Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913_3_hsa_tpiA	2,407,399	C→A	intergenic (‑758/‑162)	lrhA ← / → alaA	transcriptional repressor of flagellar, motility and chemotaxis genes/glutamate‑pyruvate aminotransferase; glutamic‑pyruvic transaminase (GPT); alanine transaminase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913_3_hsa_tpiA	2,407,399	0	C	A	100.0%	166.0 / NA	50	intergenic (‑758/‑162)	lrhA/alaA	transcriptional repressor of flagellar, motility and chemotaxis genes/glutamate‑pyruvate aminotransferase; glutamic‑pyruvic transaminase (GPT); alanine transaminase
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base A (27/23);  total (27/23)

TGAGGAAATATCATCATCGCGTTTCATTAGTGAATTCTTAAATGAGGCATTTTCACACAATTATCTTACAGATAAAAAAACCAGACTTACAATTAAGAATCAGAACAATTCACTATATAACATTGCATGTAAAGCATATACACCTCATTATTTTGTCATTATTAAGTTATTAACAGCACAATCGAGCCTTCCCCTCTGGCAAAATCTTATTCTGCAGACCTTCAAAACACCGTCCTGGGGGAGTACATTGTTCTAAGCTGACTTCCACGGCAGGGAGTGGCGATAACAGC  >  NC_000913_3_hsa_tpiA/2407254‑2407543                                                                                                                                                  |                                                                                                                                                 tGAGGAAATATCATCATCGCGTTTCATTAGTGAATTCTTAAATGAGGCATTTTCACACAATTATCTTACAGATAAAAAAACCAGACTTACAATTAAGAATCAGAACAATTCACTATATAACATTGCATGTAAAGCATATACACCTAatt                                                                                                                                               >  1:159331/1‑149 (MQ=255)  gAGGAAATATCATCATCGCGTTTCATTAGTGAATTCTTAAATGAGGCATTTTCACACAATTATCTTACAGATAAAAAAACCAGACTTACAATTAAGAATCAGAACAATTCACTATATAACATTGCATGTAAAGCATATACACCTAatta                                                                                                                                              >  1:132247/1‑149 (MQ=255)    ggAAATATCATCATCGCGTTTCACTAGTGAATTCTTAAATGAGGCATTTTCACACAATTATCTTACAGATAAAAAAACCAGACTTACAATTAAGAATCAGAACAATTCACTATATAACATTGCATGTAAAGCATATACACCTAattatt                                                                                                                                            >  2:431448/1‑149 (MQ=255)      aaaTATCATCATCGCGTTTCATTAGTGAATTCTTAAATGAGGCATTTTCACACAATTATCTTACAGATAAAAAAACCAGACTTACAATTAAGAATCAGAACAATTCACTATATAACATTGCATGTAAAGCATATACACCTAATTAtttt                                                                                                                                          <  1:448505/149‑1 (MQ=255)           tcatcatcGCGTTTCATTAGTGCATTCTTAAATGAGGCATTTTCACACAATTATCTTACAGATAAAAAAACCAGACTTACAATTAAGAATCAGAACAATTCACTATATAACATTGCATGTAAAGCATATACACCTAATTATTTTGTCat                                                                                                                                     >  2:389135/1‑149 (MQ=255)             atcatcGCGTTTCATTAGTGAATTCTTAAATGAGGCATTTTCACACAATTATCTTACAGATAAAAAAACCAGACTTACAATTAAGAATCAGAACAATTCACTATATAACATTGCATGTAAAGCATATACACCTAATTATTTTGTCatta                                                                                                                                   >  2:190660/1‑149 (MQ=255)                atcGCGTTTCATTAGTGAATTCTTAAATGAGGCATTTTCACACAATTATCTTACAGATAAAAAAACCAGACTTACAATTAAGAATCAGAACAATTCACTATATAACATTGCATGTAAAGCATATACACCTAATTATTTTGTCAttatta                                                                                                                                <  1:619730/149‑1 (MQ=255)                 