Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,632,915	T→C	pseudogene (351/414 nt)	yhiL ←	pseudogene, DUF4049 family protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,632,915	0	T	C	100.0%	251.3 / NA	70	pseudogene (351/414 nt)	yhiL	pseudogene, DUF4049 family protein
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (36/34);  total (36/34)

TACAATCGATTAAGAAAACCTATGAAATACTGGCAGGATTAAAAAGACATACCACCGTATTCATGGAGTTTTAATGTAGTTGAAAACAACTAAGCCCTGAGGAATAAATTATTTTATTATTTTTATCACGTGCTTCCTTCAGGGAATTTAGCCCCATAATACCATTATCAAATTGTTGATTATGATCTACCCCGGGCCCATGATGCCCATATTTTTGTCTAATGTATTTGCTGGGGTCTTCACCTTTGAGTGTCTCCCCACATATGAA  >  NC_000913/3632782‑3633049                                                                                                                                      |                                                                                                                                       tACAATCGATTAAGAAAACCTATGAAATACTGGCAGGATTAAAAAGACATACCACCGTATTCATGGAGTTTTAATGTAGTTGAAAACAACTAAGCCCTGAGGAATAAATTATTTTATTATTTTTATCACGTGcctcctt                                                                                                                                   >  1:833738/1‑139 (MQ=255)         aTTAAGAAAACCTATGAAATACTGGCAGGATTAAAAAGACATACCACCGTATTCATGGAGTTTTAATGTAGTTGAAAACAACTAAGCCCTGAGGAATAAATTATTTTATTATTTTTATCACGTGCCTCCTTCAGGGAAt                                                                                                                           >  1:549109/1‑139 (MQ=255)             aGAAAACCTATGAAATACTGGCAGGATTAAAAAGACATACCACCGTATTCATGGAGTTTTAATGTAGTTGAAAACAACTAAGCCCTGAGGAATAAATTATTTTATTATTTTTATCACGTGCCTCCTTCAGGGAATTTAg                                                                                                                       <  2:1408770/139‑1 (MQ=255)               aaaaCCTATGAAATACTGGCAGGATTAAAAAGACATACCACCGTATTCATGGAGTTTTAATGTAGTTGAAAACAACTAAGCCCTGAGGAATAAATTATTTTATTATTTTTATCACGTGCCTCCTTCAGGGAATTTAGcc                                                                                                                     <  1:114689/139‑1 (MQ=255)                  aCCTATGAAATACTGGCAGGATTAAAAAGACATACCACCGTATTCATGGAGTTTTAATGTAGTTGAAAACAACTAAGCCCTGAGGAATAAATTATTTTATTATTTTTATCACGTGCCTCCTTCAGGGAATTTAGCCCCa                                                                                                                  >  2:1419482/1‑139 (MQ=255)                         aaaTACTGGCAGGATTAAAAAGACATACCACCGTATTCATGGAGTTTTAATGTAGTTGAAAACAACTAAGCCCTGAGGAATAAATTATTTTATTATTTTTATCACGTGCCTCCTTCAGGGAATTTAGCCCCATAATAcc                                                                                                           <  1:943404/139‑1 (MQ=255)                             aCTGGCAGGATTAAAAAGACATACCACCGTATTCATGGAGTTTTAATGTAGTTGAAAACAACTAAGCCCTGAGGAATAAATTATTTTATTATTTTTATCACGTGCCTCCTTCAGGGAATTTAGCCCCATAATACCATTa                                                                                                       >  2:604408/1‑139 (MQ=255)                                      aTTAAAAAGACATACCACCGTATTCATGGAGTTTTAATGTAGTTGAAAACAACTAAGCCCTGAGGAATAAATTATTTTATTATTTTTATCACGTGCCTCCTTCAGGGAATTTAGCCCCATAATACCATTATCAAAttgt                                                                                              <  1:2778/139‑1 (MQ=255)                                           aaaGACATACCACCGTATTCATGGAGTTTTAATGTAGTTGAAAACAACTAAGCCCTGAGGAATAAATTATTTTATTATTTTTATCACGTGCCTCCTTCAGGGAATTTAGCCCCATAATACCATTATCAAATTGTTGAtt                                                                                         <  2:1329843/139‑1 (MQ=255)                                                cATACCACCGTATTCATGGAGTTTTAATGTAGTTGAAAACAACTAAGCCCTGAGGAGTAAATTATTTTATTATTTTTATCACGTGCCTCCTTCAGGGAATTTAGCCCCATAATACCATTATCAAAGTGTTGATtattat                                                                                    >  1:972533/1‑139 (MQ=255)                                                 aTACCACCGTATTCATGGAGTTTTAATGTAGTTGAAAACAACTAAGCCCTGAGGAATAAATTATTTTATTATTTTTATCACGTGCCTCCTTCAGGGAATTTAGc                                                                                                                      <  1:512456/104‑1 (MQ=255)                                                 aTACCACCGTATTCATGGAGTTTTAATGTAGTTGAAAACAACTAAGCCCTGAGGAATAAATTATTTTATTATTTTTATCACGTGCCTCCTTCAGGGAATTTAGc                                                                                                                      >  2:512456/1‑104 (MQ=255)                                                      accGTATTCATGGAGTTTTAATGTAGTTGAAAACAACTAAGCCCTGAGGAATAAATTATTTTATTATTTTTATCACGTGCCTCCTTCAGGGAATTTAGCCCCATAATACCATTATCAAATTGTTGATTATGATCTAccc                                                                              <  1:604408/139‑1 (MQ=255)                                                        cGTATTCATGGAGTTTTAATGTAGTTGAAAACAACTAAGCCCTGAGGAATAAATTATTTTATTATTTTTATCACGTGCCTCCTTCAGGGAATTTAGCCCCATAATACCATTATCAAATTGTTGATTATGATCTACCCCg                                                                            <  1:1419482/139‑1 (MQ=255)                                                         gTATTCATGGAGTTTTAATGTAGTTGAAAACAACTAAGCCCTGAGGAATAAATTATTTTATTCTTTTTATCACGTGCCTCCTTCAGGGAATTTAGCCCCATAATACCATTATCAAATTGTTGATTa                                                                                        <  1:958947/126‑1 (MQ=255)                                                         gTATTCATGGAGTTTTAATGTAGTTGAAAACAACTAAGCCCTGAGGAATAAATTATTTTATTATTTTTATCACGTGCCTCCTTCAGGGAATTTAg                                                                                                                       <  1:1444050/95‑1 (MQ=255)                                                         gTATTCATGGAGTTTTAATGTAGTTGAAAACAACTAAGCCCTGAGGAATAAATTATTTTATTATTTTTATCACGTGCCTCCTTCAGGGAATTTAg                                                                                                                       >  2:1444050/1‑95 (MQ=255)                                                         gTATTCATGGAGTTTTAATGTAGTTGAAAACAACTAAGCCCTGAGGAATAAATTATTTTATTATTTTTATCACGTGCCTCCTTCAGGGAATTTAGCCCCATAATACCATTATCAAAttg                                                                                               <  2:760269/119‑1 (MQ=255)                                                         gTATTCATGGAGTTTTAATGTAGTTGAAAACAACTAAGCCCTGAGGAATAAATTATTTTATTATTTTTATCACGTGCCTCCTTCAGGGAATTTAGCCCCATAATACCATTATCAAAttg                                                                                               >  1:760269/1‑119 (MQ=255)                                                         gTATTCATGGAGTTTTAATGTAGTTGAAAACAACTAAGCCCTGAGGAATAAATTATTTTATTATTTTTATCACGTGCCTCCTTCAGGGAATTTAGCCCCATAATACCATTATCAAATTGTTGATTa                                                                                        >  2:958947/1‑126 (MQ=255)                                                         gTATTCATGGAGTTTTAATGTAGTTGAAAACAACTAAGCCCTGAGGAATAAATTATTTTATTATTTTTATCACGTGCCTCCTTCAGGGAATTTAGCCCCATAATACCATTATCAAATTGTTGATTATGATCTACCCCgg                                                                           >  1:888381/1‑139 (MQ=255)                                                               aTGGAGTTTTAATGTAGTTGAAAACAACTAAGCCCTGAGGAATAAATTATTTTATTATTTTTATCACGTGCCTCCTTCAGGGAATTTAGCCCCATAATACCATTATCAAATTGTTGATTATGATCTACCCCGGGCCCat                                                                     >  1:841801/1‑139 (MQ=255)                                                               