Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913_3_hsa_tpiA	2,976,638	T→G	82.2%	S14A (TCA→GCA)	galR →	galactose‑inducible d‑galactose regulon transcriptional repressor; autorepressor

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913_3_hsa_tpiA	2,976,638	0	T	G	82.2%	108.5 / 11.4	49	S14A (TCA→GCA)	galR	galactose‑inducible d‑galactose regulon transcriptional repressor; autorepressor
Reads supporting (aligned to +/- strand):  ref base T (4/5);  new base G (22/18);  total (26/23)
Fisher's exact test for biased strand distribution p-value = 7.16e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.64e-01

CGTTTGGCTCACATTCCCACGATGAAAACACGCCACCCCTTGAACCAACGGGCGTTTTCCGTAACACTGAAAGAATGTAAGCGTTTACCCACTAAGGTATTTTCATGGCGACCATAAAGGATGTAGCCCGACTGGCAGGCGTTTCAGTCGCCACCGTTTCCCGCGTCATTAATAATTCACCCAAAGCCAGCGAAGCTTCCCGGCTGGCTGTGCATAGTGCAATGGAGTCTCTTAGCTATCACCCGAACGCCAACGCCCGTGCGCTGGCGCAGCAGACCACTGAAACG  >  NC_000913_3_hsa_tpiA/2976495‑2976781                                                                                                                                                |                                                                                                                                                cGTTTGGCTCACATTCCCACGATGAAAACACGCCACCCCTTGAACCAACGGGCGTTTTCCGTAACACTGAAAGAATGTAAGCGTTTACCCACTAAGGTATTTTCATGGCGACCATAAAGGATGTAGCCCGACTGGCAGGCGTTGCAGTc                                                                                                                                            <  2:34465/149‑1 (MQ=255) cGTTTGCCCCACATTCCCACGATGAAAACACGCCACCCCTTGAACCAACGGGCGTTTTCCGTAACACTGAAAGAATGTAAGCGTTTACCCACTAAGGTATTTTCATGGCGACCATAAAGGATGTAGCCCGACTGGCAGGCGTTTCAGTc                                                                                                                                            <  1:246021/149‑1 (MQ=255)             aTTCCCACGATGAAAACACGCCACCCCTTGAACCAACGGGCGTTTTCCGTAACACTGAAAGAATGTAAGCGTTTACCCACTAAGGTATCTTCATGGCGACCATAAAGGATGTAGCCCGACTGGCAGCCGTTGCAATCCCCCCCGTTTcc                                                                                                                                >  2:299584/1‑149 (MQ=255)                 ccACGATGAAAACACGCCACCCCTTGAACCAACGGGCGTTTTCCGTAACACTGAAAGAATGTAAGCGTTTACCCACTAAGGTATTTTCATGGCGACCATAAAGGATGTAGCCCGACTGGCAGGCGTTTCAGTCGCCACCGTTTCCcgcg                                                                                                                            <  1:478610/149‑1 (MQ=255)                    cGATGAAAACACGCCACCCCTTGAACCAACGGGCGTTTTCCGTAACACTGAAAGAATGTACGCGTTTACCCACTAAGGTATTTTCATGGCGACCATAAAGGATGTAGCCCGACTGGCAGGCGTTGCAGTCGCCCCCGTTTCCCTCGTCa                                                                                                                         >  1:444796/1‑149 (MQ=255)                      aTGAAAACACGCCACCCCTTGAACCAACGGGCGTTTTCCGTAACACTGAAAGAATGTAAGCGTTTACCCACTAAGGTATTTTCATGGCGACCATAAAGGATGTAGCCCGACTGGCAGGCGTTGCAGTCGCCACCGTTTCCCGCGTCAtt                                                                                                                       >  1:415233/1‑149 (MQ=255)                           aaCCCGCCACCCCTTGAACCAACGGGCGTTTTCCGTAACACTGAAAGAATGTAAGCGTTTACCCACTAAGGTATTTTCATGGCGACCATAAAGGATGTAGCCCGACTGGCAGGCGTTGCAGTCGCCACCGTTTCCCGCGTCATtaataa                                                                                                                  <  2:363962/149‑1 (MQ=255)                           