Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	40,525	0	C	T	40.7%	60.9 / 21.0	54	L469L (CTG→CTA)	caiT	putative transporter
Reads supporting (aligned to +/- strand):  ref base C (8/24);  new base T (22/0);  total (30/24)
Fisher's exact test for biased strand distribution p-value = 1.35e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CCATCTTTCAACCTCTTGATATTTTGGGGGTTAATTAATCTTTCCAGTTCTGTTTCGCGTCTTTAATAAAGGAGAGCGTCACCATAATGTTGACGAAGAACAGCGGGCATCCTCCGGCGATAATGGCGGTTTGAATCGGTTTCAGGCCGCCGAGCGCCAGCAGAACAATACCGATAATGCCAACCAG‑AATTGACCAACCGATACGCACCAGCAGAGGTGGTTCTTCACCATCGCGTACTTCGCGGCAAGTGGACATCGCCAGGGTATAAGAGCAGGCGTTAACCAGCGTAACG  >  NC_000913/40383‑40675                                                                                                                                               |                                                                                                                                                        ccATCTTTCAACCTCTTGATATGTTGGGGGTTAATTAATCTTTCCAGTTCGGTTTCGCGTCTTTAATAAAGGAGAGCGTCTCCATAATGTTGACGAAGAACAGCGGGCATCCTCCGGCGATAATGGCGGTTTGAATCGGTTTCAGgcctc                                                                                                                                                  <  1:873811/150‑3 (MQ=255)   aTCTTTCAACCTCTTGATATTTTGGGGGTTAATTAATCTTTCCAGTTCTGTTTCGCGTCTTTAATAAAGGAGAGCGTCACCATAATGTTGACGAAGAACAGCGGGCATCCTCCGGCGATAATGGCGGTTTGAATCGGGTTCAGgccgcc                                                                                                                                                 >  2:744152/1‑149 (MQ=255)    tCTTTCAACCTCTTGATATTTTGGGGGTTAATTAATCTTTCCAGTTCTGTTTCGCGTCTTTAATAAAGGAGAGCGTCACCATAATGTTGACGAAGAACAGCGGGCATCCTCCGGCGATAATGGCGGTTTGAATCGGTTTCAGggcggc                                                                                                                                                 >  1:667766/1‑146 (MQ=255)    tCTTTCAACCTCTTGATATTTTGGGGGTTAATTAATCTTTCCAGTTCTGTTTCGCGTCTTTAATAAAGGAGAGCGTCACCATAATGTTGACGAAGAACAGCGGGCATCCTCCGGCGATAATGGCGGTTTGAATCGGGTTTAGgccgcc                                                                                                                                                 >  2:892048/1‑148 (MQ=255)      tttCAACCTCTTGATATTTTGGGGGTTAATTAATCTTTCCAGTTCTGTTTCGCGTCTTTAATAAAGGAGAGCGTCACCATAATGTTGACGAAGAACAGCGGGCATCCTCCGGCGATAATGGCGGTTTGAATTGGTTTTAAgccgcc                                                                                                                                                 >  2:1094029/1‑146 (MQ=255)       ttCAACCTCTTGATATTTTGGGGGTTAATTAATCTTTCCAGTTCTGTTTCGCGTCTTTAATAAAGGAGAGCGTCACCATAATGTTGACGAAGAACAGCGGGCATCCTCCGGCGATAATGGCGGTTTTAATCGGGTTCAGGCCGCCCAgc                                                                                                                                             >  2:384644/1‑149 (MQ=255)       ttCAACCTCTTGATATTTTGGGGGTTAATTAATCTTTCCAGTTCTGTTTCGCGTCTTTAATAAAGGAGAGCGTCACCATAATGTTGACGAAGAACAGCGGGCATCCTCCGGCGATAATGGCGGTTTGAATCGGTTTTAAGGCGCcgcgcg                                                                                                                                            >  1:434486/1‑150 (MQ=255)         