tcGCGTTTCATTAGTTAATTCTTAAATGAGGCATTTTCACGCAATTATCTTACAGATAAAAAAACCAGACTTACAATTAAGAATCAGAACAATTCACTATATAACATTGCATGTAAAGCATATACACCTAATTATTTTGTCATTATTaa                                                                                                                               <  1:1041037/149‑1 (MQ=255)                  tgcttttCATTAGTGAATTCTTAAATGAGGCATTTTCAAACAATTATCTTACAGATAAAAAAACCAGACTTACAATTAAGAATCAGAATAATTCACTACATAACATTGCATGTAAAGCATATACACCTAATTATTTTGTCATTATTAAg                                                                                                                              <  2:637917/145‑1 (MQ=255)                   gcgTTTCATTAGTGAATTCTTAAATGAGGCATTTTCACACAATTATCTTACAGATAAAAAAACCAGACTTACAATTAAGAATCAGAACAATTCACTATATAACATTGCATGTAAAGCATATACACCTAATTATTTTGTCATTATTaatt                                                                                                                             >  1:308779/1‑147 (MQ=255)                               tGAATTCTTAAATGAGGCATTTTCACACAATTATCTTACAGATAAAAAAACCAGACTTACAATTAAGAATCAGAACAATTCACTATATAACATTGCATGTAAAGCATATACACCTAATTATTTTGTCATTATTAAGTTATTAACAGcac                                                                                                                 >  1:968547/1‑149 (MQ=255)                                  aTTCTTAAATGAGGCATTTTCAAACAATTATCTTACAGATAAAAAAACCAGACTTACAATTAAGAATCAGAACAATTCACTATATAACATTGCATGTAAAGCATATACACCTAATTATTTTGTCATTATTAAGTTATTAACAGCACAAt                                                                                                              <  1:914681/149‑1 (MQ=255)                                      ttAAATGAGTCATTTTCACACAATTATCTGACAGATAAAAAAACCAGACTTACAATTAAGAATCAGAACAATTCACTATATAACATTGCATGTAAAGCATATACACCTAATTATTTTGTCATTATTAAGTTATTAACAGCACAATCGAg                                                                                                          <  1:310900/149‑1 (MQ=255)                                      ttAAATGAGGCATTTTCACACAATTATCTTACAGATAAAAAAACCAGACTTACAATTAAGAATCAGAACAATTCACTATATAACATTGCATGTAAAGCATATACACCTAATTATTTTGTCATTATTAAGTTATTAACAGCACAATCGAg                                                                                                          >  1:984811/1‑149 (MQ=255)                                      ttAAATGAGGCATTTTCACACAATTATCTTACAGATAAAAAAACCAGACTTACAATTAAGAATCAGAACAATTCACTATATAACATTGCATGTAAAGCATATACACCTAATTATTTTGTCATTATTAAGTTATTAACAGCACAATCGAg                                                                                                          >  2:112203/1‑149 (MQ=255)                                       tAAATGAGGCATTTTCACACAATTATCTTACAGATAAAAAAACCAGACTTACAATTAAGAATCAGAACACTTCACTATATAACATTGTATGTCAAGCATATACACCTAATTATTTTGTCATTATTAAGTTATTAACAGCACAATCGAGc                                                                                                         >  1:863673/1‑149 (MQ=255)                                       tAAATGAGGCATTTTCACACAATTATCTTACAGATAAAAAAACCAGACTTACAATTAAGAATCAGAACAATTCACTATATAACATTGCATGTAAAGCATATACACCTAATTATTTTGTCATTATTAAGTTATTAACAGCACAATCGAGc                                                                                                         <  2:159331/149‑1 (MQ=255)                                                           aaTTATCTTACAGATAAAAAAACCAGACTTACAATTAAGAATCAGAACAATTCACTATATAACATTGCATGTAAAGCATATACACCTAATTATTTTGTCATTATTAAGTTATTAACAGCACAATCGAGCCTTCCCCTCTGGCAAAATCt                                                                                     <  1:389135/149‑1 (MQ=255)                                                           