aaCACGCCACCCCTTGAACCAACGGGCGTTTTCCGTAACACTGAAAGAATGTAAGCGTTTACCCACTAAGGTATTTTCATGGCGACCATAAAGGATGTAGCCCGACTGGCAGGCGTTGCAGTCGCCACCGTTTCCCGCGTCATtaataa                                                                                                                  <  2:363832/149‑1 (MQ=255)                             cacGCCACCCCTTGAACCAACGGGCGTTTTCCGTAACACTGAAAGAATGTAAGCGTTTACCCACTAAGGTATTTTCATGGCGACCATAAAGGATGTAGCCCGACTGGCAGGCGTTGCAGTCGCCACCGTTTCCCGCGTCATTAATAAtt                                                                                                                >  2:48069/1‑149 (MQ=255)                                gCCACCCCTTGAACCAACGGGCGTTTTCCGTAACACTGAAAGAATGTAAGCGTTTACCCACTAAGGTATTTTCATGGCGACCATAAAGGATGTAGCCCGACTGGCAGGCGTTGCAGTCGCACCCGTTTCCCGCGGCATTCATAATTccc                                                                                                             >  2:623765/1‑147 (MQ=255)                                    ccccTTGAACCAACGGGCGTTTTCCGTAACACTGAAAGAATGTAAGCGTTTACCCACTAAGGTATTTTCATGGCGACCATAAAGGATGTAGCCCGACTGGCAGGCGTTTCAGTCGCCACCGTTTCCCGCGTCATTAATAATTCACCCaa                                                                                                         >  1:142758/1‑149 (MQ=255)                                          gAACCAACGGGCGTTTTCCGTAACACTGAAAGAATGTAAGCGTTTACCCACTAAGGTATTTTCCTGGCCACCATAAAGGATGTAGCCCGACTGACAGGCGTTGCAGTCGCCACCCTTTCCCGCGTCATTAATAATTCACCCAAAGCCAg                                                                                                   >  2:359976/1‑149 (MQ=255)                                          gAACCAACGGGCGTTTTCCGTAACACTGAAAGAATGTAAGCGTTTACCCACTAAGGTATTTTCATGGCGACCATAAAGGATGTAGCCCGACTGGCAGGCGTTGCAGTCGCCACCGTTTCCCGCGTCATTAATAATTCACCCAAAGCCAg                                                                                                   <  2:31017/149‑1 (MQ=255)                                           aaCCAACGGGCGTTTTCCGTAACACTGAAAGAATGTAAGCGTTTACCCACTAAGGTATTTTCATGGCGACCATAAAGGATGTAGCCCGACTGGCAGGCGTTGCAGTCGCCACCGTTTCCCGCGTCATTAATAATTCACCCAAAGCCAGc                                                                                                  <  1:140578/149‑1 (MQ=255)                                              cAACGGGCGTTTTCCGTAACACTGAAAGAATGTAAGCGTTTACCCACTAAGGTATTTTCATGGCGACCATAAAGGATGTAGACCGACTGGCAAGCGTATCAGTAGCCGCCCTGTCCCCCGACCTTAATAATTACCCCCAACCCCGCGac                                                                                               >  2:73912/1‑148 (MQ=255)                                                         ttCCGTAACACTGAAAGAATGTAAGCGTTTACCCACTAAGGTATTTTCATGGCGACCATAAAGGATGTAGCCCGACTGGCAGGCGTTGCAGTCGCCACCGTTTCCCGCGTCATTAATAATTCACCCAAAGCCAGCGAAGCTTCCCggct                                                                                    <  1:168981/149‑1 (MQ=255)                                                              tAACACTGAAAGAATGTAAGCGTTTACCCACTAAGGTATTTTCATGGCGACCATAAAGGATGTAGCCCGACTGGCAGGCGTTGCAGTCGCCACCGTTTCCCGCGTCATTAATAATTCACCCAAAGCCAGCGAAGCTTCCCGgctggctg                                                                               >  1:684467/1‑149 (MQ=255)                                                                acacTGAAAGAATGTAAGCGTTTAACCACTAAGGTATTTTCATGGCGACCATAAAGGATGTAGCCCGACTGGCAAGCGTTGCAGTCGCTACCGTTGCTCGCGTCATTAATAATTCACCCACAGCCAGCGCAGCTTCCCggctgggcgta                                                                             >  2:422765/1‑144 (MQ=255)                                                                  