Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,920,950	C→T	*80* (TAG→TAA)	atpE ←	F0 sector of membrane‑bound ATP synthase, subunit c

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,920,950	0	C	T	98.7%	239.3 / NA	74	*80* (TAG→TAA)	atpE	F0 sector of membrane‑bound ATP synthase, subunit c
Reads supporting (aligned to +/- strand):  ref base C (0/0);  major base T (39/34);  minor base A (0/1);  total (39/35)
Fisher's exact test for biased strand distribution p-value = 4.73e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CGTACTTCATGCAGAACAGAACGAACAGGACAAACGCGATGGCCTGGCCGAGGATTGTTGCGTTAAGATTCACAGCACAATGCCTCTATTTAGTTAACGTTCTGATATTGCTCTTTAAATAAAAGCAACGCTTACTACGCGACAGCGAACATCACGTACAGACCCAGACCTACAGCGATCATCGGGATAGCATCCACCAGACCCATAACGATAAAGAACTGAGTACGCAGCAGAGGAATCAGATCAGGTTGACGCGCTGCGC  >  NC_000913/3920816‑3921077                                                                                                                                       |                                                                                                                                cGTACTTCATGCAGAACAGAACGAACAGGACAAACGCGATGGCCTGGCCGAGGATTGTTGCGTTAAGATTCACAGCACAATGCCTCTATTTAGTTAACGTTCTGATATTGCTCTTTAAATAAAAGCAACGCTTATTAcg                                                                                                                             <  1:863836/139‑1 (MQ=255)        cATGCAGAACAGAACGAACAGGACAAACGCGATGGCCTGGCCGAGGATTGTTGCGTTAAGATTCACAGCACAATGCCTCTATTTAGTTAACGTTCTGATATTGCTCTTTAAATAAAAGCAACGCTTATTACGCGACAGc                                                                                                                      >  2:635028/1‑139 (MQ=255)        cATGCAGAACAGAACGAACAGGACAAACGCGATGGCCTGGCCGAGGATTGTTGCGTTAAGATTCACAGCACAATGCCTCTATTTAGTTAACGTTCTGATATTGCTCTTTAAATAAAAGCAACGCTTATTACGCGACAGc                                                                                                                      >  1:786015/1‑139 (MQ=255)              gaacagaacGAACAGGACAAACGCGATGGCCTGGCCGAGGATTGTTGCGTTAAGATTCACAGCACAATGCCTCTATTTAGTTAACGTTCTGATATTGCTCTTTAAATAAAAGCAACGCTTATTACGCGACa                                                                                                                        >  2:348583/1‑131 (MQ=255)              gaacagaacGAACAGGACAAACGCGATGGCCTGGCCGAGGATTGTTGCGTTAAGATTCACAGCACAATGCCTCTATTTAGTTAACGTTCTGATATTGCTCTTTAAATAAAAGCAACGCTTATTACGCGACa                                                                                                                        <  1:348583/131‑1 (MQ=255)                    aacgaacAGGACAAACGCGATGGCCTGGCCGAGGATTGTTGCGTTAAGATTCACAGCACAATGCCTCTATTTAGTTAACGTTCTGATATTGCTCTTTAAATAAAAGCAACGCTTATTACGCGACAGCGAACATCACGTa                                                                                                          >  1:574278/1‑139 (MQ=255)                          cAGGACAAACGCGATGGCCTGGCCGAGGATTGTTGCGTTAAGATTCACAGCACAATGCCTCTATTTAGTTAACGTTCTGATATTGCTCTTTAAATAAAAGCAACGCTTATTACGCGACAGCGAACATCACGTAcagacc                                                                                                    <  2:574278/139‑1 (MQ=255)                                       aTGGCCTGGCCGAGGATTGTTGCGTTAAGATTCACAGCACAATGCCTCTATTTAGTTAACGTTCTGATATTGCTCTTTAAATAAAAGCAACGCTTATTACGCGACAGCGAACATCACGTACAGACCCAGACCTACAGCg                                                                                       <  2:1294391/139‑1 (MQ=255)                                                               ttAAGATTCACAGCACAATGCCTCTATTTAGTTAACGTTCTGATATTGCTCTTTAAATAAAAGCAACGCTTCTTACGCGACAGCGAACATCACGTACAGACCCAGACCTACAGCGATCATCGGGATAGCATCCACCAGa                                                               >  2:882405/1‑139 (MQ=255)                                                                  