aTGGAGTTTTAATGTAGTTGAAAACAACTAAGCCCTGAGGAATAAATTATTTTATTATTTTTATCACGTGCCTCCTTCAGGGAATTTAGCCCCATAATACCATTATCAAATTGTTGATTATGATCTACCCCGGGCCCat                                                                     >  2:1142001/1‑139 (MQ=255)                                                                tGGAGTTTTAATGTAGTTGAAAACAACTAAGCCCTCAGGAATAAATTATTTTATTATTTTTATCACGTGCCTCCTTCAGGGAATTTAGCCCCATAATACCATTATCAAATTGTTGATTATGATCTACCCCGGGCCCatg                                                                    <  2:888381/139‑1 (MQ=255)                                                                 ggAGTTTTAATGTAGTTGAAAACAACTAAGCCCTGAGGAATAAATTATTTTATTATTTTTATCACGTGCCTCCTTCAGGGAATTTAGCCCCATAATACCATTATCAAATTGTTGATTATGATCTACCCCGGGCCCatga                                                                   >  1:720960/1‑139 (MQ=255)                                                                 ggAGTTTTAATGTAGTTGAAAACAACTAAGCCCTGAGGAATAAATTATTTTATTATTTTTATCACGTGCCTCCTTCAGGGAATTTAGCCCCATAATACCATTATCAAATTGTTGATTATGATCTACCCCGGGCCCatga                                                                   >  2:453066/1‑139 (MQ=255)                                                                  gAGTTTTAATGTAGTTGAAAACAACTAAGCCCTGAGGAATAAATTATTTTATTATTTTTATCACGTGCCTCCTTCAGGGAATTTAGCCCCATAATACCATTATCAAATTGTTGATTATGATCTACCCCGGGCCCatgat                                                                  >  1:547441/1‑139 (MQ=255)                                                                      tttAATGTAGTTGAAAACAACTAAGCCCTGAGGAATAAATTATTTTATTATTTTTATCACGTGACTCCTTCAGGGAATTTAg                                                                                                                       >  1:658820/1‑82 (MQ=255)                                                                      tttAATGTAGTTGAAAACAACTAAGCCCTGAGGAATAAATTATTTTATTATTTTTATCACGTGACTCCTTCAGGGAATTTAg                                                                                                                       <  2:658820/82‑1 (MQ=255)                                                                       ttAATGTAGTTGAAAACAACTAAGCCCTGAGGAATAAATTATTTTATTATTTTTATCACGTGCCTCCTTCAGGGAATTTAGCCCCATAATACCATTATCAAATTGTTGATTa                                                                                        >  1:806520/1‑112 (MQ=255)                                                                       ttAATGTAGTTGAAAACAACTAAGCCCTGAGGAATAAATTATTTTATTATTTTTATCACGTGCCTCCTTCAGGGAATTTAGCCCCATAATACCATTATCAAATTGTTGATTa                                                                                        <  2:806520/112‑1 (MQ=255)                                                                       ttAATGTAGTTGAAAACAACTAAGCCCTGAGGAATAAATTATTTTATTATTTTTATCACGTGCCTCCTTCAGGGAATTTAGCCCCATAATACCATTATCAAATTGTTGATTATGATCTACCCCGGGCCCATGATGCCCa                                                             >  2:838385/1‑139 (MQ=255)                                                                             tAGTTGAAAACAACTAAGCCCTGAGGAATAAATTATTTTATTATTTTTATCACGTGCCTCCTTCAGGGAATTTAGCCCCATAATACCATTATCAAATTGTTGATTATGATCTACCCCGGGCCCatg                                                                    <  2:155039/126‑1 (MQ=255)                                                                             tAGTTGAAAACAACTAAGCCCTGAGGAATAAATTATTTTATTATTTTTATCACGTGCCTCCTTCAGGGAATTTAGCCCCATAATACCATTATCAAATTGTTGATTATGATCTACCCCGGGCCCatg                                                                    >  1:155039/1‑126 (MQ=255)                                                                               gTTGAAAACAACTAAGCCCTGAGGAATAAATTATTTTATTATTTTTATCACGTGCCTCCTTCAGGGAATTTAGCCCCata                                                                                                                >  1:440986/1‑80 (MQ=255)                                                                               gTTGAAAACAACTAAGCCCTGAGGAATAAATTATTTTATTATTTTTATCACGTGCCTCCTTCAGGGAATTTAGCCCCata                                                                                                                <  2:440986/80‑1 (MQ=255)                                                                               gTTGAAAACAACTAAGCCCTGAGGAATAAATTATTTTATTATTTTTATCACGTGCCTCCTTCAGGGAATTTAGCCCCATAATACCATTATCAAATTGTTGATTATGATCTACCCCGGGCCCATGATGCCCATATTTTTg                                                     >  1:1165054/1‑139 (MQ=255)                                                                                  gAAAACAACTAAGCCCTGAGGAATAAATTATTTTATTATTTTTATCACGTGCCTCCTTCAGGGAATTTAGCCCCATAATACCATTATCAAATTGTTGATTATGATCTACCCCGGGCCCATGATGCCCATATTTTTGTCt                                                  >  2:1078752/1‑139 (MQ=255)                                                                                   aaaaCAACTAAGCCCTGAGGAATAAATTATTTTATTATTTTTATCACGTGCCTCCTTCAGGGAATTTAGCCCCATAATACCATTATCAAATTGTTGATTATGATCTACCCCGGGCCCATGATGCCCATATTTTTGTCTa                                                 <  2:736911/139‑1 (MQ=255)                                                                                   aaaaCAACTAAGCCCTGAGGAATAAATTATTTTATTATTTTTATCACGTGCCTCCTTCAGGGAATTTAGCCCCATAATACCATTATCAAATTGTTGATTATGATCTACCCCGGGCCCATGATGCCCATATTTTTGTCTa                                                 <  2:80634/139‑1 (MQ=255)                                                                                          cTAAGCCCTGAGGAATAAATTATTTTATTATTTTTATCACGTGCCTCCTTCAgg                                                                                                                               <  1:1134224/54‑1 (MQ=255)                                                                                          cTAAGCCCTGAGGAATAAATTATTTTATTATTTTTATCACGTGCCTCCTTCAgg                                                                                                                               >  2:1134224/1‑54 (MQ=255)                                                                                                   gAGGAATAAATTATTTTATTATTTTTATCACGTGCCTCCTTCAGGGAATTTAGCCCCATAATACCATTATCAAATTGTTGATTATGATCTACCCCGGGCCCATGATGCCCATATTTTTGTCTAATGTATTTGCTGGGGt                                 >  2:834700/1‑139 (MQ=255)                                                                                                    aGGAATAAATTATTTTATTATTTTTATCACGTGCCTCCTTCAGGGAATTTAGCCCCATAATACCATTATCAAATTGTTGATTATGATCTACCCCGGGCCCatgat                                                                  >  1:659200/1‑105 (MQ=255)                                                                                                    aGGAATAAATTATTTTATTATTTTTATCACGTGCCTCCTTCAGGGAATTTAGCCCCATAATACCATTATCAAATTGTTGATTATGATCTACCCCGGGCCCatgat                                                                  <  2:659200/105‑1 (MQ=255)                                                                                                     ggAATAAATTATTTTATTATTTTTATCACGTGCCTCCTTCAGGGAATTTAGCCCCATAATACCATTATCAAATTGTTGATTATGATCTACCCCGGGCCCATGATGCCCATATTTTTGTCTAATGTATTTGCTGGGGTCt                               <  2:720960/139‑1 (MQ=255)                                                                                                        aTAAATTATTTTATTATTTTTATCACGTGCCTCCTTCAGGGAATTTAGCCCCATAATACCATTATCAAATTGTTGATTATGATCTACCCCGGGCCCatg                                                                    <  2:920923/99‑1 (MQ=255)                                                                                                        aTAAATTATTTTATTATTTTTATCACGTGCCTCCTTCAGGGAATTTAGCCCCATAATACCATTATCAAATTGTTGATTATGATCTACCCCGGGCCCatg                                                                    >  1:920923/1‑99 (MQ=255)                                                                                                         tAAATTATTTTATTATTTTTATCACGTGCCTCCTTCAGGGAATTTAGcc                                                                                                                     <  2:137960/49‑1 (MQ=255)                                                                                                         tAAATTATTTTATTATTTTTATCACGTGCCTCCTTCAGGGAATTTAGcc                                                                                                                     >  1:137960/1‑49 (MQ=255)                                                                                                         tAAATTATTTTATTATTTTTATCACGTGCCTCCTTCAGGGAATTTAGCCCCATAATACCATTATCAAATTGTTGATTATGATCTACCCCGGGCCCATGATGCCCATATTTTTGTCTAATGTATTTGCTGGGGTCTTCAc                           <  2:547441/139‑1 (MQ=255)                                                                                                         tAAATTATTTTATTATTTTTATCACGTGCCTCCTTCAGGGAATTTAGCCCCATAATACCATTATCAAATTGTTGATTATGATCTACCCCGGGCCCATGATGCCCATATTTTTGTCTAATGTATTTGCTGGGGTCTTCAc                           >  1:786382/1‑139 (MQ=255)                                                                                                            attattttattattttTATCACGTGCCTCCTTCAGGGAATTTAGCCCCATAATACCATTATCAAATTGTTGATTATGATCTACCCCGGGCCCATGATGCCCATATTTTTGTCTa                                                 <  2:123829/114‑1 (MQ=255)                                                                                                            attattttattattttTATCACGTGCCTCCTTCAGGGAATTTAGCCCCATAATACCATTATCAAATTGTTGATTATGATCTACCCCGGGCCCATGATGCCCATATTTTTGTCTa                                                 >  1:123829/1‑114 (MQ=255)                                                                                                              tattttattattttTATCACGTGCCTCCTTCAGGGAATTTAGCCCCATAATACCATTATCAAATTGTTGATTATGATCTACCCCGGGCCCATGATGCCCATATTTTTGTCTAATGTATTTGCTGGGGTCTTCACCTTTg                      <  2:841801/139‑1 (MQ=255)                                                                                                              tattttattattttTATCACGTGCCTCCTTCAGGGAATTTAGCCCCATAATACCATTATCAAATTGTTGATTATGATCTACCCCGGGCCCATGATGCCCATATTTTTGTCTAATGTATTTGCTGGGGTCTTCACCTTTg                      >  2:536475/1‑139 (MQ=255)                                                                                                                ttttattattttTATCACGTGCCTCCTTCAGGGAATTTAGCCCCATAATACCATTATCAAATTGTTGATTATGATCTACCCCGGGCCCATGATGCCCATATTTTTGTCTa                                                 >  2:834765/1‑110 (MQ=255)                                                                                                                ttttattattttTATCACGTGCCTCCTTCAGGGAATTTAGCCCCATAATACCATTATCAAATTGTTGATTATGATCTACCCCGGGCCCATGATGCCCATATTTTTGTCTa                                                 <  1:834765/110‑1 (MQ=255)                                                                                                                ttttattattttTATCACGTGCCTCCTTCAGGGAATTTAGCCCCATAATACCATTATCAAATTGTTGATTATGATCTACCCCGGGCCCATGATGCCCATATTTTTGTCTAATGTATTTGCTGGGGTCTTCACCTTTGAg                    <  1:1387921/139‑1 (MQ=255)                                                                                                                     ttattttTATCACGTGCCTCCTTCAGGGAATTTAGCCCCATAATACCATTATCAAAttgtt                                                                                             >  1:742020/1‑61 (MQ=255)                                                                                                                     