Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913_3_pae_tpiA	3,560,455	+G	intergenic (‑2/+1)	glpR ← / ← glpR	pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon/pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913_3_pae_tpiA	3,560,455	1	.	G	97.7%	133.4 / ‑2.9	44	intergenic (‑2/+1)	glpR/glpR	pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon/pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon
Reads supporting (aligned to +/- strand):  ref base . (1/0);  new base G (25/18);  total (26/18)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.00e-01

CCGATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTG‑TTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGC‑CA‑GGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATACCGTTGTGACGTTGTGTT  >  NC_000913_3_pae_tpiA/3560308‑3560597                                                                                                                                                      |                                                                                                                                                ccGATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGTCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTG‑TTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATAGcg                                                                                                                                                 >  1:832282/1‑148 (MQ=255)        cGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTG‑TTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCA‑GGATc                                                                                                                                         >  1:636394/1‑149 (MQ=255)         gATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTG‑TTAACCGAACTGGAAGGCAGCGCCGCACGGCCATGATGGCGCA‑GGATCa                                                                                                                                        >  1:573444/1‑149 (MQ=255)          aTAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTG‑TTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCA‑GGATCAg                                                                                                                                       >  1:126287/1‑149 (MQ=255)          aTAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTG‑TTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCA‑GGATCAg                                                                                                                                       <  2:975298/149‑1 (MQ=255)             agcAGCGGCGAGCAATTGGGGATTCGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGCCTGGGTGGCCTTGCGATCGTGCCACGGCGTG‑GTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCA‑GGATCAGGtt                                                                                                                                    <  2:746704/147‑1 (MQ=255)              aCAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGTTCTGGGTGGCCTTGCGATCGTGCCACGGCGTG‑TTAGCCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCA‑GGATCAGGttt                                                                                                                                   >  2:510672/1‑149 (MQ=255)                aGCGTCGAGCCATTGGGGATTTGCTCCGCCACGTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTG‑TTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCA‑GGATCAGGTTTTg                                                                                                                                 <  2:72315/149‑1 (MQ=255)                    gggggCCATGGGGGATTTGCTCCGCCACTTGGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCCCGGCGTG‑TTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCA‑GGATCAGGTTTTGCTcc                                                                                                                             <  2:811768/145‑1 (MQ=255)                      gAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTGTGCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTG‑TTAACCGGACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCA‑GGATCAGGTTTTGCTCCGc                                                                                                                           >  2:797746/1‑149 (MQ=255)                      gAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTG‑TTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCA‑GGATCAGGTTTTGCTCCGc                                                                                                                           <  1:365649/149‑1 (MQ=255)                        gCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTG‑TTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCA‑GGATCAGGTTTTGCTCCGCCa                                                                                                                         >  1:538590/1‑149 (MQ=255)                          cATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGTGCTTGCGATCGTGCCCCGGCGTG‑TTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCA‑GGATCAGGTTTTGCTCCGCCAGc                                                                                                                       >  2:119328/1‑149 (MQ=255)                             tGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTG‑TTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCA‑GGATCAGGTTTTGCTCCGCCAGCTCa                                                                                                                    >  1:313138/1‑149 (MQ=255)                                  aTTTGCTCCGCCACTTTTCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTG‑TTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCA‑GGATCAGGTTTTGCTCCGCCAGCTCATTGAg                                                                                                               <  1:596412/149‑1 (MQ=255)                                   tttGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTG‑TTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCA‑GGATCAGGTTTTGCTCCGCCAGCTCATTGAgg                                                                                                              >  1:857933/1‑149 (MQ=255)                                   taagCTCCGCCACATTGCGGGCGATGCGCTCTTTTTCTTCAGTCTGGGTGGCCGTACGATCGTGCGACGGCGGG‑TCGACCGAAAGGGAAAACAGCGCCACACCGCCATGAGGGCGCA‑GGATCACGCTAAGCTCCGCCAGCGCATCGacg                                                                                                              >  2:320299/4‑147 (MQ=255)                                       cTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTG‑TTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCA‑GGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTcgc                                                                                                          >  1:272981/1‑149 (MQ=255)                                         ccGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGTTGGCCTTGCGATCGTGCCACGGCGTG‑TTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCA‑GGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCgcgg                                                                                                        <  2:826812/149‑1 (MQ=255)                                         ccGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTG‑TTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCA‑GGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCgcgg                                                                                                        <  1:796740/149‑1 (MQ=255)                                          cGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCAACGGCCTGTTTCAACG‑ACTTTGTTGCAGCTCCTCACCGCCAAGATCGCGAA‑GGATCAGGTTTTGCCCCGCCCGCTCATTGAGGGCtcggc                                                                                                       >  2:143/1‑149 (MQ=255)                                                tttGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTG‑TTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCA‑GGATCAGGTTTTGCTCCGCCAGCTCATTGCGGTCGCCGAGAATAg                                                                                                 >  2:990456/1‑149 (MQ=255)                                                tttGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTG‑TTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCA‑GGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAg                                                                                                 >  1:945255/1‑149 (MQ=255)                                                        cGATGCGTTGTTTTTCTGCGGTGTGGGTGGCCTTGCGATCGTGCCACGGCGTG‑TTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCA‑GGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCggg                                                                                         <  2:150910/149‑1 (MQ=255)                                                          gtGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTG‑TTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCA‑GGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATGGTCTGCGGGCt                                                                                       <  1:659695/148‑1 (MQ=255)                                                            gcgcTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTG‑TTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCA‑GGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGa                                                                                     <  1:411016/149‑1 (MQ=255)                                                                    tttCTTCGGTCTGGTGGGCCTGGCGATCGTGCCACGGCGTG‑TTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCA‑GGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGaaa                                                                             <  2:163781/149‑1 (MQ=255)                                                                        ttcGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTG‑TTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCA‑GGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATgat                                                                         >  1:85112/1‑147 (MQ=255)                                                                            gTCTGGGTGGCCTTGCGATCGTGCCACGGCGTG‑TTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCA‑GGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGctctcc                                                                     >  1:1045395/1‑147 (MQ=255)                                                                             tCTGGGTGGCCTTGCGATCGTGCCACGGCGTG‑TTAACCGAAATGGAAGGCAGCGCCGCACCGCCATGATGGCGCA‑GGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTagc                                                                    >  1:274731/1‑147 (MQ=255)                                                                                     gCCTTGCGATCGTGCCCCGGCGTG‑TTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCA‑GGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTc                                                            >  1:917703/1‑149 (MQ=255)                                                                                       ctgggcgtCGTGCCACGGCGTG‑TTAACCGTACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCA‑GGATCAGGTTTTGCCCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGTGCTGACGGAGAAATGCTCTACCAGCTCTTCgg                                                          <  2:160858/142‑1 (MQ=255)                                                                                       cTTGCGATCGTGCCACGGCGTG‑TTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCA‑GGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCgg                                                          >  1:669257/1‑149 (MQ=255)                                                                                       cTTGCGATCGTGCCACGGCGTG‑TTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCA‑GGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACCGAGAAATCCACTCCCCGCTCTTCgg                                                          >  2:192618/1‑149 (MQ=255)                                                                                                   ccACGGCGTG‑TTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCA‑GGCTCAGGTCTTGCTCCGCCAGCTCCTTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGCGAAATGCTCTACCAACTCCTCGATCCTCGCATAAc                                              >  2:957561/1‑149 (MQ=255)                                                                                                         cGTG‑TTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCA‑GGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCctgct                                        <  1:439024/149‑1 (MQ=255)                                                                                                                 aCCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCA‑GGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACTTAACAGTGCTGTTTAAc                                 >  2:1003091/1‑149 (MQ=255)                                                                                                                   cGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCA‑GGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCa                               <  2:669257/149‑1 (MQ=255)                                                                                                                   cGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCA‑GGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCa                               <  1:915353/149‑1 (MQ=255)                                                                                                                      aCTGGAAGGCAGCGCCGCACCGCCATGATGGCGCA‑GGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGtt                            <  1:119328/149‑1 (MQ=255)                                                                                                                         ggAAGGCAGCGCCGCACCGCCATGATGGCGCA‑GGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGa                         <  2:284557/149‑1 (MQ=255)                                                                                                                                 gcgcCGCACCGCCATGATGGCGCA‑GGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACAAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATACCg                 >  2:73695/1‑149 (MQ=255)                                                                                                                                   gccgcACCGCCATGATGGC‑GACGAAGCAAGTTTTGCTCCGCCAGCTCATGGAGGTCGCGGCGAATAGGCTGCGGGCTAACGGAGAAATGCCCTACCAGATCTTCGGTACTGGCATAACCCTGCTGTTTAACCACTTCGATAATAACGtc               >  2:514963/1‑148 (MQ=255)                                                                                                                                            ccATGATGGCGCA‑GGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATACCGTTGTGACGTtg      >  1:226313/1‑149 (MQ=255)                                                                                                                                                gatgGCGCA‑GGAATAGGTTTTGCTCCGCCAGCTCGTTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGCAATGCTCTACCAGCTCTTCGGTACTTTCATAACCCTGCACTTTAACCACTTCGATAATACCCTTGTTACGTTGtgtt  >  2:164173/1‑149 (MQ=255)                                                                                                                                                      |                                                                                                                                                CCGATATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTG‑TTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGC‑CA‑GGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATACCGTTGTGACGTTGTGTT  >  NC_000913_3_pae_tpiA/3560308‑3560597

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