aGATTCACAGCACAATGCCTCTATTTAGTTAACGTTCTGATATTGCTCTTTAAATAAAAGCAACGCTTATTACGCGACAGCGa                                                                                                                    >  1:990334/1‑83 (MQ=255)                                                                  aGATTCACAGCACAATGCCTCTATTTAGTTAACGTTCTGATATTGCTCTTTAAATAAAAGCAACGCTTATTACGCGACAGCGa                                                                                                                    <  2:990334/83‑1 (MQ=255)                                                                      tCACAGCACAATGCCTCTATTTAGTTAACGTTCTGATATTGCTCTTTAAATAAAAGCAACGCTTATTACGCGACAGCGAACATCACGTACAGACCCAGACCTACAGCGATCATCGGGATAGCATCCACCAGACCCATaa                                                        <  1:144993/139‑1 (MQ=255)                                                                          aGCACAATGCCTCTATTTAGTTAACGTTCTGATATTGCTCTTTAAATAAAAGCAACGCTTATTACGCGACAGCGAACATCACGTACAGACCCAGACCTACAGCGATCATCGGGATAGCATccac                                                                   >  2:1108360/1‑124 (MQ=255)                                                                          aGCACAATGCCTCTATTTAGTTAACGTTCTGATATTGCTCTTTAAATAAAAGCAACGCTTATTACGCGACAGCGAACATCACGTACAGACCCAGACCTACAGCGATCATCGGGATAGCATccac                                                                   <  1:1108360/124‑1 (MQ=255)                                                                             acaATGCCTCTATTTAGTTAACGTTCTGATATTGCTCTTTAAATAAAAGCAACGCTTATTACGCGACAGCGAACATCACGTACAGACCCAGACCTACAGCGATCATCGGGATAGCATCCACCAGACCCATAACGATaaa                                                 <  2:786015/139‑1 (MQ=255)                                                                                 tGCCTCTATTTAGTTAACGTTCTGATATTGCTCTTTAAATAAAAGCAACGCTTATTACGCGACAGCGAACATCACGTACAGACCCAGACCTACAGCGATCATCGGGATAGCATccac                                                                   >  2:966527/1‑117 (MQ=255)                                                                                 tGCCTCTATTTAGTTAACGTTCTGATATTGCTCTTTAAATAAAAGCAACGCTTATTACGCGACAGCGAACATCACGTACAGACCCAGACCTACAGCGATCATCGGGATAGCATccac                                                                   <  1:966527/117‑1 (MQ=255)                                                                                 tGCCTCTATTTAGTTAACGTTCTGATATTGCTCTTTAAATAAAAGCAACGCTTATTACGCGACAGCGAACATCACGTACAGACCCAGACCTACAGCGATCATCGGGATAGCATCCACCAGACCCATAACGATAAAGAAc                                             >  1:318209/1‑139 (MQ=255)                                                                                    ctctATTTAGTTAACGTTCTGATATTGCTCTTTAAATAAAAGCAACGCTTATTACGCGACAGCGAACATCACGTACAGACCCAGACCTACAGCGatcat                                                                                  <  1:1368322/99‑1 (MQ=255)                                                                                    ctctATTTAGTTAACGTTCTGATATTGCTCTTTAAATAAAAGCAACGCTTATTACGCGACAGCGAACATCACGTACAGACCCAGACCTACAGCGatcat                                                                                  >  2:1368322/1‑99 (MQ=255)                                                                                      ctATTTAGTTAACGTTCTGATATTGCTCTTTAAATAAAAGCAACGCTTATTACGCGACAGCGAACATCACGTACAGACCCAGACCTACAGCGATCATCGGGATAGCa                                                                        <  2:879706/107‑1 (MQ=255)                                                                                      ctATTTAGTTAACGTTCTGATATTGCTCTTTAAATAAAAGCAACGCTTATTACGCGACAGCGAACATCACGTACAGACCCAGACCTACAGCGATCATCGGGATAGCa                                                                        >  1:879706/1‑107 (MQ=255)                                                                                      ctATTTAGTTAACGTTCTGATATTGCTCTTTAAATAAAAGCAACGCTTATTACGCGACAGCGAACATCACGTACAGACCCAGACCTACAGCGATCATCGGGATAGCATCCACCAGACCCAt                                                          <  1:1406898/121‑1 (MQ=255)                                                                                      ctATTTAGTTAACGTTCTGATATTGCTCTTTAAATAAAAGCAACGCTTATTACGCGACAGCGAACATCACGTACAGACCCAGACCTACAGCGATCATCGGGATAGCATCCACCAGACCCAt                                                          >  2:1406898/1‑121 (MQ=255)                                                                                      ctATTTAGTTAACGTTCTGATATTGCTCTTTAAATAAAAGCAACGCTTATTACGCGACAGCGAACATCACGTACAGACCCAGACCTACAGCGATCATCGGGATAGCATCCACCAGACCCATAACGATAAAGAACTGAGt                                        >  1:520752/1‑139 (MQ=255)                                                                                       tATTTAGTTAACGTTCTGATATTGCTCTTTAAATAAAAGCAACGCTTATTACGCGACAGCGAACATCACGTACAGACCCAGACCTACAGCGATCATCGGGATAGCATCCACCAGACCCATAACGATAAAGAACTGAGTa                                       <  1:882405/139‑1 (MQ=255)                                                                                         tttAGTTAACGTTCTGATATTGCTCTTTAAATAAAAGCAACGCTTATTACGCGACAGCGAACATCACGTACAGACCCAGACCTACAGCGATCATCGGGATAGCATCCACCAGACCCATAACGATAAAGAACTGAGTACg                                     <  2:520752/139‑1 (MQ=255)                                                                                             gTTAACGTTCTGATATTGCTCTTTAAATAAAAGCAACGCTTATTAcgcg                                                                                                                           >  2:676652/1‑49 (MQ=255)                                                                                             gTTAACGTTCTGATATTGCTCTTTAAATAAAAGCAACGCTTATTAcgcg                                                                                                                           <  1:676652/49‑1 (MQ=255)                                                                                              ttAACGTTCTGATATTGCTCTTTAAATAAAAGCAACGCTTATTACGCGACAGCGAACATCACGTAc                                                                                                         <  2:674783/66‑1 (MQ=255)                                                                                              ttAACGTTCTGATATTGCTCTTTAAATAAAAGCAACGCTTATTACGCGACAGCGAACATCACGTAc                                                                                                         >  1:674783/1‑66 (MQ=255)                                                                                               tAACGTTCTGATATTGCTCTTTAAATAAAAGCAACGCTTATTACGCGACAGCGAACATCACGTACAGACCCAGACCTACAGCGATCATCGGGATAGCATCCACCAGACCCAt                                                          <  1:703816/112‑1 (MQ=255)                                                                                               tAACGTTCTGATATTGCTCTTTAAATAAAAGCAACGCTTATTACGCGACAGCGAACATCACGTACAGACCCAGACCTACAGCGATCATCGGGATAGCATCCACCAGACCCAt                                                          >  2:703816/1‑112 (MQ=255)                                                                                                 aCGTTCTGATATTGCTCTTTAAATAAAAGCAACGCTTATTACGCGACAGCGAACATCACGTAcagacc                                                                                                    <  1:1318573/68‑1 (MQ=255)                                                                                                 aCGTTCTGATATTGCTCTTTAAATAAAAGCAACGCTTATTACGCGACAGCGAACATCACGTAcagacc                                                                                                    >  2:1318573/1‑68 (MQ=255)                                                                                                 aCGTTCTGATATTGCTCTTTAAATAAAAGCAACGCTTATTACGCGACAGCGAACATCACGTACAGACCCAGACCTACAGCGATCATCGGGATAGCATCCACCAGACCCATAACGATAAAGAACTGAGTACGCAGCagag                             >  2:869612/1‑139 (MQ=255)                                                                                                   