Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,664,360	G→A	P87S (CCC→TCC)	gadW ←	transcriptional activator of gadA and gadBC, repressor of gadX

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,664,360	0	G	A	100.0%	164.0 / NA	47	P87S (CCC→TCC)	gadW	transcriptional activator of gadA and gadBC, repressor of gadX
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (25/22);  total (25/22)

TAAGGGGATCAGTTCTTTCTTATGAGAAAACATCGATAAACAGGAAAGGTAGAGCATATTGCTCAGTATCGGTGAATTTACCCCGGATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCATGGGGGGTGACTGGTTAATTAACAAACGGTCTTTGCTGTGTAACCCTAAATTGCGTGGTAGCTGACGAATATTTTGTAAGTAATGGCAAACTGTCAGCTCATCGATATCCAGTC  >  NC_000913/3664232‑3664470                                                                                                                                 |                                                                                                               tAAGGGGATCAGTTCTTTCTTATGAGAAAACATCGATATACAGGAAAGGTAGAGCATATTGCTCAGTATCGGTGAATTTACCCCGGATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCATGGAGGGTGACt                                                                                                        >  1:161856/1‑137 (MQ=255) tAAGGGGATCAGTTCTTTCTTATGAGAAAACATCGATAAACAGGAAAGGTAGAGCATATTGCTCAGTATCGGTGAATTTACCCCGGATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCATGGAGGGTGACt                                                                                                        <  2:161856/137‑1 (MQ=255)  aaGGGGATCAGTTCTTTCTTATGAGAAAACATCGATAAACAGGAAAGGTAGAGCATATTGCTCAGTATCGGTGAATTTACCCCGGATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCATGGAGGGTGACTGGt                                                                                                     <  2:178862/139‑1 (MQ=255)           aGTTCTTTCTTATGAGAAAACATCGATAAACAGGAAAGGTAGAGCATATTGCTCAGTATCGGTGAATTTACCCCGGATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCATGGAGGGTGa                                                                                                          >  1:431559/1‑125 (MQ=255)           aGTTCTTTCTTATGAGAAAACATCGATAAACAGGAAAGGTAGAGCATATTGCTCAGTATCGGTGAATTTACCCCGGATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCATGGAGGGTGa                                                                                                          <  2:431559/125‑1 (MQ=255)           aGTTCTTTCTTATGAGAAAACATCGATAAACAGGAAAGGTAGAGCATATTGCTCAGTATCGGTGAATTTACCCCGGATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCATGGAGGGTGACTGGTTAATTAACa                                                                                            >  1:85321/1‑139 (MQ=255)                 ttcttATGAGAAAACATCGATAAACAGGAAAGGTAGAGCATATTGCTCAGTATCGGTGAATTTACCCCGGATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCATGGAGGGTGACTGGTTAATTAACAAACGGt                                                                                      <  2:85321/139‑1 (MQ=255)                           aaaaCATCGATAAACAGGAAAGGTAGAGCATATTGCTCAGTATCGGTGAATTTACCCCGGATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCATGGAGGGTGACTGGTTAATTAACAAACGGTCTTTGCtgtg                                                                            <  2:214491/139‑1 (MQ=255)                                                   agagCATATTGCTCAGTATCGGTGAATTTACCCCGGATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCATGGAGGGTGACTGGTTAATTAACAAACGGTCTTTGCTGTGTAACCCTAAATTGCGTGGTAGCTg                                                    >  2:219421/1‑139 (MQ=255)                                                           ttGCTCAGTATCGGTGAATTTACCCCGGATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCATGGAGGGTGACt                                                                                                        >  2:512286/1‑79 (MQ=255)                                                           ttGCTCAGTATCGGTGAATTTACCCCGGATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCATGGAGGGTGACt                                                                                                        <  1:512286/79‑1 (MQ=255)                                                           ttGCTCAGTATCGGTGAATTTACCCCGGATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCATGGAGGGTGACTGGTTAATTAACAAACGGTCTTTGCTGTGTAACCCTAAATTGCGTGGTAGCTGACGAatat                                            >  2:69035/1‑139 (MQ=255)                                                                cAGTATCGGTGAATTTACCCCGGATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCATGGAGGGTGACTGGTTAATTAACAAACGGt                                                                                      <  1:280325/92‑1 (MQ=255)                                                                cAGTATCGGTGAATTTACCCCGGATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCATGGAGGGTGACTGGTTAATTAACAAACGGt                                                                                      >  2:280325/1‑92 (MQ=255)                                                                 aGTATCGGTGAATTTACCCCGGATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCATGGAGGGTGACTGGTTAATTAACAAACGGTCTTTGCtgtg                                                                            >  1:15894/1‑101 (MQ=255)                                                                 aGTATCGGTGAATTTACCCCGGATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCATGGAGGGTGACTGGTTAATTAACAAACGGTCTTTGCtgtg                                                                            <  2:15894/101‑1 (MQ=255)                                                                   tATCGGTGAATTTACCCCGGATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCATGGAGGGTGACTGGTTAATTAACAAACGGTCTTTGCTGTGTAACCCTAAATTGCGTGGTAGCTGACGaa                                               >  2:442873/1‑128 (MQ=255)                                                                   tATCGGTGAATTTACCCCGGATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCATGGAGGGTGACTGGTTAATTAACAAACGGTCTTTGCTGTGTAACCCTAAATTGCGTGGTAGCTGACGaa                                               <  1:442873/128‑1 (MQ=255)                                                                      cGGTGAATTTACCCCGGATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCATGGAGGGTGACTGGt                                                                                                     >  2:146171/1‑71 (MQ=255)                                                                      cGGTGAATTTACCCCGGATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCATGGAGGGTGACTGGt                                                                                                     <  1:146171/71‑1 (MQ=255)                                                                        gTGAATTTACCCCGGATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCATGGAGGGTGACTGGTTAATTAACCAACGGTCTTTGCTGTGTAACCCt                                                                     <  1:91935/101‑1 (MQ=255)                                                                        gTGAATTTACCCCGGATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCATGGAGGGTGACTGGTTAATTAACAAACGGTCTTTg                                                                                 <  2:277573/89‑1 (MQ=255)                                                                        gTGAATTTACCCCGGATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCATGGAGGGTGACTGGTTAATTAACAAACGGTCTTTg                                                                                 >  2:144840/1‑89 (MQ=255)                                                                        gTGAATTTACCCCGGATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCATGGAGGGTGACTGGTTAATTAACAAACGGTCTTTg                                                                                 <  1:144840/89‑1 (MQ=255)                                                                        gTGAATTTACCCCGGATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCATGGAGGGTGACTGGTTAATTAACAAACGGTCTTTg                                                                                 >  1:277573/1‑89 (MQ=255)                                                                        gTGAATTTACCCCGGATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCATGGAGGGTGACTGGTTAATTAACAAACGGTCTTTGCTGTGTAACCCt                                                                     >  2:91935/1‑101 (MQ=255)                                                                        gTGAATTTACCCCGGATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCATGGAGGGTGACTGGTTAATTAACAAACGGTCTTTGCTGTGTAACCCTAAATTGCGTGGTAGCTGACGAATATTTTgt                                       <  1:576884/131‑1 (MQ=255)                                                                        gTGAATTTACCCCGGATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCATGGAGGGTGACTGGTTAATTAACAAACGGTCTTTGCTGTGTAACCCTAAATTGCGTGGTAGCTGACGAATATTTTgt                                       >  2:576884/1‑131 (MQ=255)                                                                                 ccccGGATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCATGGAGGGTGACTGGTTAATTAACAAACGGTCTTTGCTGTGTAACCCTAAATTGCGTGGTAGCTGACGAATATTTTGTAAGTAATGGCAAACTGt                      >  1:550295/1‑139 (MQ=255)                                                                                     ggATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCATGGAGGGTGACTGGTTAATTAACAAACGGTCTTTGCTGTGTAACCCTAAATTGCGTGGTAGCTGACGAATATTTTGTAAGTAATGGCAAACTGTCAGc                  <  2:255610/139‑1 (MQ=255)                                                                                      gATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCATGGAGGGTGACTGGTTAATTAACAAACGGTCTTTGCTGTGTAACCCTAAATTGCGTGGTAGCTGACGAATATTTTGTAAGTAATGGCAAACTGTCAGCt                 <  1:502447/139‑1 (MQ=255)                                                                                       aTTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCATGGAGGGTGACTGGtt                                                                                                    >  2:360594/1‑55 (MQ=255)                                                                                       aTTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCATGGAGGGTGACTGGtt                                                                                                    <  1:360594/55‑1 (MQ=255)                                                                                        ttaaTTGAAGCTATCAAAAATCGCCGTCACCAGCGGCATGGAGGGTGACTGGATAATTAACAAACGGTCTTTGCTGTGTAACCCTAAATTGCGTGGTAGCTGACGAATATTTTGTAAGTAATGGCAAACTGTCAGCTCa               >  1:336767/4‑139 (MQ=255)                                                                                         tCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCATGGAGGGTGACTGGTTAATTAACAAACGGTCTTTGCTGTGTAACCCTAAATTGCGTGGTAGCTGACGAATATTTTGTAAGTAATGGCAAACTGTCAGCTCAt              <  1:254389/139‑1 (MQ=255)                                                                                                aGCTATCAAAAATCGCCGTCACCAGCGGCATGGAGGGTGACTGGTTAATTAACAAACGGTCTTTGCTGTGTAACCCTAAATTGCGTGGTAGCTGACGAATATTTTGTAAGTAATGGCAAACTGTCAGGTCATCGATATc       >  2:375625/1‑139 (MQ=255)                                                                                                 gCTATCAAAAATCGCCGTCACCAGCGGCATGGAGGGTGACTGGTTAATTAACAAACGGTCTTTGCTGTGTAACCCTAAATTGCGTGGTAGCTGACGAATATTTTGTAAGTAATGGCAAACTGTCAGCTCATCGATATcc      >  2:197157/1‑139 (MQ=255)                                                                                                     tCAAAAATCGCCGTCACCAGCGGCATGGAGGGTGACTGGTTAATTAACaa                                                                                           >  1:442149/1‑50 (MQ=255)                                                                                                     tCAAAAATCGCCGTCACCAGCGGCATGGAGGGTGACTGGTTAATTAACaa                                                                                           <  2:442149/50‑1 (MQ=255)                                                                                                     tCAAAAATCGCCGTCACCAGCGGCATGGAGGGTGACTGGTTAATTAACAAACGGTCTTTGCTGTGTAACCCTAAATTGCGTGGTAGCTGACGAATATTTTGTAAGTAATGGCAAACTGTCAGCTCATCGATATCCAgtc  >  1:4995/1‑139 (MQ=255)                                                                                                     tCAAAAATCGCCGTCACCAGCGGCATGGAGGGTGACTGGTTAATTAACAAACGGTCTTTGCTGTGTAACCCTAAATTGCGTGGTAGCTGACGAATATTTTGTAAGTAATGGCAAACTGTCAGCTCATCGATATCCAgtc  >  1:545170/1‑139 (MQ=255)                                                                                                      cAAAAATCGCCGTCACCAGCGGCATGGAGGGTGACTGGTTAATTAACAAACGGTCTTTGCTGTGTAACCCTa                                                                    <  2:453437/72‑1 (MQ=255)                                                                                                      cAAAAATCGCCGTCACCAGCGGCATGGAGGGTGACTGGTTAATTAACAAACGGTCTTTGCTGTGTAACCCTa                                                                    >  1:453437/1‑72 (MQ=255)                                                                                                           aTCGCCGTCACCAGCGGCATGGAGGGTGACTGGTTAATTAACAAACGGTCTTTGCTGTGTAACCCTa                                                                    <  1:392124/67‑1 (MQ=255)                                                                                                           aTCGCCGTCACCAGCGGCATGGAGGGTGACTGGTTAATTAACAAACGGTCTTCGCTGTGTAACCCTa                                                                    >  2:392124/1‑67 (MQ=255)                                                                                                                         cGGCATGGAGGGTGACTGGTTAATTAACAAACGGTCTTTGCTGTGTAAcc                                                                       <  2:494185/50‑1 (MQ=255)                                                                                                                         cGGCATGGAGGGTGACTGGTTAATTAACAAACGGTCTTTGCTGTGTAAcc                                                                       >  1:494185/1‑50 (MQ=255)                                                                                                                                 |                                                                                                               TAAGGGGATCAGTTCTTTCTTATGAGAAAACATCGATAAACAGGAAAGGTAGAGCATATTGCTCAGTATCGGTGAATTTACCCCGGATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCATGGGGGGTGACTGGTTAATTAACAAACGGTCTTTGCTGTGTAACCCTAAATTGCGTGGTAGCTGACGAATATTTTGTAAGTAATGGCAAACTGTCAGCTCATCGATATCCAGTC  >  NC_000913/3664232‑3664470

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