cAACCTCTTGATATTTTGGGGGTTAATTAATCTTTCCAGTTCTGTTTCGCGTCTTTAATAAAGGAGAGCGTCACCATAATGTTGACGAAGAACAGCGGGCATCCTCCGGCGATAATGGCGGTTTTAATCGGTTTTAGGCCGCCGCGCGcc                                                                                                                                          >  2:342486/1‑150 (MQ=255)         cAACCTCTTGATATTTTGGGGGTTAATTAATCTTTCCAGTTCTGTTTCGCATCTTTAATAAAGGAGAGCGTCACCATAATGTTGACGAAGAACAGCGGGCATCCTCCGGCGATAATGGCGGTTTGAATCGGTTTCAGGCCGCCGAGCGCca                                                                                                                                         <  1:537616/151‑1 (MQ=255)          aaCCTCTTGATATTTTGGGGGTTAATTAATCTTTCCAGTTCTGTTTCGCGTCTTTAATAAAGGAGAGCGTCACCATAATGTTGACGAAGAACAGCGGGCATCCTCCGGCGATAATGGCGGTTTGAATCGGTTTCAGGCCGCCGAGCGCcag                                                                                                                                        <  1:304029/151‑1 (MQ=255)            ccTCTTGATATTTTGGGGGTTAATTAATCTTTCCAGTTCTGTTTCGCGTCTTTAATAAAGGAGAGCGTCACCATAATGTTGACGAAGAACAGCGGGCATCCTCCGGCGATAATGGCGGCTTTAATCGGTTTTAGGCCGCCCCGCGCccgcc                                                                                                                                      >  1:370783/1‑150 (MQ=255)              tctTGATATTTTGGGGGTTAATTAATCTTTCCAGTTCTGTTTCGCGTCTTTAATAAAGGAGAGCGTCACCATAATGTTGACGAAGAACAGCGGGCATCCTCCGGCGATAATGGCGGTTTTAAACGGGTTTAGGCCGCCGGGCGCccgcc                                                                                                                                      >  1:85320/1‑148 (MQ=255)                   atatTTTGGGGGTTAATTAATCTTTCCAGTTCTGTTTCGCGTCTTTAATAAAGGAGAGCGTCACCATAATGTTGACGAAGAACAGCGGGCATCCTCCGGCGATAATGGCGGTTTTAATCGGTTTTAGGCCGCCGAGCGCCCGCAGAaaaa                                                                                                                                >  2:1055696/1‑150 (MQ=255)                     atTTTGGGGGTTAATTAATCTTTCCAGTTCTGTTTCGCGTCTTTAATAAAGGAGAGCGTCACCATAATGTTGACGAAGAACAGCGGGCATCCTCCGGCGATAATGGCGGTTTTAATCGGGTTTAGGCCGCCCAGCGCCACCAGAACAATa                                                                                                                              >  2:980469/1‑150 (MQ=255)                      ttttGGGGGTTAATTAATCTTTCCAGTTCTGTTTCGCGTCTTTAATAAAGGAGAGCGTCACCATAATGTTGACGAAGAACAGCGGGCATCCTCCGGCGATAATGGCAGTTTGAATCGGGTTCAGGCCGCCGAGCGCCAGCAGAACAATAcc                                                                                                                            >  1:976352/1‑151 (MQ=255)                         tGGGGGTTAATTAATCTTTCCAGTTCTGTTTCGCGTCTTTAATAAAGGAGAGCGTCACCATAATGTTGACGAAGAACAGCGGGCATCCTCCGGCGATAATGGCGGTTTGAATCGGTTTCAGGCCGCCGAGCGCCAGCAGAACAATACCGa                                                                                                                          <  1:624407/150‑1 (MQ=255)                         tGGGGGTTAATTAATCTTTCCAGTTCTGTTTCGCGTCTTTAATAAAGGAGAGCGTCACCATAATGTTGACGAAGAACAGCGGGCATCCTCCGGCGATAATGGCGGTTTGAATCGGGTTTTGGGCGCCGAGCGCCCGCCGaaacaaaacga                                                                                                                          >  1:765349/1‑141 (MQ=255)                                          ttCCAGTTCTGTTTCGCGTCTTTAATAAAGGAGAGCGTCACCATAATGTTGACGAAGAACAGCGGGCATCCTCCGGCGATAATGGCGGTTTTTAACGGCTTTATGCCGCCCAGCGCCCACCCAACAAAACCCAGAATGTCAACCAG‑aaat                                                                                                        >  2:1096141/1‑148 (MQ=255)                                          ttCCAGTTCTGTTTCGCGTCTTTAATAAAGGAGAGCGTCACCATAATGTTGACGAAGAACAGCGGGCATCCTCCGGCGATAATGGCGGTTTGAATCGGTTTCAGGCCGCCGAGCGCCAGCAGAACAATACCGATAATGCCAACCAG‑AAtt                                                                                                        <  1:836657/150‑1 (MQ=255)                                          ttCCAGTTCTGTTTCGCGTCTTTAATAAAGGAGAGCGTCACCATAATGTTGACGAAGAACAGCGGGCATCCTCCGGCGATAATGGCGGCTTTAAACGGTTTTACGCCCCCGAGCGCCCGCCGAAAAAAACCGAAAACTCCAACCaa‑aaat                                                                                                        >  1:1076438/1‑148 (MQ=255)                                           tCCAGTTCTGTTTCGCGTCTTTAATAAAGGAGAGCGTCACCATAATGTTGACGAAGAACAGCGGGCATCCTCCGGCGATAATGGCGGTTTTTATTGGGTTTAGGGCGCCGCGCGCCCGCAGAAAAAAAACGATAAAGGCCACCAG‑aaat                                                                                                        >  2:135955/1‑147 (MQ=255)                                              aGTTCTGTTTCGCGTCTTTAATAAAGGAGAGCGTCACCATAATGTTGACGAAGAACAGCGGGCATCCTCCGGCGATAATGGCGGTTTTAATCGGTTTCAGGCCGCCCGGCGCCAGCAGAACAAAAACGATAAAGCCAACCAG‑aaattac                                                                                                     >  1:996063/1‑144 (MQ=255)                                              aGTTCTGTTTCGCGTCTTTAATAAAGGAGAGCGTCACCATAATGTTGACGAAGAACAGCGGGCATCCTCCGGCGATAATGGCGGTTTTAATAGGTTTCAGGCCGCCGGGCGCCAGCAGAAAAAAAACGGTAATGCCAACCAG‑AACTgt                                                                                                      >  1:223771/1‑147 (MQ=255)                                              aGTTCTGTTTCGCGTCTTTAATAAAGGAGAGCGTCACCATAATGTTGACGAAGAACAGCGGGCATCCTCCGGCGATAATGGCGGTTTGAATCGGTTTCAGGCCGCCGAGCGCCAGCAGAACAATACCGATAATGCCAACCAG‑AATTGACCa                                                                                                   <  1:465493/151‑1 (MQ=255)                                                ttCTGTTTCGCGTCTTTAATAAAGGAGAGCGTCACCATAATGTTGACGAAGAACAGCGGGCATCCTCCGGCGATAATGGCGGTTTGAATCGGTTTCAGGCCGCCGAGCGCCAGCAGAACAATACCGATAATGCCAACCAG‑AATTGACCaa                                                                                                  <  1:757915/150‑1 (MQ=255)                                                    gTTTCGCGTCTTTAATAAAGGAGAGCGTCACCATAATATTGACGAAGAACAGCGGGCATCCTCCGGCGATAATGGCGGTTTGAATCGGTTTCAGGCCGCCGAGCGCCAGCAGAACAATACCGATAATGCCAACCAG‑AATTGACCAACCg                                                                                               <  2:122972/149‑1 (MQ=255)                                                      ttCGCGTCTTTAATAAAGGAGAGCGTCACCATAATGTTGACGAAGAACAGCGGGCATCCTCCGGCGATAATGGCGGTTTGAATCGGGTTTCGGCCGCCGAGCGCCCGCAAAAAAAAAACGATAAAGCCAAACAA‑AAATGAACAAACCATa                                                                                            >  2:6245/1‑150 (MQ=255)                                                      ttCGCGTCTTTAATAAAGGAGAGCGTCACCATAATGTTGACGAAGAACAGCGGGCATCCTCCGGCGATAATGGCGGTTTGAATAGGGTTTTGGCCCCCCCGCGCCAGCAGAAAAAAACCGATAAAGCCAACCAA‑AAATGACCAAACGGTa                                                                                            >  1:1098452/1‑150 (MQ=255)                                                        cgcgTCTTTAATAAAGGAGAGCGTCACCATAATGTTGACGAAGAACAGCGGGCATTCTCCGGCGATAATGGCGGTTTGAATCGGTTTCAGGCCGCCGAGCGCCAGCAGAACAATACCGATAATGCCAACCAG‑AATTGACCAACCGATACg                                                                                          <  1:242079/150‑1 (MQ=255)                                                        cgcgTCTTTAATAAAGGAGAGCGTCACCATAATGTTGACGAAGAACAGCGGGCATCCTCCGGCGATAATGGCGGGTTGAATATGGTTTACGCCCCCGCGCGGCCCCCGAAGAAAACAGATAATTCCCAACAA‑AAATAACCCAGCGAt                                                                                             >  2:892520/1‑147 (MQ=255)                                                               ttAATAAAGGAGAGCGTCACCATAATGTTGACGAAGAACAGCGGGCATCCTCCGGCGATAATGGCGGTTTTAATCGGGTTTCGGCCGCCGGGGGCCAGGAGAAAAAAAACGGAAATGGCAAACAG‑AAATGACCAACCGAAAAGCACcagc                                                                                   >  1:200062/1‑150 (MQ=255)                                                               ttAATAAAGGAGAGCGTCACCATAATGTTGACGAAGAACAGCGGGCATCCTCCGGCGATAATGGCGGTTTGAATCGGTTTCAGGCCGCCGAGCGCCAGCAGAACAATACCGATAATGCCAACCAG‑AATTGACCAACCGATACGCACca                                                                                     <  2:1005969/148‑1 (MQ=255)                                                                 aataaAGGAGAGCGTCACCATAATGTTGACGAAGAACAGCGGGCATCCTCCGGCGATAATGGCGGTTTGAATCGGTTTCAGGCCGCCGAGCGCCAGCAGAACAATACCGATAATGCCAACCAG‑AATTGACCAACCGATACGCACcagcag                                                                                 <  2:867960/150‑1 (MQ=255)                                                                 aataaAGGAGAGCGTCACCATAATGTTGACGAAGAACAGCGGGCATCCTCCGGCGATAATGGCGGTTTGAATCGGTTTCAGGCCGCCGAGCGCCAGCAGAACAATACCGATAATGCCAACCAG‑AATTGACCAACCGATACGCACcagcag                                                                                 <  2:524982/150‑1 (MQ=255)                                                                 aataaAGGAGAGCGTCACCATAATGTTGACGAAGAACAGCGGGCATCCTCCGGCGATAATGGCGGATTGAATCGGGTTTAGGGCGCCCCGGGCCAGGAGAAAAAAACCCACAATGCCCACCAGAAATTGA‑CAACCGCTaaccccc                                                                                      >  1:263084/1‑139 (MQ=255)                                                                      aGGAGAGCGTCACCATAATGTTGACGAAGAACAGCGGGCATCCTCCGGCGATAATGGCGGTTTGAATCGGGTTCAGGCCGCCGAGCGCCAGCAGAACAAAACCGATAATGCCAACCAG‑AAATGACCAAACGATACGCACCAGCAGAggggg                                                                           >  2:758033/1‑151 (MQ=255)                                                                                   cATAATGTTGACGAAGAACAGCGGGCATCCTCCGGCGATAATGGCGGTTTGAATCGGGTTTAGGCCGCCCAGCGCCCGCCGAAAAATAACGATAATGCCAACCCA‑AAATGACCAACCCAAACGCACCCCCAAAGGGGGGTTTTTACCaac                                                               >  2:1078639/1‑148 (MQ=255)                                                                                       aTGTTGACGAAGAACAGCGGGCATCCTCCGGCGATAATGGCGGTTTGAATCGGTTTCAGGCCGCCGAGCGCCAGCAGAACAATACCGATAATGCCAACCAG‑AATTGACCAACCGATACGCACCAGCAGAGGTGGTTCTTCACCATCGCGTa                                                          <  1:636247/151‑1 (MQ=255)                                                                                         gTTGACGAAGAACAGCGGGCATCCTCCGGCGATAATGGCGGTTTGAATCGGGTTTCGGCCGCCCGCCGCCCGCCGAACAAAACCGATAATGGCAACCAG‑AAATCACCCCCCGCTACCCCCCCCCACAGGGGGGTCTTTAc                                                                   >  1:568885/1‑140 (MQ=255)                                                                                                      aGCGGGCATCCTCCGGCGATAATGGCGGTTTTAATTGGGTTTAAGCCGCCGCGCGCCCGCAGAACAAAAACGATAATGCCCAACAA‑AATTTACCAAACCATACGCCCCCGCAGAGGGGGGTTTTTACCAACCCGGACTTTCCGGCAAgggg                                           >  2:482472/1‑151 (MQ=255)                                                                                                      aGCGGGCATCCTCCGGCGATAATGGCGGTTTGAATCGGTTTCAGGCCGCCGAGCGCCAGCAGAACAATACCGATAATGCCAACCAG‑AATTGACCAACCGATACGCACCAGCAGAGGTGGTTCTTCACCATCGCGTACTTCGCGGCAAGTgg                                           <  1:975237/151‑1 (MQ=255)                                                                                                        cGGGCATCCTCCGGCGATAATGGCGGTTTTAATCGGTTTTAGGCCGCCCAGCGCCAGCAGAAAAATAACGATAAATACAACCAG‑AATTGACCAACCCAAACGCACCCGCAGAGGGGGTTCTTTCCCCTCCCGGACTTCGCGGCCAgggg                                           >  2:385856/1‑149 (MQ=255)                                                                                                           gCATCCTCCGGCGATAATGGCGGTTTGAATCGGTTTCAGGCCGCCGAGCGCCAGCAGAACAATACCGATAATGCCAACCAG‑AATTGACCAACCGATACGCACCAGCAGAGGTGGTTCTTCACCATCGCGTACTTCGCGGCAAGTGGACATc                                      <  2:808958/151‑1 (MQ=255)                                                                                                            cATCCTCCGGCGATAATGGCGGTTTGAATCGGTTTTATGCCCCCCCGCGCCCGCAGAAAAAAACCGATAAAATCAAACAG‑AAATGAACAACCGATACGCACCCGCAGAGGGGGGTCTTCTCCATCGCGCACTTCGCGGCAAGTgggaatc                                      >  1:18573/1‑145 (MQ=255)                                                                                                               cctccGGCGATAATGGCGGTTTGAATCGGTTTCAGGCCGCCGAGCGCCAGCAGAACAATACCGATAATGCCAACCAG‑AATTGACCAACCGATACGCACCAGCAGAGGTGGTTCTTCACCATCGCGTACTTCGCGGCAAGTGGACATCGCCa                                  <  2:85340/151‑1 (MQ=255)                                                                                                                  ccGGCGATAATGGCGGTTTGAATCGGTTTCAGGCCGCCGAGCGCCAGCAGAACAATACCGATAATGCCAACCAG‑AATTGACCAACCGATACGCACCAGCAGAGGTGGTTCTTCACCATCGCGTACTTCGCGGCAAGTGGACATCGCCAgg                                <  2:31903/150‑1 (MQ=255)                                                                                                                       gATAATGGCGGTTTGAATCGGTTTCAGGCCGCCGAGCGCCTGCAGAACAATACCGATAATGCCAACCAG‑AATTGACCAACCGATACGCACCAGCAGAGGTGGTTCTTCACCATCGCGTACTTCGCGGCAAGTGGACATCGCCAGGGTATaa                          <  2:475321/151‑1 (MQ=255)                                                                                                                        aTAATGGCGGTTTGAATCGGTTTCAGGCCGCCGAGCGCCAGCAGAACAATACCGATAATGCCAACCAG‑AATTGACCAACCGATACGCACCAGCAGAGGTGGTTCTTCACCATCGCGTACTTCGCGGCAAGTGGACATCGCCAGGGTATAag                         <  2:401923/151‑1 (MQ=255)                                                                                                                          aaTGGCGGTTTGAATCGGTTTCAGGCCGCCGAGCGCCAGCAGAACAATACCGATAATGCCAACCAG‑AATTGACCAACCGATACGCACCAGCAGAGGTGGTTCTTCACCATCGCGTACTTCGCGGCAAGTGGACATCGCCAGGGTATAaga                        <  2:597620/150‑1 (MQ=255)                                                                                                                             ggCGGTTTGAATCGGTTTCAGGCCGCCGAGCGCCAGCAGAACAATACCGATAATGCCAACCAG‑AATTGACCAACCGATACGCACCAGCAGAGGTGGTTCTTCACCATCGCGTACTTCGCGGCAAGTGGACATCGCCAGGGTATAAGAGCAg                    <  1:482751/151‑1 (MQ=255)                                                                                                                             ggCGGTTTGAATCGGTTTCAGGCCGCCGAGCGCCAGCAGAACAATACCGATAATGCCAACCAG‑AATTGACCAACCGATACGCACCAGCAGAGGTGGTTCTTCACCATCGCGTACTTCGCGGCAAGTGGACATCGCCAGGGTATAAGAGCAg                    <  1:733554/151‑1 (MQ=255)                                                                                                                                      aaTCGGTTTCAGGCCGCCGAGCGCCAGCAGAACAATACCGATAATGCCAACCAG‑AATTGACCAACCGATACGCACCAGCAGAGGTGGTTCTTCACCATCGCGTACTTCGCGGCAAGTGGACATCGCCAGGGTATAAGAGCAGGCGTTAAcc           >  2:767465/1‑151 (MQ=255)                                                                                                                                         cGGTTTCAGGCCGCCGAGCGCCAGCAGAACAATACCGATAATGCCAACCAG‑AATTGACCAACCGATACGCACCAGCAGAGGTGGTTCTTCACCATCGCGTACTTCGCGGCAAGTGGACATCGCCAGGGTATAAGAGCAGGCGTTAACCAGc        <  1:556766/151‑1 (MQ=255)                                                                                                                                          ggTTTCAGGCCGCCGAGCGCCAGCAGAACAATACCGATAATGCCAACCAG‑AATTGACCAACCGATACGCACCAGCAGAGGTGGTTCTTCACCATCGCGTACTTCGCGGCAAGTGGACATCGCCAGGGTATAAGAGCAGGCGTTAACCAGCg       <  1:214819/151‑1 (MQ=255)                                                                                                                                               cAGGCCGCCGAGCGCCAGCAGAACAATACCGATAATGCCAACCAG‑AATTGACCAACCGATACGCACCAGCAGAGGTGGTTCTTCACCATCGCGTACTTCGCGGCAAGTGGACATCGCCAGGGTATAAGAGCAGGCGTTAACCAGCGTAACg  <  1:391039/151‑1 (MQ=255)                                                                                                                                               |                                                                                                                                                        CCATCTTTCAACCTCTTGATATTTTGGGGGTTAATTAATCTTTCCAGTTCTGTTTCGCGTCTTTAATAAAGGAGAGCGTCACCATAATGTTGACGAAGAACAGCGGGCATCCTCCGGCGATAATGGCGGTTTGAATCGGTTTCAGGCCGCCGAGCGCCAGCAGAACAATACCGATAATGCCAACCAG‑AATTGACCAACCGATACGCACCAGCAGAGGTGGTTCTTCACCATCGCGTACTTCGCGGCAAGTGGACATCGCCAGGGTATAAGAGCAGGCGTTAACCAGCGTAACG  >  NC_000913/40383‑40675

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