Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913_3_pae_tpiA	4,158,704	C→T	T100I (ACA→ATA)	oxyR →	oxidative and nitrosative stress transcriptional regulator

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913_3_pae_tpiA	4,158,704	0	C	T	100.0%	92.0 / NA	29	T100I (ACA→ATA)	oxyR	oxidative and nitrosative stress transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (16/13);  total (16/13)

GCCGTAAAGTGTTGTTCACCCAGGCGGGAATGCTGCTGGTGGATCAGGCGCGTACCGTGCTGCGTGAGGTGAAAGTCCTTAAAGAGATGGCAAGCCAGCAGGGCGAGACGATGTCCGGACCGCTGCACATTGGTTTGATTCCCACAGTTGGACCGTACCTGCTACCGCATATTATCCCTATGCTGCACCAGACCTTTCCAAAGCTGGAAATGTATCTGCATGAAGCACAGACCCACCAGTTACTGGCGCAACTGGACAGCGGCAAACTCGATTGCGTGATCCTCGCG  >  NC_000913_3_pae_tpiA/4158560‑4158846                                                                                                                                                 |                                                                                                                                               ggcGTAAAGCGTTGTTCACCCAGGCGGGAATGCTGCTGGTGGATCAGGCGCGTACCGTGCTGCGTGAGGTGAAAGGCCTTAAAGTGATGGCAAGCCAGCAGGGCGAGACGATGTCCGGACCGCTGCACATTGGTTTGATTCCCATAGtt                                                                                                                                            <  2:309539/147‑1 (MQ=255) gctctcaaGTGCTGTTCAACCAGGTGGAAATGCTGGTGGTGTATCAGGCGCGTACCTTCCTGCGTGAGGTGAAAGTCCTTAAAGAGATGGCAAGCCAGCAGCCCGAGACGATGTCCGGACCGTTGCACATTTGTTTGATTCCCATAGtt                                                                                                                                            <  2:63065/143‑1 (MQ=255)                 cACCCAGGCGGGAATGCTGCTGGTGGATCAGGCGCGTACCGTGCTGCGTGAGGTGAAAGTCCTTAAAGAGATGGCAAGCCAGCAGGGCGAGACGATGTCCGGACCGCTGCACATTGGTTTGATTCCCATAGTTGGACCGTACCTGCTAc                                                                                                                            <  1:425579/149‑1 (MQ=255)                  aCCCAGGCGGGAATGCTGCTGGTGGATCAGGCGCGTACCGTGCTGCGTGAGGTGAAAGTCCTTAAAGAGATGGCAAGCCAGCAGGGCGAGACGATGTCCGGACCGCTGCACATTGGTTTGATTCCCATAGTTGGACCGTACCTGCTaac                                                                                                                           >  1:142623/1‑147 (MQ=255)                        gCGGGAATGCTGCTGGCTGAGCAGGCGCGTACCGTGCTGCGTCAGGCGAAAGTCCTTAAAGAGATGGCAAGCCAGCATGGCGAGACGATGTCCGGACCGCTGCACATTGGTTTGATTCCCATAGTTGGACCGTACCTGCTACCGCatat                                                                                                                     <  2:135971/149‑1 (MQ=255)                         cGGGAATGCTGCTGGTGGATCAGGCGCGTACCGTGCTGCGTGAGGTGAAAGTCCTTAAAGAGATGGCAAGCCAGCAGGGCGAGACGATGTCCGGACCGCTGCACATTGGTTTGATTCCCATAGTTGGACCGTACCTGCTACCGCAtatt                                                                                                                    >  2:335437/1‑149 (MQ=255)                             aaTGCTGCTGGTGGATCAGGCGCGTACCGTGCTGCGTGAGGTGAAAGTCCGTAAAGAGATGGCAAGCCAGCAGGGCGAGACGATGTCCGGACCGCTGCACATTGGTTTGATTCCCATAGTTGGACCGTACCTGCTACCGCATATTATcc                                                                                                                >  2:244621/1‑149 (MQ=255)                                            tCAGGCGCGTACCGTGCTGCGTGAGGTGAAAGTCCTTAAAGAGATGGCAAGCCAGCAGGGCGAGACGATGTCCGGACCGCTGCACATTGGTTTGATTCCCATAGTTGGACCGTACCTGCTACCGCATATTATCCCTATGCTGCACCAGa                                                                                                 >  1:299007/1‑149 (MQ=255)                                              