Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913_3_hsa_tpiA	3,815,928	+GG	pseudogene (622/669 nt)	rph ←	ribonuclease PH (defective);enzyme; Degradation of RNA; RNase PH

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913_3_hsa_tpiA	3,815,926	1	.	G	97.9%	152.8 / ‑5.1	48	pseudogene (624/669 nt)	rph	ribonuclease PH (defective);enzyme; Degradation of RNA; RNase PH
Reads supporting (aligned to +/- strand):  ref base . (0/0);  major base G (26/21);  minor base C (1/0);  total (27/21)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.78e-01
*	NC_000913_3_hsa_tpiA	3,815,926	2	.	G	100.0%	153.5 / NA	48	pseudogene (624/669 nt)	rph	ribonuclease PH (defective);enzyme; Degradation of RNA; RNase PH
Reads supporting (aligned to +/- strand):  ref base . (0/0);  new base G (27/21);  total (27/21)

CTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAAC‑‑GGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCTTCGCCGTTCACAATTCCGACAGA  >  NC_000913_3_hsa_tpiA/3815779‑3816063                                                                                                                                                     ||                                                                                                                                          ctcATCTTACTATCCTACAGAGAAAAAAAAGGCGACTTATCAGTCGCCTTAAAAATCAGTTGGCCAGCGCCGCCTGCTGCGTCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGGTCTTCATGGGTGAAC‑‑g                                                                                                                                          <  2:933621/149‑1 (MQ=255)         aCTATTATAAAGAAAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAAC‑‑ggggctcgc                                                                                                                                  <  2:918196/149‑8 (MQ=255)                tACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCTTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGGGCTCGCCTTCTGc                                                                                                                             >  1:578490/1‑149 (MQ=255)                     aCAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGGGCTCGCCTTCTGCCGTcc                                                                                                                        >  1:570986/1‑149 (MQ=255)                     aCAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGGGCTCGCCTTCTGCCGTcc                                                                                                                        <  1:483359/149‑1 (MQ=255)                      cAAAAAAAAGGCGACCCATCAGTCGCCTTAAAACTCAGTGTGCGAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGGGCTCGCCTTCTGCCGTccc                                                                                                                       <  1:392736/149‑1 (MQ=255)                          aaaaaGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACCGGGCTCGCCTACTCCCGTccacagg                                                                                                                   >  2:986313/1‑144 (MQ=255)                                 cGACTCATCAGTCGCCTTAAAAATCAGTTGGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGGGCTCGCCTTCTGCCGTCCCCTGCACTTCaa                                                                                                            <  2:94840/149‑1 (MQ=255)                                 cGACGCGTCAGTGGCGTTAAAAATCAGTTGGCCAGCGCCGCCTTCTGCGTCGCTACAGTGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGGGCTCGCCTTCTGCCGTCCCCTGCACTTCaa                                                                                                            <  2:128737/149‑1 (MQ=255)                                  gACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGGGAACGGGGCTCGCCTTCGTCCGTCCCCTGCCCTTCAat                                                                                                           >  2:5785/1‑149 (MQ=255)                                   tcacaacaGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGGGCTCGCCTTCTGCCGTCCCCTGCACTTCAatg                                                                                                          >  2:141220/7‑149 (MQ=255)                                       atcaGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATgc                                                                                                      >  2:435951/1‑149 (MQ=255)                                       atcaCTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATgc                                                                                                      <  1:141220/149‑1 (MQ=255)                                                  tAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCg                                                                                           <  2:673691/149‑1 (MQ=255)                                                       aTCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGtcat                                                                                      >  1:246331/1‑149 (MQ=255)                                                                 cAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGGGCTCGCCTTCTGCCGTCCCCTGCACTTCAat                                                                                                           >  2:168480/1‑118 (MQ=255)                                                                 cAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGGGCTCGCCTTCTGCCGTCCCCTGCACTTCAat                                                                                                           <  1:168480/118‑1 (MQ=255)                                                                           ttCTGCGTCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATAACTCCGTTCAGTTCGGgct                                                                  >  2:403512/1‑149 (MQ=255)                                                                           ttCTGCGTCGCTACAATGGATTCGATACCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGAGTGAACGGGGCTCGCCTTCTGCCGTCCACTGCAGTTCAATGATGCGCACGTCTTAGGTCGTCACTACGTTCATTTCGCtcc                                                                  >  2:222394/1‑148 (MQ=255)                                                                           ttCTGCGTAGCTCCAATGGATTCGCTTCCAGTCGGACCTGTGCCAACAAGATGAGTAGCGCTTCATGGGTGGACGGGGCTCTCCTTCTGCCGTCCCCTGCACTTCAATGATGCACCCGTCTTCGGACGTCCCTACGTTCATTTCGGcct                                                                  >  2:832495/1‑149 (MQ=255)                                                                             cTGCGTCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTctct                                                                >  1:824828/1‑149 (MQ=255)                                                                               gCGTCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGGGCTCGCCTTCTGCCGTCCCCTGCACTTCAatgat                                                                                                        >  2:609017/1‑107 (MQ=255)                                                                               gCGTCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGGGCTCGCCTTCTGCCGTCCCCTGCACTTCAatgat                                                                                                        <  1:609017/107‑1 (MQ=255)                                                                                cGTCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCg                                                             <  1:308151/149‑1 (MQ=255)                                                                                        taagggtttcgattcCCCTCGGGCCAGAGCACACAAGATGAGTAGCTCTTCATGGGTGAACGGGGCTCGCCTTCTGCCCTCCCCTGCACTTCCATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTc                                                     <  2:206811/142‑1 (MQ=255)                                                                                        cAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTc                                                     >  2:220791/1‑149 (MQ=255)                                                                                         aaTGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCt                                                    >  1:342044/1‑149 (MQ=255)                                                                                         aaTGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCt                                                    >  1:829985/1‑149 (MQ=255)                                                                                          aTGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCtt                                                   <  1:435951/149‑1 (MQ=255)                                                                                             gattcgattcCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCaa                                                >  1:612066/1‑149 (MQ=255)                                                                                              attcgattcCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAAc                                               <  1:906785/149‑1 (MQ=255)                                                                                              attcgattcCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAAc                                               <  1:60518/149‑1 (MQ=255)                                                                                                    ttcCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTc                                         <  2:246331/149‑1 (MQ=255)                                                                                                    tcccccTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTc                                         <  1:893631/147‑1 (MQ=255)                                                                                                       cccTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGGGCTAGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAg                                      >  2:929825/1‑149 (MQ=255)                                                                                                        ccTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACTTTCATGTCGGTCTCTGCGGCAGAGTCTTCGACGTGTTCCAGa                                     >  1:47353/1‑149 (MQ=255)                                                                                                         cTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGAt                                    <  1:268860/149‑1 (MQ=255)                                                                                                              gCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCaa                               >  1:618772/1‑149 (MQ=255)                                                                                                                aagagCCAACAATATGAGTAGCGTTTAATGGGTGAACGGGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAAc                             <  2:389365/148‑1 (MQ=255)                                                                                                                     ccAACAAGATGAGTAGCTCTTCATGGGTGAACGGGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCtt                        >  1:502670/1‑149 (MQ=255)                                                                                                                       aacaaGATGAGTAGCTCTTCATGGGTGAACGGGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCaga                                                        <  1:135271/115‑1 (MQ=255)                                                                                                                       aacaaGATGAGTAGCTCTTCATGGGTGAACGGGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCaga                                                        >  2:135271/1‑115 (MQ=255)                                                                                                                       aacaaGATGAGTAGCTCTTCATGGGTGAACGGGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCTTCg                      >  1:774597/1‑149 (MQ=255)                                                                                                                       aacaaGATGAGTAGCTCTTCATGGGTGAACGGGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCTTCg                      >  1:940491/1‑149 (MQ=255)                                                                                                                           aGATGAGTAGCTCTTCATGGGTGAACGGGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCTTCGCCGt                  <  2:839872/149‑1 (MQ=255)                                                                                                                           aGATGAGTAGCTCTTCATGGGTGAACGGGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCAAGATCGCAAACCGCTTcacagt                  >  1:589975/1‑144 (MQ=255)                                                                                                                             aTGAGTAGCTCTTCATGGGTGAACGGGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCCACGTATTCCAGATCGCAAACCGCTTCGCCGTTc                >  1:121750/1‑149 (MQ=255)                                                                                                                                     ctctTCATGGGTGAACGGGGCTTGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCTTCGCCGTTCACAATTcc        <  1:20636/149‑1 (MQ=255)                                                                                                                                       ctTCATGGGTGAACGGGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCTTCGCCGTTCACAATTCCGa      <  2:612066/149‑1 (MQ=255)                                                                                                                                           aTGGGTGAACGGGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCTTCGCCGTTCACAATTCCGACAGa  >  2:567974/1‑149 (MQ=255)                                                                                                                                                     ||                                                                                                                                          CTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAAC‑‑GGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCTTCGCCGTTCACAATTCCGACAGA  >  NC_000913_3_hsa_tpiA/3815779‑3816063

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