Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913_3_hsa_tpiA	4,604,698	C→A	100%	A186E (GCA→GAA)	bglJ →	bgl operon transcriptional activator

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913_3_hsa_tpiA	4,604,698	0	C	A	100.0%	140.1 / ‑6.7	51	A186E (GCA→GAA)	bglJ	bgl operon transcriptional activator
Reads supporting (aligned to +/- strand):  ref base C (0/1);  new base A (33/16);  total (33/18)
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

CCGACCGACTGAACAATCAGTGGTACATTAACCAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATC‑AAAACGATCCGTGCA‑CA‑TAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGTTGCATCCCTATTAATCCGCATGATGCCGGGTTTACTTC  >  NC_000913_3_hsa_tpiA/4604554‑4604843                                                                                                                                                  |                                                                                                                                                    ccgaccgacTGAACAATCAGTGGTACATTAACCAAAGCCGGACGTTAAGCCCGTCGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGAAACAAATTGCCGAGCAGCTTAAACGCAATAGC‑AAAACGATCCGTGAA‑CA‑t                                                                                                                                               >  1:549423/1‑149 (MQ=255)      cgacTGAACAATCAGTGGTACATTAACCAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAAGATC‑AAAACGATGCGTGAA‑CA‑TAAAtt                                                                                                                                          >  1:68125/1‑149 (MQ=255)        acTGAACAATCAGTGGTACATTAACCAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAGTATC‑AAAACGATCCGTGAA‑CA‑TAAATTTa                                                                                                                                        >  1:429113/1‑149 (MQ=255)         cTGAACAATCAGTGGTACATTAACCAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTACGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCGATATC‑AACACGATCCGTGAA‑CA‑TAAATTTaa                                                                                                                                       >  1:403353/1‑149 (MQ=255)          tGAACAATCAGTGGTACATTAACCAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATC‑AAAACGATCCGTGAA‑CA‑TAAATTTAAt                                                                                                                                      <  1:297171/149‑1 (MQ=255)          tGAACAATCAGTGGTACATTAACCAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATC‑AAAACGATCCGTGAA‑CA‑AAAATTTAAt                                                                                                                                      >  2:623622/1‑149 (MQ=255)          tGAACAATCAGTGCTACACTAACCAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATGGCGCCTTATGTCGCGTGGCTACTTGATGACACAAATTGCCGAGCAGCTTAAACGCAATATC‑AAAACGATCCGTGAA‑CA‑TAAATTTAAt                                                                                                                                      <  1:233327/149‑1 (MQ=255)                  cAGTGGAACATTAACCAAAGGCGGACGTTAAGCCAGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATC‑AAAACGATCCGTGAA‑CA‑TAAATTTAATGTGATGTc                                                                                                                              <  1:329802/149‑1 (MQ=255)                       gTACATTAACCAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATC‑AAAACGATCCGTGAA‑CA‑TAAATTTAATGTGATGTCGAAAc                                                                                                                         >  1:641328/1‑149 (MQ=255)                          caatAAACAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTCTGTCGCGTGGCGACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATC‑AAATCTATCCGTGAA‑CA‑TAAATTTAATGTGATGTCGAAACTgg                                                                                                                      <  1:375/146‑1 (MQ=255)                           aTTAACCAAAGCCGGACGTTAAGCCCGTCGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATA‑AAAACGATCCGTGAA‑CA‑TAAATTTAATGTGATGTCGAAACTggt                                                                                                                     >  2:389101/1‑148 (MQ=255)                           aTTAACCAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATC‑AAAACGATCCGTGAA‑CA‑TAAATTTAATGTGATGTCGAAACTggg                                                                                                                     >  2:544372/1‑149 (MQ=255)                            ttAACCAAAGCCGGACGTTAAGCCGGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATC‑AAAACGATCCGTGAA‑CA‑TAAATTTAATGTGATGTCGAAACTGGGc                                                                                                                    <  1:318712/149‑1 (MQ=255)                                gcAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATC‑AAAACGATCCGTGAA‑CA‑TAAATTTAATGTGATGTCGAAACTGGGCGTCa                                                                                                                <  1:804428/148‑1 (MQ=255)                                ccAACGCCGGGCGAGAGGCTCGAGGGAGGGAGAAATATTGCGGATTATCTAGTGGGGCTACTCAATGACACAAATTGCCGAGCAGGTTAAACGCAAGATC‑AAAACGATCCGTGAA‑CA‑TAAATTTAATGTGATGTCGAAACTGGGCGTCa                                                                                                                <  2:115881/149‑1 (MQ=255)                                ccAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATC‑AAAACGATCCGTGAA‑CA‑TAAATTTAATGTGATGTCGAAACTGGGCGTCa                                                                                                                >  1:313606/1‑149 (MQ=255)                                 cAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATCAAAAACGATCCGTGAA‑CA‑TAAATTTAATGTGATGTCGCAACTGGCCGTCa                                                                                                                >  2:543009/1‑149 (MQ=255)                                      ccGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTACGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATC‑AAAACGATCCGTGAA‑CA‑TAAATTTAATGTGATGTCGAAACTTGGCGTCAGTTCTg                                                                                                          >  2:385473/1‑149 (MQ=255)                                                    cGACGGAGGAGGAAGTATTGCGCTTTGTGTCGCGTGGCTACTCAACGACACAAATTGCCGAGCAGCTTAACCGCAATATC‑ATATTGCT‑GTTCCAGCT‑TGAGTTCAATGTGTTGTCGAAACTGGGCGTCAGCGGTGACGCTGGGttgttg                                                                                            <  2:176003/149‑1 (MQ=255)                                                    cGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATC‑AAAACGATCCGTGAA‑CA‑TAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGgtgttg                                                                                            >  1:669910/1‑149 (MQ=255)                                                             gagaAATATAACGGTTAATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATGTC‑AAAACGATCCGTGAA‑CA‑TAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCa                                                                                   >  2:647897/1‑149 (MQ=255)                                                                     tttcgttttATGTCGCGTGGCTCTGCAATGACAAAAATTGCCGAGCAGCTTAAACGCAATATC‑AAAACGATCCGTGAA‑CC‑TAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCt                                                                           <  2:125176/143‑1 (MQ=255)                                                                     ttGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATC‑AAAACGATCCGTGAA‑CA‑TAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGAGATTCt                                                                           >  2:87148/1‑149 (MQ=255)                                                                        tcgtttATGTCGGGTGGGTACTCAAAGACACAAATTGCCGAGCAGCTTAAACGCAATATC‑AAAACGATCCGTGAA‑CA‑TAAAGTTAATGTGATGTCGAAACTGGGCGTCAGTGCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGtt                                                                        <  2:743421/146‑1 (MQ=255)                                                                        cgcTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATC‑AAAACGATCCGTGAA‑CA‑TAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGtt                                                                        <  1:146082/149‑1 (MQ=255)                                                                         gcTTTATGGCGCGTGGCTACTCAATGGCACAAATTGCCGAGCAGCTTAAACGCAATATC‑AAAACGATCCGTGAA‑CA‑TAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTta                                                                       <  1:225402/149‑1 (MQ=255)                                                                           tttATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATC‑AAAACGATCCGTGAA‑CA‑TAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTtatg                                                                     >  1:412986/1‑149 (MQ=255)                                                                           tttATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATC‑AAAACGATCCGTGAA‑CA‑TAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTtatg                                                                     >  1:414385/1‑149 (MQ=255)                                                                                     gTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATC‑AAAACGATCCGTTAA‑CA‑TAGATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATCCTGTTATGTATGCGGCAt                                                           >  1:515913/1‑149 (MQ=255)                                                                                             tCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATC‑AAAACGATCCGTG‑A‑CAGTAATCTTAATTTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTTGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAAc                                                   <  1:400593/149‑1 (MQ=255)                                                                                               aaTGACACAAATTGCCGAGCAGCTTAAACGCAATAGA‑AACACGAGCCGAGAA‑CA‑TAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACaa                                                 >  1:406584/1‑149 (MQ=255)                                                                                                   acacAAATTGCCGAGCAGCTTAAACGCAATATC‑AAAACGATCCGTGAA‑CA‑TAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTGGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTaa                                             >  1:576154/1‑149 (MQ=255)                                                                                                         aTTGCCGAGCAGCTTAAACGCAATATC‑AAAACGATCCGTGAA‑CA‑TAAATTTAATGTGATGTCGAAAGTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGGAACAAGTAATGTGtt                                       >  2:435915/1‑149 (MQ=255)                                                                                                          ttGCCGAGCAGCTTAAACGCAATATC‑AAAACGATCCGTGAA‑CA‑TAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGTTg                                      <  1:301078/149‑1 (MQ=255)                                                                                                           tGCCGAGCAGCTTAAACGCAATATC‑AAAACGATCCGTGAA‑CA‑TAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGTTGc                                     <  1:424667/149‑1 (MQ=255)                                                                                                               gAGCAGCTTAAACGCAATATC‑AAAACGATCCGTGAA‑CA‑TAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGTTGCATcc                                 >  1:650628/1‑149 (MQ=255)                                                                                                               gAGCAGCTTAAACGCAATATC‑AAAACGATCCGTGAA‑CA‑TAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGTTGCATcc                                 >  1:387129/1‑149 (MQ=255)                                                                                                                   agcTTAAACGCAATATC‑AAAACGATCCGTGAA‑CA‑TAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGTTGCATCCCTAt                             <  2:124628/149‑1 (MQ=255)                                                                                                                    gcTTAAACGCAATATC‑AAAACGATCCGTGAA‑CA‑TAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTTACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGTTGAATCCCTAtt                            >  1:641779/1‑149 (MQ=255)                                                                                                                     cTTAAACGCAATATC‑AAAACGATCCGTGAA‑CA‑TAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGTTGCATCCCTATTa                           >  1:714873/1‑149 (MQ=255)                                                                                                                       tAAACGCAATATC‑AAAACGATCCGTGAA‑CA‑TAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTAACGCAGGGGTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACACGTAATTTGTTGCATCCCTATTAAt                         >  1:648254/1‑149 (MQ=255)                                                                                                                       tAAACGCAACATC‑AAGACGATCCGCGAA‑CA‑TAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCGGGGTTGTTGGAGGCCTCACATATCCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGTTGCATCCCTATTAAt                         <  1:659786/149‑1 (MQ=255)                                                                                                                           cGCAATATC‑AAAACGATCCGTGAA‑CA‑TAAATTTAATGTGATATCGAAACTGGACTACAGATCTGACGAAGAGTAGTAGGACGCCGCAGACATTCAGTTATGTATGTGTCATTGCGAAACAAGTAATATGTTGCATCCCTATTAATCCGc                     >  2:19141/1‑149 (MQ=255)                                                                                                                            gCAATATC‑AAAACGATCCGTGAA‑CA‑TAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATTTGTTGCATTCCTATTAATCCGCa                    >  2:825160/1‑149 (MQ=255)                                                                                                                                  tC‑AAAACGATCCGTGAA‑CA‑TAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGTTGCATCCCTATTAATCCGCATGATGc              >  1:23809/1‑149 (MQ=255)                                                                                                                                     aaaaCGATCCGTGAA‑CA‑TAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATTCGGCATTGCGAAACAAGTAATGTGTTGCATCCCTATTAATCCGCATGATGACg            >  1:276436/1‑149 (MQ=255)                                                                                                                                      aaaCGATCCGTGAA‑CA‑TAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCCTTGCGCAACCAGTAATGTGTTGCAGCCCTATTAATCCGCATAATGCCgg           >  2:655426/1‑149 (MQ=255)                                                                                                                                       aaCGATCCGTGAA‑CA‑TAAATTTAATGTGATGTCGAAACTGAACGTCAGTTCTGACACAGGGCTGTTGGAGGCAGCAGATATTCTATTATGTATGGGTCATTGAAAGATGAGTAATCTGTTGTAGCACTATTAATACCGATGATGCCggg          >  2:242444/1‑149 (MQ=255)                                                                                                                                        aCGATCCGTGAA‑CA‑TAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGTTGCATCCCTATTAATCCGCATGATGCCGGGt         >  1:101344/1‑149 (MQ=255)                                                                                                                                         cGATCCGTGAA‑CA‑TAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGTTGCATCCCTATTAATCCGCATGATGCCGGGtt        <  1:40341/149‑1 (MQ=255)                                                                                                                                               gTGAA‑CA‑TAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGTTGCATCCCTATTAATCCGCATGATGCCGGGTTTACTTc  >  1:654228/1‑149 (MQ=255)                                                                                                                                                  |                                                                                                                                                    CCGACCGACTGAACAATCAGTGGTACATTAACCAAAGCCGGACGTTAAGCCCGACGGAGAGAGAAATATTGCGCTTTATGTCGCGTGGCTACTCAATGACACAAATTGCCGAGCAGCTTAAACGCAATATC‑AAAACGATCCGTGCA‑CA‑TAAATTTAATGTGATGTCGAAACTGGGCGTCAGTTCTGACGCAGGGTTGTTGGAGGCCGCAGATATTCTGTTATGTATGCGGCATTGCGAAACAAGTAATGTGTTGCATCCCTATTAATCCGCATGATGCCGGGTTTACTTC  >  NC_000913_3_hsa_tpiA/4604554‑4604843

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