aGGCGCGTACCGTGCTGCGTGAGGTGAAAGTCCTTAAAGAGATGGCAAGCCAGCAGGGCGAGACGATGTCCGGACCGCTGCACATTGGTTTGATTCCCATAGTTGGACCGTACCTGCTACCGCATATTATCCCTATGCTGCACCAGAcc                                                                                               >  2:178845/1‑149 (MQ=255)                                                      aCCGTGCTGCGTGAGGTGAAAGTCCTTAAAGAGATGGCAAGCCAGCAGGGCGAGACGATGTCCGGACCGCTGCACATTGGTTTGATTCCCATAGTTGGACCGTACCTGCTACCGCATATTATCCCTATGCTGCACCAGACCTTTCCaaa                                                                                       >  2:395453/1‑149 (MQ=255)                                                          tgctgcGTGAGGGGAAAGGCCTTAAAGAGATGGCAAGCCAGCAGGGCGAGACGATGTCCGGACCGCTGCACATTGGTTTGATTCCCATAGTTGGACCGTACCTGCTACCGCATATTATCCCTATGCTGCACCAGACCTTTCCAAAGCTg                                                                                   <  2:243806/149‑1 (MQ=255)                                                                           gTCCTTAAAGAGATGGCAAGCCAGCAGGGCGAGACGATGTCCGGACCGCTGCACATTGGTTTGATTCCCATAGTTGGACCGTACCTGCTACCGCATATTATCCCTATGCTGCACCAGACCTTTCCAAAGCTGGAAATGTATCTGCATGa                                                                  >  1:340701/1‑149 (MQ=255)                                                                             ccTTAAAGAGATGGCGAGCGAGCAGGGCGAGACGATGTCCGGACCGCTGCACATTGGTTTGATTCCCATAGTTGGACCGTACCTGCTACCGCATATTATCCCTATGCTGCACCAGACCTTTCCAAAGCTGGAAATGTATCTGCATGAAg                                                                >  2:420968/1‑149 (MQ=255)                                                                               ttAAAGAGATGGCAAGGCAGCAGGGCGAGACGATGTCCGGACCGCTGCACATTGGTTTGATTCCCATAGTTGGACCGTACCTGCTACCGCATATTATCCCTATGCTGCACCAGACCTTTCCAAAGCTGGAAATGTATCTGCCTGAAGca                                                              >  1:436573/1‑149 (MQ=255)                                                                                gaaaGAGATGGCAAGCCAGCAGGGCGAGACGATGTCCGGACCGCTGCACATTGGTTTGATTCCCATAGTTGGACCGTACCTGCTACCGCATATTATCCCTATGCTGCACCAGACCTTTCCAAAGCTGGAAATGTATCTGCATGAAGcac                                                             <  1:184613/148‑1 (MQ=255)                                                                                  aaGAGATGGCAAGCCAGCAGGGCGAGACGATGTCCGGACCGCTGCACATTGGTTTGATTCCCATAGTTGGACCGTACCTGCTACCGCATATTATCCCTATGCTGCACCAGACCTTTCCAAAGCTGGAAATGTATCTGCATGAAGcacgg                                                           >  1:230725/1‑147 (MQ=255)                                                                                    gagaTTGCAATCCAGCAGGGCGAGACGATGTCCGGACCGCTGCACATTGGTTTGATTCCCATAGTTGGACCGTACCTGCTACCGCATATTATCCCTATGCTGCACCAGACCTTTCCAAAGCTGGAAATGTATCTGCATGAAGCACAGAc                                                         <  2:418634/149‑1 (MQ=255)                                                                                    gagaTGGCAAGCCAGCAGGGCGAGACGATGTCCGGACCGCTGCACATTGGTTTGATTCCCATAGTTGGACCGTACCTGCTACCGCATATTATCCCTATGCTGCACCAGACCTTTCCAAAGCTGGAAATGTATCTGCATGACGCACAGAc                                                         >  2:439114/1‑149 (MQ=255)                                                                                       aTGGCAAGCCAGCAGGGCGAGACGATGTCCGGACCGCTGCACATTGGTTTGATTCCCATAGTTGGACCGTACCTGCTACCGCATATTATCCCTATGCTGCACCAGACCTTTCCAAAGCTGGAAATGTATCTGCATGAAGCACAGACcca                                                      <  2:340701/149‑1 (MQ=255)                                                                                              gCCAGCAGGGCGAGACGATGTCCGGACCGCTGCACATTGGTTTGATTCCCATAGTTGGACCGTACCTGCTACCGCATATTATCCCTATGCTGCACCAGACCTTTCCAAAGCTGGAAATGTATCTGCATGAAGCACAGACCCACCAGTTa                                               >  1:347407/1‑149 (MQ=255)                                                                                                 agcagGGCGAGACGATGTCCGGACCGCTGCACATTGGTTTGATTCCCATAGTTGGACCGTACCTGCTACCGCATATTATCCCTATGCTGCACCAGACCTTTCCAAAGCTGGAAATGTATCTGCATGAAGCACAGCCCCACCAGTTACTg                                            >  2:1200/1‑149 (MQ=255)                                                                                                 agcagGGCGAGACGATGTCCGGACCGCTGCACATTGGTTTGATTCCCATAGTTGGACCGTACCTGCTACCGCATATTATCCCTATGCTGCACCAGACCTTTCCAAAGCTGGAAATGTATCTGCATGAAGCACAGACCCACCAGTTACTg                                            <  1:395453/149‑1 (MQ=255)                                                                                                   cagGGGGAGCCGATGTCGGGAGCGCTGCAATTTGGTTTGATTCCCATAGTTGGATCGTACCTGCTACCGCATATTAGCCCTATGCTGCACCAGACCTTTCCAAAGCTGGAAATGTATCTGCATGAAGCACATACCCACCAGTTGCTGgc                                          <  2:9569/149‑1 (MQ=255)                                                                                                   cagGGCGAGACGATGTCCGGACCGCTGCACATTGGTTTGATTCCCATAGTTGGACCGTACCTGCTACCGCATATTATCCCTATGCTGCACCAGACCTTTCCAAAGCTGGAAATGTATCTGCATGAAGCACAGACCCACCAGTTACTGgc                                          <  2:347407/149‑1 (MQ=255)                                                                                                              gATGTCCGGACCGCTGCACATTGGTTTGATTCCCATAGTTGGACCGTACCTGCTACCGCATATTATCCCTATGCTGCACCAGACCTTTCCAAAGCTGGAAATGTATCTGCATGAAGCACAGACCCACCAGTTACTGGCGCAACTGGACa                               <  1:400241/149‑1 (MQ=255)                                                                                                                 gTCCGGAACGCTGCACGGTGGGTTGGTTCCCGTAGTTGGACCGTAACTGGTACCGCATATTATCCCTATGCTGCACCAGTCCTTTCCGAAGCTGGAAATGTATCTGCATGAAGCACAGGCCCACCAGTTACTGGCGCAACTGGACAGCg                            <  2:356481/149‑1 (MQ=255)                                                                                                                  tCCGGACCGCTGCACATTGGTTTGATTCCCATAGTTGGACCGTACCTGCTACCGCATATTATCCCTATGCTGCACCAGACCTTTCCAAAGCTGGAAATGTATCTGCATGAAGCACAGACCCACCAGTTACTGGCGCAACTGGACAGCgc                           >  2:369219/1‑148 (MQ=255)                                                                                                                                 aTTGGTTTGATTCCCATAGTTGGACCGTACCTGCTACCGCATATTATCCCTATGCTGCACCAGACCTTTCCAAAGCTGGAAATGTATCTGCATGAAGCACAGACCCACCAGTTACTGGCGCAACTGGACAGCGGCAAACTCGATTGCGt            >  1:137994/1‑149 (MQ=255)                                                                                                                                           ttCCCATAGTTGGACCGTACCTGCTACCGCATATTATCCCTATGCTGCGCCAGACCTTTCCAAAGCTGGAAATGTATCTGCATGAAGCACGGACCCACCAGTTACTGGCGCAACTGGGCAGCGGCAAACTCGATTGCGTGGTCCTcgcg  >  2:10797/1‑149 (MQ=255)                                                                                                                                                 |                                                                                                                                               GCCGTAAAGTGTTGTTCACCCAGGCGGGAATGCTGCTGGTGGATCAGGCGCGTACCGTGCTGCGTGAGGTGAAAGTCCTTAAAGAGATGGCAAGCCAGCAGGGCGAGACGATGTCCGGACCGCTGCACATTGGTTTGATTCCCACAGTTGGACCGTACCTGCTACCGCATATTATCCCTATGCTGCACCAGACCTTTCCAAAGCTGGAAATGTATCTGCATGAAGCACAGACCCACCAGTTACTGGCGCAACTGGACAGCGGCAAACTCGATTGCGTGATCCTCGCG  >  NC_000913_3_pae_tpiA/4158560‑4158846

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: ‑