGCCATAAAatatat                                                                                 >  1:354653/1‑143 (MQ=255)                                                                 ttaGTTTGTAGATCAAGGTATTGTCAGTGAGACACAAATCCACACTTAGCAATTGTTGGTGCCATCGGGTACGACGCCATTTCGTTGTGTGCACTAATTCTCTATTTTATTCATTAAACAAATCCATTGCCATAAAagatctc                                                                                >  1:568483/1‑140 (MQ=255)                                                                      ttGTATATTAAGGTATTGTCAGTGAGACGAAAATCCACGCTTCGCTATTTTTGGTGCCATCAGCTAAGAGGACAGTCCTCTTAGACCCATCCTTTCCCCGCTCATTCATTAAACAAATCCATTGCCATAAAATATATaaaaaa                                                                           <  2:109903/143‑1 (MQ=255)                                                                      ttGTAGATCAAGGTATTGTCAGTGAGACGAAAATCCAGGCTTCGCTATTTTTGTTGCCATCAGCTGAGAGGACAGTCCTCATAGCCCCCTCCTTTCCCCGATCGCTCATTAAACAAATCCATTGCCATAAAATATATaaaaaa                                                                           >  2:149509/1‑143 (MQ=255)                                                                         tAGCTCAAGGTACTGCTAGTGATCCGCAAATCCAGTCTTCGCTATTTCTGGTGCCATCAGCTAAGAGGACAGTCCTCTTAGCCCCCTCCTTTCCCCGCTCATTCATTAAACAAATCCATTGCCATAAAATATATAACAACGct                                                                        <  2:235760/143‑2 (MQ=255)                                                                         tAGATCAAGGTATTGTCAGTGAGACGAAAATCCAGGCTTCGCTATTTTTGGTGCCATCAGCTAAGAGGACAGTCCTCTTAGCCCCCTCCTTTCCACGCGCATTCATTAAACAAATCCATTGCCATGAAATGTATAGAAAAGcc                                                                        >  1:735940/1‑143 (MQ=255)                                                                            aTCAAGGTATTGTCAGTGAGACGAAAATCCAGGCTTCGCTATTTTTGGTGCCATCAGCTAAGAGGACAGTCCTCTTAGCCCCCTCCTTTCCCCGCTCATTCATTAAACAAATCCATTGCCATAAAATATATAAAAAAGCCCtt                                                                     >  2:347129/1‑143 (MQ=255)                                                                             tCAAGGTATTGTCAGTGAGACGAAAATCCAGGCTTCGCTATTTTTGGTGCCATCAGCTAAGAGGACAGTCCTCTTAGCCCCCTCCTTTCCCCGCTCATTCATTAAACAAATCCATTGCCATAAAATATATAAAAAAGCCCTTg                                                                    <  1:614095/143‑1 (MQ=255)                                                                             tCAAGGTATTGTCAGTGAGACGAAAATCCAGGCTTCGCTATTTTTGGTGCCATCAGCTAAGAGGACAGTCATCTTAGCCCACTCCTTTCCCCGCTCATTCATTAAACAACTCCATTGCCATCAAATATATAAAAAAGACCtcg                                                                    >  2:404840/1‑141 (MQ=255)                                                                              cAAGGTATTGTCAGTGAGACGAAAATCCAGGCTTCGCTATTTTTGGTGCCATCAGCTAAGAGGACAGTCCTCTTAGCCACCTCCTTTCCCCGCTCATTCATTACACAAATCCATTGCCATACAATATATAAAAAAGCCCTTGc                                                                   >  2:736128/1‑143 (MQ=255)                                                                                      tctcggtgtGACGGAAATCCAGGCTTCGCTATTTTTGGTGCCATCAGCTAAGAGGACAGTCCTCTTAGCCCCCTTCTTTCCCCGCTCATTCATTAAACAAATCCATTGCCATAAAATATATATTAAAGCCCTTGCTTTCTAAc                                                           <  2:95033/138‑1 (MQ=255)                                                                                            tGAGACGAAAATCCAGGCTTCGCTATTTTTGGTGCCATCAGCTAAGAGGACAGTCCTCTTAGCCCCCTCCTTTCCCCGCTCATTCATTAAACAAATCCATTGCCATAAAATATATAAAAAAGCCCTTGCTTTCTAACGTGaaa                                                     <  1:897376/143‑1 (MQ=255)                                                                                            tGAGACGAAAAGCCAGGCTTCGCTATTTTTGGTGCCATCAGCTAAGAGGACAGTCCTCTTATCCCCCTCCTTTCCCCGCTCATTCATTAAACAAATCCATTGCCATAAAATATATAAAAAAGCCCTTGCTTTCTAACGTGaaa                                                     <  2:317188/143‑1 (MQ=255)                                                                                                  gAAAATCCAGGCTTCGCTATTTTTGGTGCCATCAGCTAAGAGGACAGTCCTCTTAGCCCCCTCCTTTCCCCGCTCATTCATTAACCAAATCCATTGCCATAAAATATCTCAAAAAGCCCTTGCTTTCTAACGTGAAAGAggat                                               >  1:329733/1‑141 (MQ=255)                                                                                                  gAAAATCCAGGCTTCGCTATTTTTGGTGCCATCAGCTAAGAGGACAGTCCTCTTAGCCCCCTCCTTTCCCCGCTCATTCATTAAACAAATCCATTGCCATAAAATATATAAAAAAGCCCTTGCTTTCTAACGTGAAAGTGGtg                                               >  1:212480/1‑142 (MQ=255)                                                                                                      