aaTTATCTTACAGATAAAAAAACCAGACTTACAATTAAGAATCAGAACAATTCACTATATAACATTGCATGTAAAGCATATACACCTAATTATTTTGTCATTATTAAGTTATTAACAGCACAATCGAGCCTTCCCCTCTGGCAAAATCt                                                                                     >  2:447578/1‑149 (MQ=255)                                                             ttATCTTACAGATAAAAAAACCAGACTTACAATTAAGAATCAGAACAATTCACTATATAACATTGCATGTAAAGCATATACACCTAATTATTTTGTCATTATTAAGTTATTAACAGCACAATCGAGCCTTCCCCTCTGGCAAAATCTTa                                                                                   <  1:190660/149‑1 (MQ=255)                                                             ttATCGTACAGATAAAAAAACCAGACGTACAGTTAAGAATCAGAAAAATTCACTATATAACATTGCATGTAAAGCATATACACCTAATTATTTTGTCATTATTAAGTTATTAACAGCACAATCGATCCTTCCCCTCTGGCAAAATCTTa                                                                                   <  2:408715/149‑1 (MQ=255)                                                                     cAGATAAAAAAACCAGACTTACAATTAAGAATCAGAACAATTCACTATATAACATTGCATGTAAAGCATATACACCTAATTATTTTGTCATTATTAAGTTATTAACAGCACAATCGAGCCTTCCCCTCTGGCAAAATCTTATTCTGCAg                                                                           <  2:968547/149‑1 (MQ=255)                                                                       gATAAAAAAACCAGACTTACAATTAAGAATCAGAACAATCAACTATAGAACATTGCATGTAAAGCATATACACCTAATTATTTTGTCATTATTAAGTTATTAACAGCACAATCGAGCCTTCCCCTCTGGCAAAATCTTATTCTGCAGAc                                                                         <  1:781105/149‑1 (MQ=255)                                                                          aaaaaaaCCAGACTTACAATTAAGAATCAGAACAATTCACTATATAACATTGCATGTAAAGCATATACACCTAATTATTTTGTCATTATTAAGTTATTAACAGCACAATCGAGCCTTCCCCTCTGGCAAAATCTTATTCTGCAGACCtt                                                                      >  1:7225/1‑149 (MQ=255)                                                                            aaaaaCCAGACTTACAATTAAGAATCAGAACAATTCACTATATAACATTGCATGTAAAGCATATACAACTAATTATTTTGTCATTATTAAGTTATTAAAAGCAGAATAGAGCATTCCCCTCTGGCAAAATCTTATTCTGCAGACTTTCa                                                                    >  2:892620/1‑149 (MQ=255)                                                                             aaaaCCAGCCTTACAATTAAGAATCAGAACAATTCACTATATAACATTGCATGTAAAGCATATACACCTAATTATTTTGTCATTATTAAGTTATTAACAGCACAATCGAGCCTTCCCCTCTGGCAAAATCTTATTCTGCAGACCTTCaa                                                                   <  1:537218/149‑1 (MQ=255)                                                                                    gACTTACAATTAAGAATCAGAACAATTCACTATATAACATTGCATGTAAAGCATATACACCTAATTATTTTGTCATTATTAAGTTATTAACAGCACAATCGAGCCTTCCCCTCTGGCAAAATTTTATTTTGCAGACCTTCAAAACACCg                                                            >  1:1042494/1‑149 (MQ=255)                                                                                      cTTACAATTAAGAATCAGAACAATTCACTATATAACATTGCATGTAAAGCATATACACCTAATTATTTTGTCat                                                                                                                                     >  1:912003/1‑74 (MQ=255)                                                                                      cTTACAATTAAGAATCAGAACAATTCACTATATAACATTGCATGTAAAGCATATACACCTAATTATTTTGTCat                                                                                                                                     <  2:912003/74‑1 (MQ=255)                                                                                        tACAATTAAGAATCAGAACAATTCACTATATAACATTGCATGTAAAGCATATACACCTAATTATTTTGTCATTATTAAGTTATTAACAGca                                                                                                                  <  2:429827/91‑1 (MQ=255)                                                                                        tACAATTAAGAATCAGAACAATTCACTATATAACATTGCATGTAAAGCATATACACCTAATTATTTTGTCATTATTAAGTTATTAACAGca                                                                                                                  >  1:429827/1‑91 (MQ=255)                                                                                            aTTAAGAATCAGAACAATTCACTATATAACATTGCATGTAAAGCATATACACCTAATTATTTTGTCATTATTAAGTTATTAACAGCACAATCGAGCCTTCCCCTCTGGCAAAATCTTATTCTGCAGACCTTCAAAACACCGTCCTgggg                                                    <  2:132247/149‑1 (MQ=255)                                                                                            aTTAAGAATCAGAACAATTCACTATATAACATTGCATGTAAAGCATATACACCTAATTATTTTGTCATTATTAAGTTATTAACAGCACAATCGAGCCTTCCCCTCTGGCAAAATCTTATTCTGCAGACCTTCAAAACACCGTCCTgggg                                                    <  1:431448/149‑1 (MQ=255)                                                                                            aTTAAGAATCAGAACAATTCACTATATAACATTGCATGTAAAGCATATACACCTAATTATTTTGTCATTATTAAGTTATTAACAGCACAATCGAGCCTTCCCCTCTGGCAAAATCTTATTCTGCAGACCTTCAAAACACCGTCCTgggg                                                    >  2:278574/1‑149 (MQ=255)                                                                                                       gAACAATTCACTATATAACATTGCATGTAAAGCATATACACCTAATTATTTTGTCATTATTAAGTTATTAACAGCACAATCGAGCCTTCCCCTCTGGCAGAATCTAATTCTGCAGACCTTCAAAACACCGTCCTGGGGGGGTACATTGt                                         >  1:719744/1‑149 (MQ=255)                                                                                                        aaCAATTCACTATATAACATTGCATGTAAAGCATATACACCTAATTATTTTGTCATTATTAAGTTATTAACAGCACAATCGAGCCTTCCCCTCTGGCAAAATCTTATTCTGCAGACCTTCAAAACACCGTCCTGGGGGAGTACATCGtt                                        >  2:964310/1‑149 (MQ=255)                                                                                                        aaCAATTCAATATATAACATTGCATGTAAAGCATATACACCTAATTATTTTGTCATTATTAAGTTATTAACAGCACAATCGAGCCTTCCCCTCTGGCAAAATCTTATTCTGCAGACCTTCAAAACACCGTCCTGGGGGAGTACATTGtt                                        <  1:847578/149‑1 (MQ=255)                                                                                                             ttCACTATATAACATTGCATGTAAAGCATATACACCTAATTATTTTGTCATTATTAAGTTATTAACAGCACAATCGAGCCTTCCCCTCTGGCAAAATCTTATTCTGCAGACCTTCACAACACCGTCCTGGGGGAGTACATTGTTCTAAg                                   >  2:159186/1‑149 (MQ=255)                                                                                                             ttCACTATATAACATTGCATGTAAAGCATATACACCTAATTATTTTGTCATTATTAAGTTATTAACAGCACAATCGAGCCTTCCCCTCTGGCAAAATCTTATTCTGCAGACCTTCAAAACACCGTCCTGGGGGAGTACATTGTTCTAAg                                   >  1:800610/1‑149 (MQ=255)                                                                                                              tCACTATATAACATTGCATGTAAAGCATATACACCTAATTATTTTGTCATTATTAAGTTATTAACAGCACAATCGAGCCTTGCCGTCAGGAAGTAGCTTATTCTGCCGAACTTCAAAACACCGTCCTGAGGGAGTGCATTCTTTTAAGc                                  >  2:123424/1‑149 (MQ=255)                                                                                                                    tataACATTGCATGTAAAGCATATACACCTAATTATTTTGTCATTATTAAGTTATTAACAGCACAATCGAGCCTTCCCCTCTGGCAAAATCTTATTCTGCAGACCTTCAAAac                                                                <  2:562652/113‑1 (MQ=255)                                                                                                                    tataACATTGCATGTAAAGCATATACACCTAATTATTTTGTCATTATTAAGTTATTAACAGCACAATCGAGCCTTCCCCTCTGGCAAAATCTTATTCTGCAGACCTTCAAAac                                                                >  1:562652/1‑113 (MQ=255)                                                                                                                    tataACATTGCATGTAAAGCATATACACCTAATTATTTTGTCATTATTAAGTTATTAACAGCACAATCGAGCCTTCCCCTCTGGCAAAATCTTATTCTGCAGACCTTCAAAACACCGTCCTGGGGGAGTACATTTTTCTAAGCTGACtt                            >  1:666992/1‑149 (MQ=255)                                                                                                                                    aaGCATACACGCCTAATTATTTTGTCATTATTAAGTTATTAACAGCACAATCGAGCCTTCCCCTCTGGCAAAATCTTATTCTGCAGACCTTCAAAACACCGTCCTGGGGGAGTACATTGTTCTAAGCTGACTTCCACGGCAGGGAGTgg            <  1:233723/149‑1 (MQ=255)                                                                                                                                            acacCTAATTATTTTGTCATTATTAAGTTATTAACAGCACAATCGAGCCTTCCCCTCTGGCAAAATCTTATTCTGCAGACCTTCAAAACACCGTCCTGGGGGAGTACATTGTTCTAAGCTGACTTCCACGGCAGGGAGTGGCGATAACa    <  2:550753/149‑1 (MQ=255)                                                                                                                                             cacCTAATTATTTTGTCATTATTAAGTTATTAACAGCACAATCGAGCCTTCCCCTCTGGCAAAATCTTATTCTGCAGACCTTCAAAACACCGTCCTGGGGGAGTACATTGTTc                                       <  1:484917/113‑1 (MQ=255)                                                                                                                                             cacCTAATTATTTTGTCATTATTAAGTTATTAACAGCACAATCGAGCCTTCCCCTCTGGCAAAATCTTATTCTGCAGACCTTCAAAACACCGTCCTGGGGGAGTACATTGTTc                                       >  2:484917/1‑113 (MQ=255)                                                                                                                                              acCTAATTATTTTGTCATTATTAAGTTATTAACAGCACAATCGAGCCTTCCCCTCTGGCAAAATCTTATTCTGCAGACCTTCAAAACACCGTCCTGGGGGAGTACATTGTTCTAAGCTGACTTCCACGGCAGGGAGTGGc           <  1:166081/140‑1 (MQ=255)                                                                                                                                              acCTAATTATTTTGTCATTATTAAGTTATTAACAGCACAATCGAGCCTTCCCCTCTGGCAAAATCTTATTCTGCAGACCTTCAAAACACCGTCCTGGGGGAGTACATTGTTCTAAGCTGACTTCCACGGCAGGGAGTGGc           >  2:166081/1‑140 (MQ=255)                                                                                                                                              acCTAATTATTTTGTCATTATTAAGTTATTAACAGCACAATCGAGCCTTCCCCTCTGGCAAAATCTTATTCTGCAGACCTTCAAAACACCGTCCTGGGGGAGTACATTGTTCTAAGCTGACTTCCACGGCAGGGAGTGGCGATAACAGc  >  2:550504/1‑149 (MQ=255)                                                                                                                                                  |                                                                                                                                                 TGAGGAAATATCATCATCGCGTTTCATTAGTGAATTCTTAAATGAGGCATTTTCACACAATTATCTTACAGATAAAAAAACCAGACTTACAATTAAGAATCAGAACAATTCACTATATAACATTGCATGTAAAGCATATACACCTCATTATTTTGTCATTATTAAGTTATTAACAGCACAATCGAGCCTTCCCCTCTGGCAAAATCTTATTCTGCAGACCTTCAAAACACCGTCCTGGGGGAGTACATTGTTCTAAGCTGACTTCCACGGCAGGGAGTGGCGATAACAGC  >  NC_000913_3_hsa_tpiA/2407254‑2407543

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