Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,921,515	C→T	T179T (ACG→ACA)	atpB ←	F0 sector of membrane‑bound ATP synthase, subunit a

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,921,515	0	C	T	100.0%	208.6 / NA	65	T179T (ACG→ACA)	atpB	F0 sector of membrane‑bound ATP synthase, subunit a
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (32/33);  total (32/33)

GAATGAAAATCAGCTCACCGGCATACATGTTACCGAACAGTCGCAAACCGAGTGAAACTGGTTTGGACAGCAGGCTTACCCCTTCAAGGATTAAGTTGACAGGAATGAACGCCCAGTGATTGAACGGCTGCAGCGTCAACTCTTTCGTGAAGCCGCCGATGCCTTTCATTTTGATGCTGTAGAACAGAATCAGGATAAATACGCCCAGTGCCATAGACAGCGTTACGTTCACGTCCGCAGACGGAACCACACGCAGTGCAGGCAGACCC  >  NC_000913/3921382‑3921650                                                                                                                                      |                                                                                                                                        gAATGAAAATCAGCTCACCGGCATACATGTTACCGAACAGTCGCAAACCGAGTGAAACTGGTTTGGACAGCAGGCTTACCCCTTCAAGGATTAAGTTGACAGGAATGAACGCCCAGTGATTGAACGGCTGCAGTGTCaa                                                                                                                                    <  2:1096569/139‑1 (MQ=255) gAATGAAAATCAGCTCACCGGCATACATGTTACCGAACAGTCGCAAACCGAGTGAAACTGGTTTGGACAGCAGGCTTACCCCTTCAAGGATTAAGTTGACAGGAATGAACGCCCAGTGATTGAACGGCTGCAGTGTCaa                                                                                                                                    <  2:1147191/139‑1 (MQ=255)                      cATACATGTTACCGAACAGTCGCAAACCGAGTGAAACTGGTTTGGACAGCAGGCTTACCCCTTCAAGGATTAAGTTGACAGGAATGAACGCCCAGTGATTGAACGGCTGCAGTGTCaa                                                                                                                                    <  1:1080721/118‑1 (MQ=255)                      cATACATGTTACCGAACAGTCGCAAACCGAGTGAAACTGGTTTGGACAGCAGGCTTACCCCTTCAAGGATTAAGTTGACAGGAATGAACGCCCAGTGATTGAACGGCTGCAGTGTCaa                                                                                                                                    >  2:1080721/1‑118 (MQ=255)                            tGTTACCGAACAGTCGCAAACCGAGTGAAACTGGTTTGGACAGCAGGCTTACCCCTTCAAGGATTAAGTTGACAGGAATGAACGCCCAGTGATTGAACGGCTGCAGTGTCAACTCTTTCGTGAAGCCGCCGATGCCttt                                                                                                         <  2:697591/139‑1 (MQ=255)                             gTTACCGAACAGTCGCAAACCGAGTGAAACTGGTTTGGACAGCAGGCTTATCCCTTCAAGGATTAAGTTGACAGGAATGAACGCCCAGTGATTGAACGGCTGCAGTGTCAACTCTTTCGTGAAGCCGCCGATGCCTTTc                                                                                                        >  1:1097787/1‑139 (MQ=255)                                    aaCAGTCGCAAACCGAGTGAAACTGGTTTGGACAGCAGGCTTACCCCTTCAAGGATTAAGTTGACAGGAATGAACGCCCAGTGATTGAACGGCTGCAGTGTCAACTCTTTCGTGAAGCCGCCGATGCCTTTCATTTTGa                                                                                                 >  2:1186074/1‑139 (MQ=255)                                     aCAGTCGCAAACCGAGTGAAACTGGTTTGGACAGCAGGCTTACCCCTTCAAGGATTAAGTTGACAGGAATGAACGCCCAGTGATTGAACGGCTGCAGTGTCAACTCTTTCGTGAAGCCGCCGATGCCTTTCATTTTGAt                                                                                                >  1:832246/1‑139 (MQ=255)                                         tCGGAAAACGATTGAAACTGGTTTGGACAGCAGGCTTACCACTTCAAGGATTAAGTTGACAGGAATGAACGCCCAGTGATTGAACGGCTGCAGTGTCAACTCTTTCGTGAAGCCGCCGATGCCTTTCATTTTGATGCTg                                                                                            <  2:683622/139‑1 (MQ=255)                                         tCGCAAACCGAGTGAAACTGGTTTGGACAGCAGGCTTACCCCTTCAAGGATTAAGTTGACAGGAATGAACGCCCAGTGATTGAACGGCTGCAGTGTCAACTCTTTCGTGAAGCCGCCGATGcc                                                                                                            >  1:460551/1‑123 (MQ=255)                                         tCGCAAACCGAGTGAAACTGGTTTGGACAGCAGGCTTACCCCTTCAAGGATTAAGTTGACAGGAATGAACGCCCAGTGATTGAACGGCTGCAGTGTCAACTCTTTCGTGAAGCCGCCGATGcc                                                                                                            <  2:460551/123‑1 (MQ=255)                                              aaCCGAGTGAAACTGGTTTGGACAGCAGGCTTACCCCTTCAAGGATTAAGTTGACAGGAATGTACGCCCAGTGATTGAACGGCTGCAGTGTCAACTCTTTCGTGAAGCCGCCGATGCCTTTCATTTTGATGCTGTAGaa                                                                                       <  2:928600/139‑1 (MQ=255)                                              aaCCGAGTGAAACTGGTTTGGACAGCAGGCTTACCCCTTCAAGGATTAAGTTGACAGGAATGAACGCCCAGTGATTGAACGGCTGCAGTGTCAACTCTTTCGTGAAGCCGCCGATGCCTTTCATTTTGATGCTGTAGaa                                                                                       <  2:1097787/139‑1 (MQ=255)                                              aaCCGAGTGAAACTGGTTTGGACAGCAGGCTTACCCCTTCAAGGATTAAGTTGACAGGAATGAACGCCCAGTGATTGAACGGCTGCAGTGTCAACTCTTTCGTGAAGCCGCCGATGCCTTTCATTTTGATGCTGTAGaa                                                                                       <  2:586204/139‑1 (MQ=255)                                                   aGTGAAACTGGTTTGGACAGCAGGCTTACCCCTTCAAGGATTAAGTTGACAGGAATGAACGCCCAGTGATTGAACGGCTGCAGTGTCAACTCTTTCGTGAAGCCGCCGATGCCTTTCATTTTGATGCTGTAGAACAGaa                                                                                  >  1:943083/1‑139 (MQ=255)                                                   aGTGAAACTGGTTTGGACAGCAGGCTTACCCCTTCAAGGATTAAGTTGACAGGAATGAACGCCCAGTGATTGAACGGCTGCAGTGTCAACTCTTTCGTGAAGCCGCCGATGCCTTTCATTTTGATGCTGTAGAACAGaa                                                                                  >  2:1239419/1‑139 (MQ=255)                                                       aaaCTGGTTTGGACAGCAGGCTTACCCCTTCAAGGATTAAGTTGACAGGAATGAACGCCCAGTGATTGAACGGCTGCAGTGTCAACTCTTTCGTGAAGCCGCCGATGCCTTTCATTTTGATGCTGTAGAACAGAATCAg                                                                              >  2:1080620/1‑139 (MQ=255)                                                               ttGGACAGCAGGCTTACCCCTTCAAGGATTAAGTTGACAGGAATGAACGCCCAGTGATTGAACGGCTGCAGTGTCAACTCTTTCGTGAAGCCGCCGATGCCTTTCATTTTGATGCTGTAGAACAGAATCAGGATAAATa                                                                      >  1:194947/1‑139 (MQ=255)                                                                  gACAGCAGGCTTACCCCTTCAAGGATTAAGTTGACAGGAATGAACGCCCAGTGATTGAACGGCTGCAGTGTCAACTCTTTCGTGAAGCCGCCGATGCCTTTCATTTTGATGCTGTAGAACAGAATCAGGATAAATACGc                                                                   >  2:989787/1‑139 (MQ=255)                                                                     aggagGCTTACCCCTTCAAGGAGTATGTTGACAGGAAGGAACGCCCAGTTATTGAACGGCTGCAGTGTCAGCTCTTTCGTGAAGCCGCCTTTGCCTTTCATTTTGATGCTGTAGAACAGAATCAGGGTAGAGACGCCCa                                                                <  2:615300/136‑1 (MQ=255)                                                                     agcagGCTTACCCCTTCAAGGATTAAGTTGACAGGAATGAACGCCCAGTGATTGAACGGCTGCAGTGTCAACTCTTTCGTGAAGCCGCCGATGCCTTTCATTTTGATGCTGTAGAACAGAATCAGGATAAATACGCCCa                                                                <  1:989787/139‑1 (MQ=255)                                                                     agcagGCTTACCCCTTCAAGGATTAAGTTGACAGGAATGAACGCCCAGTGATTGAACGGCTGCAGTGTCAACTCTTTCGTGAAGCCGCCGATGCCTTTCATTTTGATGCTGTAGAACAGAATCAGGATAAATACGCCCa                                                                <  1:1158812/139‑1 (MQ=255)                                                                                    tCAAGGATTAAGTTGACAGGAATGAACGCCCAGTGATTGAACGGCTGCAGTGTCAACTCTTTCGTGAAGCCGCCGATGCCTTTCATTTTGATGCTGTAGAACAGAATCAGGATAAATACGcc                                                                  >  2:102019/1‑122 (MQ=255)                                                                                    tCAAGGATTAAGTTGACAGGAATGAACGCCCAGTGATTGAACGGCTGCAGTGTCAACTCTTTCGTGAAGCCGCCGATGCCTTTCATTTTGATGCTGTAGAACAGAATCAGGATAAATACGcc                                                                  <  1:102019/122‑1 (MQ=255)                                                                                    tCAAGGATTAAGTTGACAGGAATGAACGCCCAGTGATTGAACGGCTGCAGTGTCAACTCTTTCGTGAAGCCGCCGATGCCTTTCATTTTGATGCTGTAGAACAGAATCAGGATAAATACGCCCa                                                                >  2:1219692/1‑124 (MQ=255)                                                                                    tCAAGGATTAAGTTGACAGGAATGAACGCCCAGTGATTGAACGGCTGCAGTGTCAACTCTTTCGTGAAGCCGCCGATGCCTTTCATTTTGATGCTGTAGAACAGAATCAGGATAAATACGCCCa                                                                <  1:1219692/124‑1 (MQ=255)                                                                                            tAAGTTGACAGGAATGAACGCCCAGTGATTGAACGGCTGCAGTGTCAACTCTTTCGTGAAGCCGCCGATGCCTTTCATTTTGATGCTGTAGAACAGAATCAGGATAAATACGCCCAGTGcc                                                           <  1:993201/121‑1 (MQ=255)                                                                                            tAAGTTGACAGGAATGAACGCCCAGTGATTGAACGGCTGCAGTGTCAACTCTTTCGTGAAGCCGCCGATGCCTTTCATTTTGATGCTGTAGAACAGAATCAGGATAAATACGCCCAGTGcc                                                           >  2:993201/1‑121 (MQ=255)                                                                                             aaGTTGACAGGAATGAACGCCCAGTGATTGAACGGCTGCAGTGTCAACTCTTTCGTGAAGCCGCCGATGCCttt                                                                                                         <  1:881499/74‑1 (MQ=255)                                                                                             aaGTTGACAGGAATGAACGCCCAGTGATTGAACGGCTGCAGTGTCAACTCTTTCGTGAAGCCGCCGATGCCttt                                                                                                         >  2:881499/1‑74 (MQ=255)                                                                                                    cAGGAATGAACGCCCAGTGATTGAACGGCTGCAGTGTCaa                                                                                                                                    <  2:878789/40‑1 (MQ=255)                                                                                                    cAGGAATGAACGCCCAGTGACTGAACGGCTGCAGTGTCaa                                                                                                                                    >  1:878789/1‑40 (MQ=255)                                                                                                       gAATGAACGCCCAGTGATTGAACGGCTGCAGTGTCAACTCTTTCGTGAAGCCGCCGATGCCTTTCATTTTGATGCTGTAGAACAGAATCAGGATAAATACGCCCAGTGCCATAGACAGCGTTACGTTCACGTCCGCAGa                              >  1:185275/1‑139 (MQ=255)                                                                                                             aCGCCCAGTGATTGAACGGCTGCAGTGTCAACTCTTTCGTGAAGCCGCCGATGCCTTTCATTTTGATGCTGTAGAACAGAATCAGGATAAATACGCCCAGTGCCATAGACAGCGTTACGTTCACGTCCGCAGACGGAAc                        >  2:528205/1‑139 (MQ=255)                                                                                                             aCGCCCAGTGATTGAACGGCTGCAGTGTCAACTCTTTCGTGAAGCCGCCGATGCCTTTCATTTTGATGCTGTAGAACAGAATCAGGATAAATACGCCCAGTGCCATAGACAGCGTTACGTTCACGTCCGCAGACGGAAc                        >  2:141138/1‑139 (MQ=255)                                                                                                                  cAGTGATTGAACGGCTGCAGTGTCAACTCTTTCGTGAAGCCGCCGATGCCTTTCATTTTGATGCTGTAGAACAGAATCAGGATAAATACGCCCAGTGCCATAGACAGCGTTACGTTCACGTCCGCAGACGGAACCacac                   <  2:846906/139‑1 (MQ=255)                                                                                                                  cAGTGATTGAACGGCTGCAGTGTCAACTCTTTCGTGAAGCCGCCGATGCCTTTCATTTTGATGCTGTAGAACAGAATCAGGATAAATACGCCCAGTGCCATAGACAGCGTTACGTTCACGTCCGCAGACGGAACCacac                   <  1:141138/139‑1 (MQ=255)                                                                                                                    gTGATTGAACGGCTGCAGTGTCAACTCTTTCGTGAAGCCGCCGATGCCTTTCATTTTGa                                                                                                 <  1:574862/59‑1 (MQ=255)                                                                                                                    gTGATTGAACGGCTGCAGTGTCAACTCTTTCGTGAAGCCGCCGATGCCTTTCATTTTGa                                                                                                 >  2:574862/1‑59 (MQ=255)                                                                                                                    gTGATTGAACGGCTGCAGTGTCAACTCTTTCGTGAAGCCGCCGATGCCTTTCATTTTGATGCTGTAGAACAGAATCAGGATAAATACGCCCAGTGCCATAGACAGCGTTACGTTCACGTCCGCAGACGGAACCACACGc                 >  2:391024/1‑139 (MQ=255)                                                                                                                     tGATTGAACGGCTGCAGTGTCAACTCTTTCGTGAAGCCGCCGATGCCTTTCATTTTGATg                                                                                               >  1:507005/1‑60 (MQ=255)                                                                                                                     tGATTGAACGGCTGCAGTGTCAACTCTTTCGTGAAGCCGCCGATGCCTTTCATTTTGATg                                                                                               <  2:507005/60‑1 (MQ=255)                                                                                                                     tGATTGAACGGCTGCAGTGTCAACTCTTTCGTGAAGCCGCCGATGCCTTTCATTTTGATGCTGTAGaa                                                                                       <  1:240644/68‑1 (MQ=255)                                                                                                                     tGATTGAACGGCTGCAGTGTCAACTCTTTCGTGAAGCCGCCGATGCCTTTCATTTTGATGCTGTAGaa                                                                                       >  2:240644/1‑68 (MQ=255)                                                                                                                           aaCGGCTGCTGTGTCAACTCTTTCGTGAAGCCGCCGATGCCTTTCATTTTGATGCTGTAGAACAGAATCAGGATAAATACGCCCa                                                                <  1:779870/85‑1 (MQ=255)                                                                                                                           aaCGGCTGCAGTGTCAACTCTTTCGTGAAGCCGCCGATGCCTTTCATTTTGATGCTGTAGAACAGAATCAGGATAAATACGcc                                                                  >  1:1038622/1‑83 (MQ=255)                                                                                                                           aaCGGCTGCAGTGTCAACTCTTTCGTGAAGCCGCCGATGCCTTTCATTTTGATGCTGTAGAACAGAATCAGGATAAATACGcc                                                                  <  2:1038622/83‑1 (MQ=255)                                                                                                                           aaCGGCTGCAGTGTCAACTCTTTCGTGAAGCCGCCGATGCCTTTCATTTTGATGCTGTAGAACAGAATCAGGATAAATACGCCCa                                                                >  2:779870/1‑85 (MQ=255)                                                                                                                           aaCGGCTGCAGTGTCAACTCTTTCGTGAAGCCGCCGATGCCTTTCATTTTGATGCTGTAGAACAGAATCAGGATAAATACGCCCAGTGCCATAGACAGCGTTACGTTCACGTCCGCAGACGGAACCACACGCAGTgcag          >  2:206617/1‑139 (MQ=255)                                                                                                                             cGGCTGCAGTGTCAACTCTTTCGTGAAGCCGCCGATGCCTTTCATTTTGATGCTGTAGAACAGAATCAGGATAAATACGCCCAGTGCCATAGACAGCGTTACGTTCACGTCCGCAGACGGAACCACACGCAGTgcaggc        <  2:194947/139‑1 (MQ=255)                                                                                                                              ggCTGCAGTGTCAACTCTTTCGTGAAGCCGCCGATGCCTTTCATTTTGATGCTGTAGAACAGAATCAGGATAAATACGCCCAGTGCCATAGACAGCGTTACGTTCACGTCCGCAGACGGAACCACACGCAGTgcaggca       <  2:943083/139‑1 (MQ=255)                                                                                                                              ggCTGCAGTGTCAACTCTTTCGTGAAGCCGCCGATGCCTTTCATTTTGATGCTGTAGAACAGAATCAGGATAAATACGCCCAGTGCCATAGACAGCGTTACGTTCACGTCCGCAGACGGAACCACACGCAGTgcaggca       <  1:391024/139‑1 (MQ=255)                                                                                                                               gCTGCAGTGTCATCTCTTTCGTGAAGCCGCCGATGCCTTTCATTTTGATGCTGTAGAACAGAATCAGGATAAATACGCCCa                                                                >  2:1291033/1‑81 (MQ=255)                                                                                                                               gCTGCAGTGTCATCTCTTTCGTGAAGCCGCCGATGCCTTTCATTTTGATGCTGTAGAACAGAATCAGGATAAATACGCCCa                                                                <  1:1291033/81‑1 (MQ=255)                                                                                                                               gCTGCAGTGTCAACTCTTTCGTGAAGCCGCCGATGCCTTTCATTTTGa                                                                                                 <  2:684151/48‑1 (MQ=255)                                                                                                                               gCTGCAGTGTCAACTCTTTCGTGAAGCCGCCGATGCCTTTCATTTTGa                                                                                                 >  1:684151/1‑48 (MQ=255)                                                                                                                               gCTGCAGTGTCAACTCTTTCGTGAAGCCGCCGATGCCTTTCATTTTGATGCTGTAGAACAGAATCAGGATAAATACGCCCa                                                                <  2:938762/81‑1 (MQ=255)                                                                                                                               gCTGCAGTGTCAACTCTTTCGTGAAGCCGCCGATGCCTTTCATTTTGATGCTGTAGAACAGAATCAGGATAAATACGCCCa                                                                >  1:938762/1‑81 (MQ=255)                                                                                                                               gCTGCAGTGTCAACTCTTTCGTGAAGCCGCCGATGCCTTTCATTTTGATGCTGTAGAACAGAATCAGGATAAATACGCCCAGTGCCATAGACAGCGTTACGTTCACGTCCGCAGACGGAACCACACGCAGTgcaggcag      >  1:1191443/1‑139 (MQ=255)                                                                                                                               gCTGCAGTGTCAACTCTTTCGTGAAGCCGCCGATGCCTTTCATTTTGATGCTGTAGAACAGAATCAGGATAAATACGCCCAGTGCCATAGACAGCGTTACGTTCACGTCCGCAGACGGAACCACACGCAGTgcaggcag      >  1:1125065/1‑139 (MQ=255)                                                                                                                                 tGCAGTGTCAACTCTTTCGTGAAGCCGCCGATGCCTTTCATTTTGATGCTg                                                                                            >  1:296141/1‑51 (MQ=255)                                                                                                                                 tGCAGTGTCAACTCTTTCGTGAAGCCGCCGATGCCTTTCATTTTGATGCTg                                                                                            <  2:296141/51‑1 (MQ=255)                                                                                                                                 tGCAGTGTCAACTCTTTCGTGAAGCCGCCGATGCCTTTCATTTTGATGCTGTAGAACAGAATCAGGATAAATACGCCCAGTGCCATAGACAGCGTTACGTTCACGTCCGCAGACGGAACCACACGCAGTGCAGGCAGAc    <  1:528205/139‑1 (MQ=255)                                                                                                                                   cAGTGTCAACTCTTTCGTGAAGCCGCCGATGCCTTTCATTTTGATGCTGTAGAACAGAATCAGGATAAATACGCCCAGTGCCATAGACAGCGTTACGTTCACGTCCGCAGACGGAACCACACGCAGTGCAGGCAGAccc  <  1:1186074/139‑1 (MQ=255)                                                                                                                                   cAGTGTCAACTCTTTCGTGAAGCCGCAGATGCCTTTCATTTTGATGCTGTAGAACAGAATCAGGATAAATACTCCCAGTGCCATAGATAGCGTTACGTTCACGTCCGCAGACGGAACCACACGCAGTGCAGGCAGActc  >  2:676921/1‑137 (MQ=255)                                                                                                                                      |                                                                                                                                        GAATGAAAATCAGCTCACCGGCATACATGTTACCGAACAGTCGCAAACCGAGTGAAACTGGTTTGGACAGCAGGCTTACCCCTTCAAGGATTAAGTTGACAGGAATGAACGCCCAGTGATTGAACGGCTGCAGCGTCAACTCTTTCGTGAAGCCGCCGATGCCTTTCATTTTGATGCTGTAGAACAGAATCAGGATAAATACGCCCAGTGCCATAGACAGCGTTACGTTCACGTCCGCAGACGGAACCACACGCAGTGCAGGCAGACCC  >  NC_000913/3921382‑3921650

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