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	100.0%	85.7 / NA	27	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 . (0/0);  new base G (11/16);  total (11/16)

TATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGC‑CAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATACCGTTGTGACGTT  >  NC_000913_3_pae_tpiA/3560312‑3560592                                                                                                                                                 |                                                                                                                                          tatCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGcgcagg                                                                                                                                       <  1:255940/149‑6 (MQ=255)  atCGATAAACAGCGTAGGGCCGTTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTTTGTTTCTTCGGGCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGTATCGCCATGATTGcgtaggt                                                                                                                                      <  2:421151/149‑7 (MQ=255)       tAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCAGGATCAgg                                                                                                                                 <  1:256591/149‑1 (MQ=255)                               tttGCTCCGGCAGTTTGCGGGCGATGGGGTCTTTTCCGTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAgg                                                                                                         <  2:12020/149‑1 (MQ=255)                                     ccGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCgcgg                                                                                                   <  1:167242/149‑1 (MQ=255)                                     ccGCCACTGTGCTGGCGATGCTCTCTTTTTCTGCGGTCTGGGTGGCCTTGCGATCGTGCCACGGGGTGTTAACCGAACGGGAAGGCAGCGCCGCACCGCCATGATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCgcgg                                                                                                   <  1:103770/149‑1 (MQ=255)                                         cACTTTGCGGGCGAAGCGCTCTTTTTCTTCGGTCCGGGTGGCCTTGCGATCGTGCCACGGCGTGCTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGaa                                                                                               <  2:117688/149‑1 (MQ=255)                                           cTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATa                                                                                             >  1:194322/1‑149 (MQ=255)                                            tttGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCATTGCGATCGTGAAACCGCGAGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAg                                                                                            >  2:358120/1‑149 (MQ=255)                                                    cGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCggg                                                                                    <  1:259062/149‑1 (MQ=255)                                                     gATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCAGGACCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGc                                                                                   >  2:56305/1‑149 (MQ=255)                                                             tgttttCTGCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCTTGTTAACCGAACTGGAAGGCAGCCCTGCACCGCCATGATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGgag                                                                           <  2:432633/147‑1 (MQ=255)                                                                 ttcttcGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAAt                                                                       >  2:297898/1‑149 (MQ=255)                                                                       ggTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTTGTTGAACGGGTACGCAGCGCCGCACCGCCATGATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTa                                                                 <  2:356021/149‑1 (MQ=255)                                                                                ggCCTTGCGATCGTGCCACGGCGAGATAGGGGAACGGGAAGGCAGCGCCGATTTGCCATGATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCtt                                                        <  1:441444/149‑1 (MQ=255)                                                                                 gCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTc                                                       <  1:398900/149‑1 (MQ=255)                                                                                   cTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCAGGATCAGGTTTTGCACCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCgg                                                     <  1:381625/149‑1 (MQ=255)                                                                                    ttGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGCAATGCTCTACCAGCTCTTCGGt                                                    >  2:466200/1‑149 (MQ=255)                                                                                     tGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTa                                                   >  1:384181/1‑149 (MQ=255)                                                                                          tCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTAACAGCAAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGAc                                              >  1:116457/1‑149 (MQ=255)                                                                                             tGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAGATGCTCTACCATCTCTTCGGTACTGACaga                                           >  1:137829/1‑147 (MQ=255)                                                                                                    gCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTGTACCAGCTCTTCGGTACTGACATAACCctgc                                    >  1:144398/1‑149 (MQ=255)                                                                                                                 aCTGGAAGGCAGCGCCGCACCGCCATGATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGtt                       <  1:56305/149‑1 (MQ=255)                                                                                                                  cTGGAAGGCAGCGCCGCACCGCCATGATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTc                      <  2:194322/149‑1 (MQ=255)                                                                                                                           aGCGCCGCACCGCCATGATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTAc                                                                <  1:310352/98‑1 (MQ=255)                                                                                                                           aGCGCCGCACCGCCATGATGGCGCAGGATCAGGCTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTAc                                                                >  2:310352/1‑98 (MQ=255)                                                                                                                             cgccgcACCGCCATGATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATACCGt           >  2:64269/1‑149 (MQ=255)                                                                                                                              gccgcACCGCCATGATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATACCGtt          <  1:358120/149‑1 (MQ=255)                                                                                                                                      gCCATGATGGCGCAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATACCGTTGTGACGtt  <  1:111752/149‑1 (MQ=255)                                                                                                                                                 |                                                                                                                                          TATCGATAAACAGCGTCGAGCCATTGGGGATTTGCTCCGCCACTTTGCGGGCGATGCGCTCTTTTTCTTCGGTCTGGGTGGCCTTGCGATCGTGCCACGGCGTGTTAACCGAACTGGAAGGCAGCGCCGCACCGCCATGATGGC‑CAGGATCAGGTTTTGCTCCGCCAGCTCATTGAGGTCGCGGCGAATAGTCTGCGGGCTGACGGAGAAATGCTCTACCAGCTCTTCGGTACTGACATAACCCTGCTGTTTAACCAGTTCGATAATACCGTTGTGACGTT  >  NC_000913_3_pae_tpiA/3560312‑3560592

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: ‑