gTTCTGATATTGCTCTTTAAATAAAAGCAACGCTTATTACGCGACAGCGAACATCACGTACAGACCCAGACCTACAGCGATCATCGGGATAGCATCCACCAGACCCa                                                           >  2:335794/1‑107 (MQ=255)                                                                                                   gTTCTGATATTGCTCTTTAAATAAAAGCAACGCTTATTACGCGACAGCGAACATCACGTACAGACCCAGACCTACAGCGATCATCGGGATAGCATCCACCAGACCCa                                                           <  1:335794/107‑1 (MQ=255)                                                                                                       tGATATTGCTCTTTAAATAAAAGCAACGCTTATTACGCGACAGCGAACATCACGTACAGACCCAGACCTACAGCGATCATCGGGATAGCATCCACCAGACCCATAACGATAAAGAACTGAGTACGCAGCAGAGGAatca                       >  1:1183515/1‑139 (MQ=255)                                                                                                       tGATATTGCTCTTTAAATAAAAGCAACGCTTATTACGCGACAGCGAACATCACGTACAGACCCAGACCTACAGCGATCATCGGGATAGCATCCACCAGACCCATAACGATAAAGAACTGAGTACGCAGCAGAGGAatca                       >  2:1117420/1‑139 (MQ=255)                                                                                                        gATATTGCTCTTTAAATAAAAGCAACGCTTATTACGCGACAGCGAACATCACGTa                                                                                                          <  1:1116621/55‑1 (MQ=255)                                                                                                        gATATTGCTCTTTAAATAAAAGCAACGCTTATTACGCGACAGCGAACATCACGTa                                                                                                          >  2:1116621/1‑55 (MQ=255)                                                                                                        gATATTGCTCTTTAAATAAAAGCAACGCTTATTACGCGACAGCGAACATCACGTACAGACCCAGACCTACAGCGATCATCGGGATAGCATCCACCAGACCCATAACGATAAAGAACTGAGTACGCAGCAGAGGAatcag                      >  2:620372/1‑139 (MQ=255)                                                                                                               ctctTTAAATAAAAGCAACGCTTATTACGCGACAGCGAACATCACGTa                                                                                                          >  2:378678/1‑48 (MQ=255)                                                                                                               ctctTTAAATAAAAGCAACGCTTATTACGCGACAGCGAACATCACGTa                                                                                                          <  1:378678/48‑1 (MQ=255)                                                                                                               ctctTTAAATAAAAGCAACGCTTATTACGCGACAGCGAACATCACGTACAGACCCAGACCTACAGCGATCATCGGGATAGCATCCACCAGACCCATAACGATAAAGAACTGAGTACGCAGCAGAGGAATCAGATCAGGt               >  2:837137/1‑139 (MQ=255)                                                                                                               ctctTTAAATAAAAGCAACGCTTATTACGCGACAGCGAACATCACGTACAGACCCAGACCTACAGCGATCATCGGGATAGCATCCACCAGACCCATAACGATAAAGAACTGAGTACGCAGCAGAGGAATCAGATCAGGt               >  1:907068/1‑139 (MQ=255)                                                                                                                 ctTTAAATAAAAGCAACGCTTATTACGCGACAGCGa                                                                                                                    <  2:1189954/36‑1 (MQ=255)                                                                                                                 ctTTAAATAAAAGCAACGCTTATTACGCGACAGCGa                                                                                                                    >  1:1189954/1‑36 (MQ=255)                                                                                                                 