ttattttTATCACGTGCCTCCTTCAGGGAATTTAGCCCCATAATACCATTATCAAAttgtt                                                                                             <  2:742020/61‑1 (MQ=255)                                                                                                                     ttattttTATCACGTGCCTCCTTCAGGGAATTTAGCCCCATAATACCATTATCAAATTGTTGATTATGAt                                                                                    <  2:1239689/70‑1 (MQ=255)                                                                                                                     ttattttTATCACGTGCCTCCTTCAGGGAATTTAGCCCCATAATACCATTATCAAATTGTTGATTATGAt                                                                                    >  1:1239689/1‑70 (MQ=255)                                                                                                                      tattttTATCACGTGCCTCCTTCAGGGAATTTAGCCCCATAATACCATTATCAAATTGTTGATTATGATCTACCCCGGGCCCATGATGCCCa                                                             <  1:245238/92‑1 (MQ=255)                                                                                                                      tattttTATCACGTGCCTCCTTCAGGGAATTTAGCCCCATAATACCATTATCAAATTGTTGATTATGATCTACCCCGGGCCCATGATGCCCa                                                             >  2:245238/1‑92 (MQ=255)                                                                                                                        tttttATCACGTGCCTCCTTCAGGGAATTTAGCCCCATAATACCATTATCAAATTGTTGATTATGATCTACCCCGGGCCCATGATGCCCATATTTTTGTCTAATGTATTTGCTGGGGTCTTCACCTTTGAGTGTCTccc            <  2:1165054/139‑1 (MQ=255)                                                                                                                        tttttATCACGTGCCTCCTTCAGGGAATTTAGCCCCATAATACCATTATCAAATTGTTGATTATGATCTACCCCGGGCCCATGATGCCCATATTTTTGTCTAATGTATTTGCTGGGGTCTTCACCTTTGAGTGTCTccc            >  1:1421191/1‑139 (MQ=255)                                                                                                                           ttATCACGTGCCTCCTTCAGGGAATTTAGCCCCATAATACCATTATCAAATTGTTGATTATGATCTACCCCGGGCCCATGATGCCCATATTTTTGTCTAATGTATTTGCTGGGGTCTTCACCTTTGAGTGTCTCCCcac         <  2:1247943/139‑1 (MQ=255)                                                                                                                             aTCACGTGCCTCCTTCAGGGAATTTAGCCCCATAATACCATTATCAAATTGTTGATTATGATCTACCCCGGGCCCATGATGCCCATATTTTTGTCTAATGTATTTGCTGGGGTCTTCACCTTTGAGTGTCTCCCCACat       >  2:364803/1‑139 (MQ=255)                                                                                                                                  gTGCCTCCTTCAGGGAATTTAGCCCCATAATACCATTATCAAATTGTTGATTATGATCTACCCCGGGCCCATGATGCCCATATTTTTGTCTAATGTATTTGCTGGGGTCTTCACCTTTGAGTGTCTCCCCACATATGaa  >  2:315637/1‑139 (MQ=255)                                                                                                                                   tGCCTCCTTCAGGGAATTTAGCCCCATAATACCATTATCAAATTGTTGATTATGATCTACCCCGGGCCCATGATGCCCa                                                             <  1:1450718/79‑1 (MQ=255)                                                                                                                                      |                                                                                                                                       TACAATCGATTAAGAAAACCTATGAAATACTGGCAGGATTAAAAAGACATACCACCGTATTCATGGAGTTTTAATGTAGTTGAAAACAACTAAGCCCTGAGGAATAAATTATTTTATTATTTTTATCACGTGCTTCCTTCAGGGAATTTAGCCCCATAATACCATTATCAAATTGTTGATTATGATCTACCCCGGGCCCATGATGCCCATATTTTTGTCTAATGTATTTGCTGGGGTCTTCACCTTTGAGTGTCTCCCCACATATGAA  >  NC_000913/3632782‑3633049

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