Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913_3_pae_pgi	4,160,733	C→T	G20S (GGC→AGC)	sthA ←	pyridine nucleotide transhydrogenase, soluble

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913_3_pae_pgi	4,160,733	0	C	T	100.0%	153.4 / NA	48	G20S (GGC→AGC)	sthA	pyridine nucleotide transhydrogenase, soluble
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (24/24);  total (24/24)

TTGATTGAATTCTATAATGCGGCTGACGGCGTGACGGAGAGCTTTCGACGGGATGGTGCCCCAGTGGGTGCAACCGCCGCCAACATTTTGATAACGCTCGATAACTGCGACGCGCGCACCTTGCTTAACCAGGCCCATTGCAGCGCCTTCGCCGCCGGGGCCGGAACCTATTACTATGGCATCGTAATCGTAGGAATGTGGCATGGTAGGGCTTACCTGTTCTTATACATAAAAGCAACAGAATGGTAACATTTTATCGCGGGTAAGCCAATTGATC  >  NC_000913_3_pae_pgi/4160587‑4160863                                                                                                                                                   |                                                                                                                                   ttgattgaATTCTATAATGCGGCTGACGGCGTGACGGAGAGCTTTCGACGGGATGGTGCCCCAGTGGGTGCAACCGCCGCCAACATTTTGATAACGCTCGATAACTGCGACGCGCGCACCTTGCTTAACCAGGCCCATTGCAGCGCttt                                                                                                                                  <  1:447179/149‑1 (MQ=255) ttgattgaATTCTATAAGGCGGCTGACGGCGTGACGGAGAGCTTTCGACGGGATGGTGCCCCAGTGGGTGCAACCGCCGCCAACATTTTGATAACGCTCGATAACTGCGACGCGCGCACCTTGCTTAACCAGGCCCATTGCAGCGCttt                                                                                                                                  <  1:572274/149‑1 (MQ=255)   gattgaATTCTATAATGCGGCTGACGGCGTGACGGAGAGCTTTCGACGGGATGGTGCCCCAGTGGGTGCAACCGCCGCCAACATTTTGATACCGCTCGATAACTGCGACGCGCGCACCTTGCTTAACCCGGCCGCTTGCAGCGCTTTcg                                                                                                                                >  2:487267/1‑149 (MQ=255)    attgaATTCTATAATGCGGCTGACGGCGTGACGGAGAGCTTTCGACGGGATGGTGCCCCAGTGGGTGCAACCGCCGCCAACATTTGGATAACGCTCGATAACTGCGACGCGCGCACCTTGCTTAACCAGGCCCATTGCAGCGCTTTcgc                                                                                                                               >  2:1040736/1‑149 (MQ=255)     ttgaATTCTATAATGCGGCTGACGGCGTGACGGAGAGCTTTCGACGGGATGGTGCCCCAGTGGGTGCAACCGCCGCCAACATTTTGATAACGCTCGATAACTGCGACGCGCGCACCTTGCTTAACCAGGCCCATTGCAGCGCTTTcgcc                                                                                                                              >  2:696287/1‑149 (MQ=255)         aTTCTATAATGCGGCTGACGGCGTGACGGAGAGCTTTCGACGGGATGGTGCCCCAGTGGGTGCAACCGCCGCCAACATTTTGATAACGCTCGATAACTGCGACGCGCCCTCATGCAGTAACCAGGCCCATTGCAGCGCTTTCGccgccg                                                                                                                          <  1:1196645/149‑1 (MQ=255)            cTATAATGCGGCTGACGGCGTGACGGAGAGCTTCCACCCGGATGGTGCTCCAGTGGGTGCAACCGCCGCCAACATTTTGATAACGCTCGATAACTGCGACGCGCGCACCTTGCTTAACCAGGCCCATTGCAGCGCTTTCGCCGCCgggg                                                                                                                       <  1:641061/149‑1 (MQ=255)              ataATGCGGCTGACGGCGTGACGGAGAGCTTTCGACGGGATGGTGCCCCAGTGGGTGCAACCGCCGCCAACATTTTGATAACGCTCGATAACTGCGACGCGCGCACCTTGCTTAACCAGGCCCATTGCAGCGCTTTCGCCGCCGGGGcc                                                                                                                     >  1:619739/1‑149 (MQ=255)                  tGCGGCTGACGGCGTGACGGAGAGCTTTCGACGGGATGGTGCCCCAGTGGGTGCAACCGCCGCCAACATTTTGATAACGCTCGATAACTGCGACGCGCGCACCTTGCTTAACCAGGCCCATTGCAGCGCTTTCGCCGCCGGGGCCGGaa                                                                                                                 <  2:619739/149‑1 (MQ=255)                  tGCGGCTGACGGCGTGACGGAGAGCTTTCGACGGGATGGTGCCCCAGTGGGTGCAACCGCCGCCAACATTTTGATAACGCTCGATAACTGCGACGCGCGCACCTTGCTTAACCAGGCCCATTGCAGCGCTTTCGCCACCGGGGCCGGaa                                                                                                                 <  2:146067/149‑1 (MQ=255)                         gACGGCGTGACGGAGAGCTTTCGACGGGATGGCGCCCCAGTGGGTGCAACCGCCGCCAACATTTTGATAACGCTCGATAACTGCGACGCGCGCACCTTGCTTAACCAGGCCCATTGCAGCGCTTTCGCCGCCGGGGCCGGAACCTATTa                                                                                                          <  1:161761/149‑1 (MQ=255)                                          cTTTCGACGGGATGGTGCCCCAGTGGGTGCAACCGCCGCCAACATTTTGATAACGCTCGATAACTGCGACGCGCGCACCTTGCTTAACCAGGCCCATTGCAGCGCTTTCGCCGCCGGGGCCGGAACCTATTACTATGGCatcgtaatcg                                                                                         >  2:885147/1‑149 (MQ=255)                                            ttCGACGGGATGGTGGCCCAGTGGGTGCAACCGACGCCAACATTTTGATAACGCTCGATAACGGCGACGCGCGCACCTTGCTTAACCAGGCCCATTGCAGCGCTTTCGCCGCCGGGGCCGGAACCTATTACTATGGCatcgtaatcgta                                                                                       <  2:158861/149‑1 (MQ=255)                                               gACGGGATGGTGCCCCAGTGGGTGCAACCGCCGCCAACATTTTGATAACGCTCGATAACTGCGACGCGCGCACCTTGCTTAACCAGGCCCATTGCAGCGCTTTCGCCGCCGGGGCCGGAACCTATTACCATGGCATCGTAATCGTAGGa                                                                                    >  1:1209475/1‑149 (MQ=255)                                                     aTGGTGCGCCAGTGGGTGCAACCGCCGCCAACATTTTGACACCGCTCGATAATTGCGACGCGCGCACCTTAATAAACCAGGCCCATTGCAGCGCTTTCGCCGCCGGGGCCGGAACCTATTACCATGGCATCGTAATCGTAGGAATGTgg                                                                              <  2:656/149‑1 (MQ=255)                                                       ggTGCCCCAGTGGGTGCAACCGCCGCCAACATTTTGATAACGCTCGATAACTGCGACGCGCGCACCTTGCTTAACCAGGCCCATTGCAGCGCTTTCGCCGCCGGGGCCGGAACCTATTACTATGGCATCGTAATCGTAGGAATGTGGCa                                                                            <  2:104452/149‑1 (MQ=255)                                                       ggTGCCCCAGTCGGCGCAACCGCCGCCAACATTTTGATAACGCTCGATAACTGCGACGCGCGCACCTTGCTTAACCAGGCCCATTGCAGCGCTTTCGCCGCCGGGGCCGGAACCTATTACTATGGCATCGTAATCGTAGGAATGTGGCa                                                                            <  1:420372/149‑1 (MQ=255)                                                        gTGCCCCAGTGGGTGCAACCGCCGCCAACATTTTGATAACGCTCGATAACTGCGACGCGCGCACCTTGCTTAACCAGGCCCATTGCAGCGCTTTCGCCGCCGGGGCCGGAACCTATTACTATGGCATCGTAATCGTAGGAATGTGGCAt                                                                           >  1:693185/1‑149 (MQ=255)                                                              cAGTGGGTGCAACCGCCGCCAACATTTTGATAACGCTCGATAACTGCGACGCGCGCACCTTGCTTAACCAGGCCCATTGCAGCGCTTTCGCCGCCGGGGCCGGAACCTATTACTATGGCATCGTAATCGTAGGAATGTGGCATGGTAgg                                                                     >  1:421945/1‑149 (MQ=255)                                                                    gTGCAACCGCCGCCAACATTTTGATAACGCTCGATAACTGCGACGCGCGCACCTTGCTTAACCAGGCCCATTGCAGCGCTTTCGCCGCCGGGGCCGGAACCTATTACTATGGCATCGTAATCGTAGGAATGTGGCATGGTAGGGCTTAc                                                               <  1:353850/149‑1 (MQ=255)                                                                     tGCAACCGCCGCCAACATTTTGATAACGCTCGATAACTGCGACGCGCGCACCTTGCTTAACCAGGCCCATTGCAGCGCTTTCGCCGCCGGGGCCGGAACCTATTACTATGGCATCGTAATCGTAGGAATGTGGCATGGTAGGGCTTAcc                                                              >  1:378865/1‑149 (MQ=255)                                                                          ccgccgCCAACATTTTGATAACGCTCGATAACTGCGACGCGCGCACCTTGCTTAACCAGGCCCATTGCAGCGCTTTCGCCGCCGGGGCTAGAACCTATTACTATGGCATCGTAATCGTAGGAATGTGGCATGGTAGGGCTTACCTGTTc                                                         <  2:1163203/149‑1 (MQ=255)                                                                          ccgccgCCAACATTTTGATAACGCTCGATAACTGCGACGCGCGCACCTTGCTTAACCAGGCCCATTGCAGCGCTTTCGCCGCCGGGGCCGGAACCTAtt                                                                                                           >  1:475216/1‑99 (MQ=255)                                                                          ccgccgCCAACATTTTGATAACGCTCGATAACTGCGACGCGCGCACCTTGCTTAACCAGGCCCATTGCAGCGCTTTCGCCGCCGGGGCCGGAACCTAtt                                                                                                           <  2:475216/99‑1 (MQ=255)                                                                          ccgccgCCAACATTTTGATAACGCTCGATAACTGCGACGCGCGCACCTTGCTTAACCAGGCCCATTGCAGCGCTTTCGCCGCCGGGGCCGGAACCTATTACTATGGCATCGTAATCGTAGGAATGTGGCATGGTAGGGCTTACCTGTTc                                                         >  1:86518/1‑149 (MQ=255)                                                                          ccgccgCCAACATTTTGATAACGCTCGATAACTGCGACGCGCGCACCTTGCTTAACCAGGCCCATTGCAGCGCTTTCGCCGCCGGGGCCGGAACCTAATACTATGGAATGGTAATCGTGGGAATGTGGCATGGTGGGGCTTACCTGTTc                                                         >  2:408390/1‑149 (MQ=255)                                                                           cgccgcCAACATTTTGATAACGCTCGATAACTGCGACGCGCGCACCTTGCTTAACCAGGCCCATTGCAGCGCTTTCGCCGCCGGGTCCGGAACCTATTACTATGGCATCGTAATCGTAGGAATGTGGCATGGTAGGGCTTACCTGTTCt                                                        >  1:1080141/1‑149 (MQ=255)                                                                               gccAACATTTTGATAACGCTCGATAACTGCGACGCGCGCACCTTGCTTAACCAGGCCCATTGCAGCGCTTTCGCCGCCGGGGCCGGAACCTATTACTATGGCATCGTAATCGTAGGAATGTGGCATGGTAGGGCTTACCTGTTCTtata                                                    <  2:931214/149‑1 (MQ=255)                                                                               gccAACATTTTGATAACGCTCGATAACTGCGACGCGCGCACCTTGCTTAACCAGGCCCATTGCAGCGCTTTCGCCGCCGGGGCCGGAACCTATTACTATGGCATCGTAATCGTAGGAATGTGGCATGGTAGGGCTTACCTGTTCTtata                                                    <  1:756589/149‑1 (MQ=255)                                                                                ccAACATTTTGATAACGCTCGATAACTGCGACGCGCGCACCTTGCTTAACCAGGCCCATTGCAGCGCTTTCGCCGCCGGGGCCGGCACCTATTACCATGGCATCGTAATCGTAGGAATGTGGCATGGTAGGGCTTACCTGTTCTTATAc                                                   <  1:346944/149‑1 (MQ=255)                                                                                  aaCATTTTGATAACGCTCGATAACTGCGACGCGCGCACCTTGCTTAACCAGGCCCATTGCAGCGCTTTCGCCGCCGGGGCCGGAACCTATTACTATGGCATCGTCATCGTAGGAATGTGGCATGGTAGGGCTTACCTGTTTTTTTACAt                                                 >  1:143388/1‑149 (MQ=255)                                                                                      ttttGATAACGCTCGATAACTGCGACGCGCGCACCTTGCTTAACCAGGCCCATTGCAGCGCTTTCGCCGCCGGGGCCGGAACCTATTACTATGGCATCGTAATCGTAGGAATGTGGCATGGTAGGGCTTACCTGTTCTTATACATaaaa                                             >  2:1103400/1‑149 (MQ=255)                                                                                      ttttGATAACGCTCGATAACTGCGACGCGCGCACCTTGCTTAACCAGGCCCATTGCAGCGCTTTCGCCGCCGGGGCCGGAACCTATTACTATGGCATCGTAATCGTAGGAATGTGGCATGGTAGGGCTTACCTGTTCTTATACATaaaa                                             >  1:318839/1‑149 (MQ=255)                                                                                       tttGATAACGCTCGATAACTGCGACGCGCGCACCTTGCTTAACCAGGCCCATTGCAGCGCTTTCGccgccg                                                                                                                          <  2:169012/71‑1 (MQ=255)                                                                                       tttGATAACGCTCGATAACTGCGACGCGCGCACCTTGCTTAACCAGGCCCATTGCAGCGCTTTCGccgccg                                                                                                                          >  1:169012/1‑71 (MQ=255)                                                                                            tAACGCTCGATAACTGCGACGCGCACACCTTGCTTAACCAGGCCCATTGCAGCGCTTTCGCCGCCGGGGCCGGAACCTATTACTATGGCATCGTAATCGTAGGAATGTGGCATGGTAGGGCTTACCTGTTCTTATTCATAAAAGCAACa                                       >  1:1048746/1‑149 (MQ=255)                                                                                               cGCTCGATAACTGCGACGCGCGCACCTTGCTTAACCAGGCCCATTGCAGCGCTTTCGCCGCCGGGGCCGGAACCTATTACTATGGCATCGTAATCGTAGGAATGTGGCATGGTAGGGCTTACCTGTTCTTATACATAAAAGCAACAGaa                                    >  2:552993/1‑149 (MQ=255)                                                                                                gCTCGATAACTGCGACGCGCGCACCTTGCTTAACCAGGCCCATTGCAGCGCTTTCGCCGCCGGGGCCGGAACCTATTCCTATGGCATCGTAATCGTAGGAATGTGGCATGGTAGGGCTTACCTGTTCTTATACATAAAAGCAACAGAAt                                   <  1:416320/149‑1 (MQ=255)                                                                                                    gagaaCTGCGACGCGCGCACCTTGCTTAACCAGGCCCATTGCAGCGCTTTCGCCGCCGGGGCCGGAACCTATTACTATGGCATCGTAATCGTAGGAATGTGGCATGGTAGGGCTTACCTGTTCTTATACATAAAAGCAACAGAATGGTa                               <  2:1105148/146‑1 (MQ=255)                                                                                                              aCGCGCGCACCTTGCTTAACCAGGCCCATTGCAGCGCTTTCGCCGCCGGGGCCGGAACCTATTACTATGGCATCGTAATCGTAGGAATGTGGCATGGTAGGGCTTACCTGTTCTTATACATAAAAGCAACAGAATGGTAACATTTTATc                     <  2:1010304/149‑1 (MQ=255)                                                                                                              aCGCGCGCACCTTGCTTAACCAGGCCCATTGCAGCGCTTTCGCCGCCGGGGCCGGAACCTATTACTATGGCATCGTAATCGTAGGAATGTGGCATGGTAGGGCTTACCTGTTCTTATACATAAAAGCAACAGAATGGTAACATTTTATc                     <  1:537218/149‑1 (MQ=255)                                                                                                                     cACCTTGCTTAACCAGGCCCATTGCAGCGCTTTCGCCGCCGGGGCCGGAACCTATTACTATGGCATCGTAATCGTAGGAATGTGGCATGGTAGGGCTTACCTGTTCTTATACATAAAAGCAACAGAATGGTAACATTTTATCGCGGGTa              >  2:217050/1‑149 (MQ=255)                                                                                                                        cTTGCTTAACCAGGCCCATTGCAGCGCTTTCGCCGCCGGGGACGGAACCTATTACTGTGGCATCGTAATAGTAGGAATGTGGCATGGTAGGGCTTACCTGTTCTTATACATAAAAGCACCAGAATGGTAACATTTTATCGCAGGTagcc           >  1:320472/1‑146 (MQ=255)                                                                                                                           gCTTAACCAGGCCCATTGGAGCGCTTTCGCCGCCGGGGCCGGAACCTATTACTATGGCATCGTAATCGTAGGAATGTGGCATGGTAGGGCTTACCTGTTCTTATACATAAAAGCAACAGAATGGTAACATTTTATCGCGGGTAAGCCaa        <  1:464342/149‑1 (MQ=255)                                                                                                                             ttAACCAGGCCCATTGCAGCGCTTTCGCCGCCGGGGCCGGAACCTATTACTATGGCATCGTAATCGTAGGAATGTGGCATGGTAGGGCTTACCTGTTCTTATACATAAAAGCAACAGAATGGTAACATTTTATCGCGGGTAAGCCAAtt      >  1:704329/1‑149 (MQ=255)                                                                                                                               aaCCAGGCCCATTGCAGCGCTTTCGCCGCCGGGGCCGGAACCTATTACTATGGCATCGTAATCGTAGGAATGTGGCATGGTAGGGCTTACCTGTTCTTATACATAAAAGCAACAGAATGGTAACATTTTATCGCGGGTACGCCAATTGa    >  2:806416/1‑149 (MQ=255)                                                                                                                               aaCCAGGCCCATTGCAGCGCTTTCGCCGCCGGGGCCGGAACCTATTACTATGGCATCGTAATCGTAGGAATGTGGCATGGTAGGGCTTACCTGTTCTTATACATAAAAGCAACAGAATGGTAACATTTTATCGCGGGTAAGCCAATTGa    <  2:802617/149‑1 (MQ=255)                                                                                                                                 ccAGGCCCATTGCAGCGCTTTCGCCGCCGGGGCCGGAACCTATTACTATGGCATCGTAATCGTAGGAATGTGGCATGGTAGGGCTTACCTGTTCTTATACATAAAAGCAACAGAATGGTAACATTTTATCGCGGGTAAGCCAATTGATc  <  2:86518/149‑1 (MQ=255)                                                                                                                                       ccATTGCAGCGCTTTCGCCGCCGGGGCCGGAACCTATTACTATGGCATCGTAATCGTAGGAATGTGGCATGGTAGGGCTTACCTGTTCTTATACATAAAAGCAACAGAATGGTAACATTTTa                       <  2:981791/122‑1 (MQ=255)                                                                                                                                       ccATTGCAGCGCTTTCGCCGCCGGGGCCGGAACCTATTACTATGGCATCGTAATCGTAGGAATGTGGCATGGTAGGGCTTACCTGTTCTTATACATAAAAGCAACAGAATGGTAACATTTTa                       >  1:981791/1‑122 (MQ=255)                                                                                                                                                   |                                                                                                                                   TTGATTGAATTCTATAATGCGGCTGACGGCGTGACGGAGAGCTTTCGACGGGATGGTGCCCCAGTGGGTGCAACCGCCGCCAACATTTTGATAACGCTCGATAACTGCGACGCGCGCACCTTGCTTAACCAGGCCCATTGCAGCGCCTTCGCCGCCGGGGCCGGAACCTATTACTATGGCATCGTAATCGTAGGAATGTGGCATGGTAGGGCTTACCTGTTCTTATACATAAAAGCAACAGAATGGTAACATTTTATCGCGGGTAAGCCAATTGATC  >  NC_000913_3_pae_pgi/4160587‑4160863

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