ctTTAAATAAAAGCAACGCTTATTACGCGACAGCGAACATCACGTACAGACCCAGACCTACAGCGATCATCGGGATAGCATCCACCAGa                                                               <  2:1113465/89‑1 (MQ=255)                                                                                                                 ctTTAAATAAAAGCAACGCTTATTACGCGACAGCGAACATCACGTACAGACCCAGACCTACAGCGATCATCGGGATAGCATCCACCAGa                                                               >  1:1113465/1‑89 (MQ=255)                                                                                                                 ctTTAAATAAAAGCAACGCTTATTACGCGACAGCGAACATCACGTACAGACCCAGACCTACAGCGATCATCGGGATAGCATCCACCAGACCCATAACGATAAAGAACTGAGTACgcagca                                <  1:1006755/120‑1 (MQ=255)                                                                                                                 ctTTAAAAAAAAGCAACGCTTATTACGCGACAGCGAACATCACGTACAGACCCAGACCTACAGCGATCATCGGGATAGCATCCACCAGACCCATAACGATAAAGAACTGAGTACgcagca                                >  2:1006755/1‑120 (MQ=255)                                                                                                                   ttAAATAAAAGCAACGCTTATTACGCGACAGCGAACATc                                                                                                               >  1:852413/1‑39 (MQ=255)                                                                                                                   ttAAATAAAAGCAACGCTTATTACGCGACAGCGAACATCACGTACAGACCCAGACCTa                                                                                            >  1:1186140/1‑58 (MQ=255)                                                                                                                   ttAAATAAAAGCAACGCTTATTACGCGACAGCGAACATCACGTACAGACCCAGACCTa                                                                                            <  2:1186140/58‑1 (MQ=255)                                                                                                                   ttAAATAAAAGCAACGCTTAATACGCGACAGCGAACATc                                                                                                               <  2:852413/39‑1 (MQ=255)                                                                                                                    taaataaaAGCAACGCTTATTACGCGACAGCGAACATCACGTACAGACCCAGACCTACAGCGATCATCGGGATa                                                                           <  2:837955/74‑1 (MQ=255)                                                                                                                    taaataaaAGCAACGCTTATTACGCGACAGCGAACATCACGTACAGACCCAGACCTACAGCGATCATCGGGATa                                                                           >  1:837955/1‑74 (MQ=255)                                                                                                                    taaataaaAGCAACGCTTATTACGCGACAGCGAACATCACGTACAGACCCAGACCTACAGCGATCATCGGGATAGCATccac                                                                   >  1:66665/1‑82 (MQ=255)                                                                                                                    taaataaaAGCAACGCTTATTACGCGACAGCGAACATCACGTACAGACCCAGACCTACAGCGATCATCGGGATAGCATccac                                                                   <  2:66665/82‑1 (MQ=255)                                                                                                                    taaataaaAGCAACGCTTATTACGCGACAGCGAACATCACGTACAGACCCAGACCTACAGCGATCATCGGGATAGCATCCACCAGACCCATAACGATAAAGAACTGAGTACg                                     >  1:106846/1‑112 (MQ=255)                                                                                                                    taaataaaAGCAACGCTTATTACGCGACAGCGAACATCACGTACAGACCCAGACCTACAGCGATCATCGGGATAGCATCCACCAGACCCATAACGATAAAGAACTGAGTACg                                     <  2:106846/112‑1 (MQ=255)                                                                                                                      aataaaAGCAACGCTTATTACGCGACAGCGAACATCACGTACAGACCCAGACCTACAGCGATCATCGGGATAGCATCCACCAGACCCATAACGATAAAGAACTGAGTACGCAGCAGAGGAATCAGATCAGGTTGAcgcg        <  1:620372/139‑1 (MQ=255)                                                                                                                         aaaaGCAACGCTTATTACGCGACAGCGAACATCACGTACAGACCCAGACCTACAGCGATCATCGGGATAGCATCCACCAGACCCATAACGATAAAGAACTGAGTACGCAGCAGAGGAATCAGATCAGGTTGACGCGCTg     <  1:1117420/139‑1 (MQ=255)                                                                                                                         aaaaGCAACGCTTATTACGCGACAGCGAACATCACGTACAGACCCAGACCTACAGCGATCATCGGGATAGCATCCACCAGACCCATAACGATAAAGAACTGAGTACGCAGCAGAGGAATCAGATCAGGTTGACGCGCTg     >  1:461618/1‑139 (MQ=255)                                                                                                                          aaaGCAACGCTTATTACGCGACAGCGAATATCACGTACAGACCCAGACCTACAGCGATCATCGGGATATCATCCACCAGACCCATAACGATAAAGAACTGAGTACGCAGCAGAGGAATCAGATCAGGTTGACGAGCTgc    >  1:952482/1‑139 (MQ=255)                                                                                                                           aaGCAACGCTTATTACGCGACAGCGAACATCACGTACAGACCCAGACCTACAGCGATCATCGGGATAGCATCCACCAGACCCATAACGATAAAGAACTGAGTACGCAGCAGAGGAATCAGATCAGGTTGACGCGCTgcg   <  1:837137/139‑1 (MQ=255)                                                                                                                           aaGCAACGCTTATTACGCGACAGCGAACATCACGTACAGACCCAGACCTACAGCGATCATCGGGATAGCATCCACCAGACCCATAACGATAAAGAACTGAGTACGCAGCAGAGGAATCAGATCAGGTTGACGCGCTgcg   <  2:461618/139‑1 (MQ=255)                                                                                                                            aGCAACGCTTATTACGCGACAGCGAACATCACGTACAGACCCAGACCTACAGCGATCATCGGGATAGCATCCACCAGACCCATAACGATAAAGAACTGAGTACGCAGCAGAGGAATCAGATCAGGTTGACGCGCTgcgc  >  2:341115/1‑139 (MQ=255)                                                                                                                                aCGCTTATTACGCGACAGCGAACATCACGTACAGACCCAGACCTACAGCGATCATCGGGATAGCATccac                                                                   <  2:1517663/70‑1 (MQ=255)                                                                                                                                aCGCTTATTACGCGACAGCGAACATCACGTACAGACCCAGACCTACAGCGATCATCGGGATAGCATccac                                                                   >  1:1517663/1‑70 (MQ=255)                                                                                                                                 cGCTTATTACGCGACAGCGAACATCACGTACAGACCCAGACCTACAGCGATCATCGGGATAGCATCCACCAGACCCATAACGATAAAGAACTGAGTACGCAGCAGAGGAatcagatca                  <  1:969355/118‑1 (MQ=255)                                                                                                                                 cGCTTATTACGCGACAGCGAACATCACGTACAGACCCAGACCTACAGCGATCATCGGGATAGCATCCACCAGACCCATAACGATAAAGAACTGAGTACGCAGCAGAGGAatcagatca                  >  2:969355/1‑118 (MQ=255)                                                                                                                                       |                                                                                                                                CGTACTTCATGCAGAACAGAACGAACAGGACAAACGCGATGGCCTGGCCGAGGATTGTTGCGTTAAGATTCACAGCACAATGCCTCTATTTAGTTAACGTTCTGATATTGCTCTTTAAATAAAAGCAACGCTTACTACGCGACAGCGAACATCACGTACAGACCCAGACCTACAGCGATCATCGGGATAGCATCCACCAGACCCATAACGATAAAGAACTGAGTACGCAGCAGAGGAATCAGATCAGGTTGACGCGCTGCGC  >  NC_000913/3920816‑3921077

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