agccAGGCTTCGCTATTTTTGGTGCCATCAGCTAAGAGCACAGTCCTCTTAGCCCCCTCCTTTCCCCGCTCATTCATTAAACAAATCCATTGCCATAAAATATATAAAAAAGCCCTTGCTTTCTAACGTGAAAGTGGTTTAgg                                           <  1:138154/141‑1 (MQ=255)                                                                                                          aGGCTTCGCTATTTTTGGTGCCATCAGCTAAGAGGTCAGTCCTCTTAGCCCCCTCCTTTCCCCGCTCATCCAACAAACAAATCCATTGCCATAAAATATATAAAAAAGCCCTTGCTTTCTAACATGAAAGTGGATTAGGTTaa                                       >  2:440550/1‑143 (MQ=255)                                                                                                           tgCTTCGCTATTTTTGGTGCCATCAGCTAAGAGGACAGTCCTCTTAGCCCCCTCCTTTCCCCGCTCATTCATTAAACAAATCCAGTGCCATAAAATATATAAAAAAGCCCTTGCTTTCTAACGTGAAAGTGGTTTAGGTTaaa                                      <  1:283640/142‑1 (MQ=255)                                                                                                                        ttGGTGCCATCAGCTAAGAGGACAGTCCTCTTAGCCCCCTCCTTTCCCCGCTCATTCATTAAACAAATCCATTGCCATAAAATATATAAAAAAGCCCTTGCTTTCTTACGTGAAAGTGGTTTAGGTTAAAAGACATCAGTTGa                         <  1:591443/143‑1 (MQ=255)                                                                                                                         tGGTGCCATCAGCTAAGAGGACAGTCCTCTTAGCCCCCTCCTTTCCCCGCTCATTCATTAAACAAATCCATTGCCATAAAATATATAAAAAAGCCCTTGCTTTCTAACGTGAAAGTGGTTTAGGTTAAAAGACATCAGTTGaa                        <  1:915687/143‑1 (MQ=255)                                                                                                                             gCCATCAGCTAAGAGGACAGTCCTCTTAGCCCCCTCCTTTCCCCGCTCATTCATTAAACAAATCCATTGCCATAAAATATATAAAAAAGCCCTTGCTTTCTCCCGTGAAAGTGGTTTAGGTTAAAAGACATCAGTTGAATaca                    >  1:642810/1‑141 (MQ=255)                                                                                                                                    gCTAATAGCACAGTCCTCTTAGCCTCCTCCTTTCCCCGCTCATTCATTAAACAAATCCATTGCCATAAAATATATAAAAAAGCCCTGGCTTTCTAACGTGAAAGTGGTTTAGGTTAAAAGACATCAGTTGAATAAACATTcac             <  1:64364/143‑1 (MQ=255)                                                                                                                                     cTAAGAGGACAGTGCTCTTAGGCCGCTCCTTTCCCCGCTCATTCATTAAACAAATCCATTGCCATAAAATATATAAAAAAGCCCTTGCTTTCTAACGTGAAAGTGGTTTAGGTTAAAAGACATCAGTTGAATAAACATTcaca            <  2:90758/143‑1 (MQ=255)                                                                                                                                      tAAGAGGACTGTCCTCTTAGCCCCCTCCTTTCCCCGCTCATTCATTAAACAAATCCATTGCCATAAAATATATAAAAAAGCCCTTGCTTTCTAACGTGAAAGTGGTTTAGGTTAAAAGACATCAGTTGACTAAACATTCACag           >  2:700839/1‑143 (MQ=255)                                                                                                                                      tAAGAGGACTGTCCTCTTAGCCCCCTCCTTTCCCCGCTCATTCATTAAACAAATCCATTGCCATAAAATATATAAAAAAGCCCTTGCTTTCTAACGTGAAAGTGGTTTAGGTTAAAAGACATCAGTTGAATAAACATTCACag           >  1:53428/1‑143 (MQ=255)                                                                                                                                       acgagGACCGCCCTCTGAGCCCCCTCCTTTCGCCGCGCAATCAGTAACAAAATCCAGTTCCATAAAATATAGAAGAAAGCCCTTGCTTTCTCACGTGAAAGTTGTTTAGGTTAAAAGACATCAGTTGAATAAACATTCACaga          <  2:808477/141‑1 (MQ=255)                                                                                                                                            gACAGTCCTCTTAGCCCCCTCCTTTCCCCGCTCATTCATTAAACAAATCCATTGCCATAAAATATATAAAAAAGCCCTTGCTTTCTAACGTGAAAGTGGTTTAGGTTAAAAGACATCAGTTGAATAAACATTCACAGAGACtt     >  1:182328/1‑143 (MQ=255)                                                                                                                                               aGTCCTCTTAGCCCCCTCCTTTCCCCGCTCATTCATTAAACAAATCCATTGCCATAAAATATATAAAAAAGCCCTTGCTTTCTAACGTGAAAGTGGTTTAGGTTAAAAGACATCAGTTGAATAAACATTCACAGAGACTTTTa  >  1:828441/1‑143 (MQ=255)                                                                                                                                               |                                                                                                                                               ATGTCAATCTCCTCTTTTGTACAGTTCATTGTACAATGATGAGCGTTAATTAACTATTTATTAATTAGTTTGTAGATCAAGGTATTGTCAGTGAGACGAAAATCCAGGCTTCGCTATTTTTGGTGCCATCAGCTAAGAGGACAGTCCTCTTAGCCCCCTCCTTTCCCCGCTCATTCATTAAACAAATCCATTGCCATAAAATATATAAAAAAGCCCTTGCTTTCTAACGTGAAAGTGGTTTAGGTTAAAAGACATCAGTTGAATAAACATTCACAGAGACTTTTA  >  NC_000913/2089712‑2089996

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