accgAAAGAATGTAAGCGTTTACCCACTAAGGTATTTTCATCGCGACCATAAACGATGTACCCCGACGCGCAGTCGTCTCAGTCGCCACCGTCTCCCGCAGCAATAATAATTCACTCACAGCCATCGAACCTTCCCGCCTGCCTGTGCa                                                                           >  2:316933/4‑149 (MQ=255)                                                                    tGAAAGAATGTAAGCGTTTACCCACTAAGGTATTTTCATGGCGACCATAAAGGATGTAGCCCGACTGGCAGGCGTTTCAGTCGCCACCGTTTCCCGCGTCATTAATAATTCACCCAAAGCCAGCGAAGCTTCCCGGCTGGCTGTGCATa                                                                         >  2:376242/1‑149 (MQ=255)                                                                        aGAATGTAAGCGTTTACCCACTAAGGTATTTTCATGGCGACCATAAAGGATGTAGCCCGACTGGCAGGCGTTGCAGTCGCCACCGTTTCCCGCGTCATTAATAATTCACCCAAAGCCAGCGAAGCTTCCCGGCTGGCTGTGCATAGTGc                                                                     >  1:562823/1‑149 (MQ=255)                                                                            tGTAAGCCTTTACCCACTAAGGTATTTTCATGGCGACCATAAAGGATGTAGCCCGACTGACAGACGTTTCAGTCGCCACCGTTTCCCGCGTCATTAATAATTCACCCAAAGCCATCGAAGCTTCCTGGCTGGCTGTGCATAGTGCAATg                                                                 <  2:641654/149‑1 (MQ=255)                                                                              tAAGTGGTTACCCCCTAAGGTATTTTCATGGCGACCATAAAGGATGTAGCCCGACTGGCAGGCGTTGCAGTCGCCACCGTTTCCCGCGTCATTAATAATTCACCCAAAGCCAGCGAAGCTTCCCGGCTGGCTGTGCATAGTGCAATGGa                                                               <  2:625308/149‑1 (MQ=255)                                                                              tAAGCGTTTACCCACTAAGGTATTTTCATGGCGACCATACCGGATGTAGCCCGACTGGCAGGCGTTGCAGTCGCCACCGTTTCCCGCGTCATTAATAATTCACCCAAAGCCAGCGAAGCTTCCCGGCTGGCTGTGCATAGTGCAATGGa                                                               <  1:650990/149‑1 (MQ=255)                                                                              tAAGCGTTTACCCACTAAGGTATTTTCATGGCGACCATAAAGGATGTAGCCCGACTGGCAGGCGTTGCAGTCGCCCCCGTTTCCCGCGTCATTCATCATTGACCCAAAGCCAGCGAAGCTTCCCGGCTGGCTGTGCATCGTGGCATGGa                                                               >  1:65344/1‑149 (MQ=255)                                                                              tAAGCGTTTACCCACTAAGGTATTTGCATGGCGACCATAAAGGATGTAGCCCGACTGGCAGGCGTTGCAGTCGCCACCGTTTCCCGCGTCATTAATAATTCACCCAAAGCCAGCGAAGCTTCCCGGCTGGCTGTGCATAGTGCAATGGa                                                               <  1:425072/149‑1 (MQ=255)                                                                               aaGCGTTTACCGACTAAGGTATTCTCATGGCGACCATAAAGGATGTAGCCCGACTGGCAGGCGTTTCAGTCGCCACCGTTTCCCGCGTCATTAATAATTCACCCAAAGCCAGCGAAGCTTCCCGGCTGGCTGTGCATAGTGCAATGGAg                                                              <  1:375110/149‑1 (MQ=255)                                                                                aGCGTTTACCCACTGAGGTATTTTCATGGCGACCATAAAGGATGTAGCCCGACTGGCAGGCGTTGCAGTCGCCACCGTTTCCCGCGTCATTAATAATTCACCCAAAGCCAGCGAAGCTTCCCGGCTGGCTGTGCATAGTGCAATGGAGt                                                             <  1:97515/149‑1 (MQ=255)                                                                                aGCGTGTACCCACTAAGGTATTTTCATGGCGACCATAAAGGATGTAGCCCGACTGGCAGGCGTTGCAGTCGCCACCGTTTCCCGCGTCATTAATAATTCACCCAAAGCCAGCGAAGCTTCCCGGCTGGCTGTGCATAGTGCAATGGAGt                                                             <  1:19689/149‑1 (MQ=255)                                                                                    tttGCCCACGAGGGTATTTTCATGGCGACCATAAAGGATGTAGCCCGACTGGCAGGCGTTGCAGTCGCCACCGTTTCCCGCGTCATTAATAATTCACCCAAAGCCAGCGAAGCTTCCCGGCTGGCTGTGCATAGTGCAATGGAGTctct                                                         <  2:145410/149‑1 (MQ=255)                                                                                    tttACCCACTAAGGTATTTTCATGGCGACCATAAAGGATGTAGCCCGACTGGCAGGCGTTGCAGTCGCCACCGTTTCCCGCGTCATTAATAATTCACCCAAAGCCAGCGAAGCTTCCCGGCTGGCTGTGCATAGTGCAATGGAGTctct                                                         >  2:415896/1‑149 (MQ=255)                                                                                    tttACCCACTAAGGTATTTTCATGGAGACCATAAAGGATGTAGCCCGACTGGCAGGCGTTGCAGTCGCCACCGTTTCCCGCGTCATTAATAATTCACCCAAAGCCAGCGAAGCTTCCCGGCTGGCTGTGCATAGTGCAATGGAGTctct                                                         >  1:528168/1‑149 (MQ=255)                                                                                       aCCCACTAAGGTATTTTCATGGCGACCATAAAGGATGTAGCCCGACTGGCAGGCGTTGCAGTCGCCACCGTTTCCCGCGTCATTAATAATTCACCCACAGCCAGCGAAGCTTCCCGGCTGGCTGTGCATAGTGCGATGGAGTCTCTTAg                                                      >  1:123532/1‑149 (MQ=255)                                                                                       aCCCACTAAGGTATTTTCATGGCGACCATAAAGGATGTAGCCCGACTGGCAGGCGTTGCAGTCGCCACCGTTTCCCGCGTCATTAATAATTCACCCAAAGCCAGCGAAGCTTCCCGGCTGGCTGTGCATAGTGCAATGGAGTCTCTTAg                                                      <  1:437365/149‑1 (MQ=255)                                                                                         ccACTAAGGTATTTTCATGGCGACCATAAAGGATGTAGCCCGACTGGCAGGCGTTGCAGTTGCCACCGTTTCCCGCGTCATTAATAATTCACCCAAAGCCAGCGAAGCTTCCCGGCTGGCTGTGCATAGTGCAATGGAGTCTCTTAGCt                                                    >  1:446614/1‑149 (MQ=255)                                                                                               aGGTATTTTCATGGCGACCATAAAGGATGTAGCCCGACTGGCAGGCGTTGCAGTCGCCACCGTTTCCCGCGTCATTAATAATTCACCCAAAGCCAGCGAAGCTTCCCGGCTGGCTGTGCATAGTGCAATGGAGTCTCTTAGCTATCAcc                                              <  2:177195/149‑1 (MQ=255)                                                                                                  tATTTTCATGGCGACCATAAAGGATGTAGCCCGACTGGCAGGCGTTGCAGTCGCCACCGTTTCCCGCGTCATTAATAATTCACCCAAAGCCAGCGAAGCTTCCCGGCTGGCTGTGCATAGTGCAATGGAGTCTCTTAGCTATCACCCGa                                           >  1:591021/1‑149 (MQ=255)                                                                                                   aTTTTCATGGCGACCATAAAGGATGTAGCCCGACTGGCAGGCGTTTCAGTCGCCACCGTTTCCCGCGTCATTAATAATTCACCCAAAGCCATCGAAGCTTCCCGGCTGGCTGTGCATAGTGCAATGGAGTCTCTTAGCTATCACCCGaa                                          <  1:270650/149‑1 (MQ=255)                                                                                                         aTGGCGACCATAAAGGATGTAGCCCGACTGGCAGGCGTTGCAGTCGCCACCGTTCCCCGCGTCATTAATAATTCACCCAAAGCCAGCGAAGCTTCCCGGCTGGCTGTGCATAGTGCAATGGAGTCTCTTAGCTATCACCCGaacgccaa                                    <  1:108712/149‑1 (MQ=255)                                                                                                                   tAAAGGATGTAGCCCGACTGGCAGGCGTTGCAGTCGCCACCGTTTCCCGCGTCATTAATAATTCACCCAAAGCCAGCGAAGCTTCCCGGCTGGCTGTGCATAGTGCAATGGAGTCTCTTAGCTATCACCCGAACGCCAACGCCCGTgcg                          >  1:652415/1‑149 (MQ=255)                                                                                                                   tAAAGGATGTAGCCCGACTGGCAGGCGTTGCAGTCGCCACCGTTTCCCGCGTCATTAATAATTCACCCAAAGCCAGCGAAGCTTCCCGGCTGGCTGTGCATAGTGCAATGGAGTCTCTTAGCTATCACCCGAACACCAACGCCCGTgcg                          >  1:623827/1‑149 (MQ=255)                                                                                                                             aGCCCGACTGGCAGGCGTTGCAGTCGCCACCGTTTCCCGCGTCATTAATAATTCACCCAAAGCCAGCGAAGCTTCCCGGCTGGCTGTGCATAGTGCAATGGAGTCTCTTAGCTATCACCCGAACGCCAACGCCCGTGCGCTGGCgcagc                <  1:432419/149‑1 (MQ=255)                                                                                                                                ccGACTGGCAGGCGTTGCAGTCGCCACCGTTTCCCGCGTCATTAATAATTCACCCAAAGCCAGCGAAGCTTCCCGGCTGGCTGTGCATAGTGCAATGGAGTCTCTTAGCTATCACCCGAACGCCAACGCCCGTGCGCTGGCGCAGCAGa             <  1:196832/149‑1 (MQ=255)                                                                                                                                 cGACTGGCAGGCGTTGCAGTCGCCACCGTTTCCCGCGTCATTAATAATTCACCCAAAGCCAGCGAAGCTTCCCGGCTGGCTGTGCATAGTCCAATGGAGTCTCTTAGCTATCACCCGAACGCCAACGCCCGTGCGCTGGCGCAGCAGAc            <  2:684467/149‑1 (MQ=255)                                                                                                                                     tGGCAGGCGTTGCAGTCGCCACCGTTTCCCGCGTCATTAATAATTCACCCAAAGCCAGCGAAGCTTCCCGGCTGGCTGTGCATAGTGCAATGGAGTCTCTTAGCTATCACCCGAACGCCAACGCCCGTGCGCTGGCGCAGCAGACCACt        >  1:260884/1‑149 (MQ=255)                                                                                                                                       gCAGGCGTTGCAGTCGCCACCGTTTCCCGCGTCATTAATAATTCACCCAAAGCCAGCGAAGCTTCCCGGCTGGCTGTGCATAGTGCAATGGAGTCTCTTGGCTATCACCCGAACGCCAACGCCCGTGCGCTGGCGCAGCAGACCACTGa      >  1:184028/1‑149 (MQ=255)                                                                                                                                       gCAGGCGTTGCAGTCGCCACCGTTTCCCGCGTCATTAATAATTCACCCAAAGCCAGCGAAGCTTCCCGGCTGGCTGTGCATAGTGCAATGGAGTCTCTTAGCTATCACCCGAACGCCAACGCCCGTGCGCTGGCGCAGCAGACCACTGa      >  1:298757/1‑149 (MQ=255)                                                                                                                                          ggCGTTGCAGTCGCCACCGTTTCCCGCGTCATTAATAATTCACCCAAAGCCAGCGAAGCTTCCCGGCTGGCTGTGCATAGTGCAATGGAGTCTCTTAGCTATCACCCGAACGCCAACGCCCGTGCGCCGGCGCCGCAGACCACTGAAAc   >  2:186534/1‑149 (MQ=255)                                                                                                                                           gCGTTGCAGTCGCCACCGTTTCCCGCGTCATTAATAATTCACCCAAAGCCAGCGAAGCTTCCCGGCTGGCTGTGCATAGTGCAATGGAGTCTCTTAGCTATCACCCGAACGCCAACGCCCGTGCGCTGGCGCAGCAGACCACTGAAAcg  >  2:602784/1‑149 (MQ=255)                                                                                                                                                |                                                                                                                                                CGTTTGGCTCACATTCCCACGATGAAAACACGCCACCCCTTGAACCAACGGGCGTTTTCCGTAACACTGAAAGAATGTAAGCGTTTACCCACTAAGGTATTTTCATGGCGACCATAAAGGATGTAGCCCGACTGGCAGGCGTTTCAGTCGCCACCGTTTCCCGCGTCATTAATAATTCACCCAAAGCCAGCGAAGCTTCCCGGCTGGCTGTGCATAGTGCAATGGAGTCTCTTAGCTATCACCCGAACGCCAACGCCCGTGCGCTGGCGCAGCAGACCACTGAAACG  >  NC_000913_3_hsa_tpiA/2976495‑2976781

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