Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913_3_vch_tpiA	2,214,152	A→T	Y165N (TAT→AAT)	yehU ←	inner membrane putative sensory kinase in two‑component system with YehT

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913_3_vch_tpiA	2,214,152	0	A	T	100.0%	161.9 / NA	51	Y165N (TAT→AAT)	yehU	inner membrane putative sensory kinase in two‑component system with YehT
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base T (26/25);  total (26/25)

GCGCAGTGGCAGAAAAAGCCGAAGTGTATTTTTCAAACATCGCGCGTTTATCGAGCAATATACGCATAAACAGCGCCGCGCCGACGGTATTGGTGACCATCATTGGCGCAGCAATATTACTCACCAGACGCACCGCATCTTCATAAGGTCGGGCGATCGCAAGGATGATCAGCATTTGCACCATTTCAGCGACGAACGTGACGGCACCGGCGGTAATGGGGTTAAAGACTTTATCAGTGCGCCCGCGGCGGATCAGGATGCTGTGTACCAGGCCACCGAGTAATCC  >  NC_000913_3_vch_tpiA/2214008‑2214293                                                                                                                                                 |                                                                                                                                              gcgcAGTGGCAGAAAAAGCCGAAGTGTATTTTTCAAACATCGCGCGTTTATCGAGCAATATACGCATAAACAGCGCCGCGCCGACGGTATTGGTGACCATCATTGGCGCAGCAATATTACTCACCAGACGCACCGCATCTTCATTAGGt                                                                                                                                           <  1:419662/149‑1 (MQ=255)   gcAGTGGCAGAAAAAGCCGAAGTGTATTTTTCAAACATCGCGCGTTTATCGAGCAATATACGCATAAACAGCGCCGCGCCGACGGTATTGGTGACCATCATTGGCGCAGCAATATTACTCACCAGACGCACCGCATCTTCATTAGGTCg                                                                                                                                         <  2:333068/149‑1 (MQ=255)   gcAGTGGCAGAAAAAGCCGAAGTGTATTTTTCAAACATCGCGCGTTTATCGAGCAATATACGCATAAACAGCGCCGCGCCGACGGTATTGGTGACCATCATTGGCGCAGCAATATTACTCACCAGACGCACCGCATCTTCATTAGGTCg                                                                                                                                         <  1:673552/149‑1 (MQ=255)         gCAGAAAAAGCCGAAGTGTATTTTTCAAACATCGCGCGTTTATCGAGCAATATACGCATAAACAGCGCCGCGCCGACGGTATTGGTGACCATCATTGGCGCAGCAATATTACTCACCAGACGCACCGCATCTTCATTAGGTCGTGCGAt                                                                                                                                   >  2:147563/1‑149 (MQ=255)                 aGCCGAAGTGTATTTTTCAAACATCGCGCGTTTATCGAGCAATATACGCATAAACAGCGCCGCGCCGACGGTATTGGTGACCATCATTGGCGCAGCAATATTACTCACCAGACGCACCGCATCTTCATTAGGTCGGGCGATCGCAAGga                                                                                                                           <  2:1023515/149‑1 (MQ=255)                  gCCGAAGTGTATTTTTCAAACATCGCGCGTTTATCGAGCAATATACGCATAAACAGCGCCGCGCCGACGGTATTGGTGACCATCATTGGCGCAGCAATATTACTCACCAGACGCACCGCATCTTCATTAGGTCGGGCGATCGCAAGgat                                                                                                                          >  2:831968/1‑149 (MQ=255)                   ccGAAGTGTATTTTTCAAACATCGCGCGTTTATCGAGCAATATACGCATAAACAGCGCCGCGCCGACGGTATTGGTGACCATCATTGGCGCAGCAATATTACTCCCCAAAGGCACCGCATCTTCATTAGGTCGGGCGATCGCAAGgatg                                                                                                                         >  1:195416/1‑149 (MQ=255)                       aGTGTATTTTTCAAACATCGCGCGTTTATCGAGCAATATACGCATAAACAGCGCCGCGCCGACGGTATTGGTGACCATCATTGGCGCAGCAATATTACTCACCAGACGCACCGCATCTTCATTAGGTCGGGCGATCGCAAGGATGATCa                                                                                                                     <  1:722667/149‑1 (MQ=255)                           tATTTTTCAAACATCGCGCGTTTATCGAGCAATATACGCATAAACCACGCCGCGCCGACGGTATTGGTGGACATCATTGGCGCAGCAATATTACTCACCAGACGCACGGCGTCTTCATTAGGTCCGGGCATCGCAAGGAAGAGCAGCAt                                                                                                                 >  2:287930/1‑149 (MQ=255)                           tATTTTTCAAACATCGCGCGTTTATCGAGCAATATACGCATAAACAGCGCCGCGCCGACGGTATTGGTGACCATCATTGGCGCAGCAATATTACTCACCAGACGCACCGCATCTTCATTAGGTCGGGCGATCGCAAGGATGATCAGCAt                                                                                                                 >  2:31446/1‑149 (MQ=255)                            aTTTTCCAAACATCGCGCGTTTATCGAGCAATATACGCATAAACAGCGCCGCGCCGACGGTATTGGTGACCATCATTGGCGCAGCAATATTACTCACCAGACGCACCGCATCTTCATTAGGTCAGGCGATCGCAAGGATGATCAGCAtt                                                                                                                <  2:236300/149‑1 (MQ=255)                                           cgcgTTTATCGAGCAATATACGCATAAACAGCGCCGCGCCGACGGTATTGGTGACCATCATTGGCGCAGCACTCTTACTCACCACACGCACCGCATCTTCCTTAGGTCGGGCGCCCGCCAGCCTGATCATCATTTGCACCATTTAAGcg                                                                                                 >  2:558617/1‑149 (MQ=255)                                                   tCGAGCAATATACGCATAAACAGCGCCGCGCCGACGGTATTGGTGACCATCATTGGCGCAGCAATATTACTCACCAGACGCACCGCATCTTCATTAGGTCGGGCGATCGCAAGGATGATCAGCATTTGCGCCATTTCAGCGACGAACGt                                                                                         >  1:336049/1‑149 (MQ=255)                                                     gAGCAATATACGCATAAACAGCGCCGCGCCGACGGTATTGGTGACCATCATTGGCGCAGCAATATTACTCACCAGACGCACCGCATCTTCATTAGGTCGGGCGATCGCAAGGATGATCAGCATTTGCACCATTTCAGCGACGAACGTGa                                                                                       <  1:498819/149‑1 (MQ=255)                                                      ggCAATATACGCATAAACAGCGCCGCGCCGACGGTATTGGTGACCATCATTGGCGCAGCAATATTACTCACCAGACGCACCGCATCTTCATTAGGTCGGGCGATCGCAAGGATGATCAGCATTTGCACCATTTCAGCGACGAACGTGAc                                                                                      <  2:142355/148‑1 (MQ=255)                                                      aGCAATATACGCATAAACAGCGCCGCGCCGACGGTATTGGTGACCATCATTGGCGCAGCAATATTACTCACCAGACGCACCGCATCTTCATTAGGTCGGGCGATCGCAAGGCTGATCAGCGTTTGCACCCTTTCAGCGACGAACCTGAc                                                                                      >  1:33013/1‑149 (MQ=255)                                                               cGCATAAACAGCGCCGCGCCGACGGTATTGGTGACCATCATTGGCGCAGCAATATTACTCACCAGACGCACCGCATCTTCATTAGGTCGGGCGATCGCAAgg                                                                                                                            <  1:921256/102‑1 (MQ=255)                                                               cGCATAAACAGCGCCGCGCCGACGGTATTGGTGACCATCATTGGCGCAGCAATATTACTCACCAGACGCACCGCATCTTCATTAGGTCGGGCGATCGCAAgg                                                                                                                            >  2:921256/1‑102 (MQ=255)                                                                gCATAAACAGCGCCGCGCCGACGGTATTGGTGACCATCATTGGCGCAGCAATATTACTCACCGGACGCACCGCATCTTCAATAGGTCGGGCGATCGCAAGGATGATACGCATTTGCACCATTTCGTCGGCGCACGTGACGGCACcgacg                                                                            >  1:433804/1‑149 (MQ=255)                                                                gCATAAACAGCGCCGCGCCGACGGTATTGGTGACCATCATTGGCGCAGCAATATTACTCACCAGACGCACCGCATCTTCATTAGGTCGGGCGATCGCAAGGATGATCAGCATTTGCACCATTTCAGCGACGAACGTGACGGCACcggcg                                                                            >  2:876816/1‑149 (MQ=255)                                                                  aTAAACAGCGCCGCGCCGACGGTATTGGTGACCATCATTGGCGCAGCAATATTACTCACCAGACGCACCGCATCTTCATTAGGTCGGGCGATCGCAAGGATGATCAGCATTTGCACCATTTCAGCGACGAACGTGACGGCACCGGCGGt                                                                          >  1:13166/1‑149 (MQ=255)                                                                   tAAACAGCGCCGCGCCGACGGTATTGGTGACCATCATTGGCGCAGCAATATTACTCACCAGACGCACCGCATCTTCATTAGGTCGGGCGATCGCAAGGATGATCAGCATTTGCACCATTTCAGCGACGAACGTGACGGCACCGGCGGTa                                                                         <  1:478892/149‑1 (MQ=255)                                                                   tAAACAGCGCCGCGCCGACGGTATTGGTGACCATCATTGGCGCAGCAATATTACTCACCAGACGCACCGCATCTTCATTAGGTCGGGCGATCGCAAGGATGATCAGCATTTGCACCATTTCAGCGACGAACGTGACGGCACCGGCGGTa                                                                         >  1:382011/1‑149 (MQ=255)                                                                    aaaCAGCGCCGCGCCGACGGTATTGGTGACCATCATTGGCGCAGCAATATTACTCACCAGACGCACCGCATCTTCATTAGGTCGGGCGATCGCAGGAATCGTCAGAATGTGCACCTTTTAAGTGACAAACGTGACGGCACCGGCGGTat                                                                        >  1:1021485/1‑148 (MQ=255)                                                                      aCAGCGCCGCGCCGACGGTATTGGTGACCATCATTGGCGCAGCAATATTACTCACCAGACGCACCGCATCTTCATTAGGTCGGGCGATCGCAAGGATGATCAGCATTTGCACCATTTCAGCGACGAACGTGACGGCACCGGCGGTAATg                                                                      >  1:931641/1‑149 (MQ=255)                                                                      aCAGCGCCGCGCCGACGGTATTGGTGACCATCATTGGCGCAGCAATATTACTCACCAGACGCACCGCATCTTCATTAGGTCGGGCGATCGCAAGGATGAGCAGCATTTGCACCCTTTCAGCGACGAACGTGACGGCACCGGCGGTAATg                                                                      >  2:891048/1‑149 (MQ=255)                                                                       cAGCGCCGCGCCGACGGGATTGGTGACCATCATTGGCGCAGCAATATTACTCACCAGACGCACCGCATCTTCATTAGGTCGGGCGATCGCAAGGATGATCAGCATTTGCACCATTTCAGCGACGAACGTGACGGCACCGGCGGTAATgg                                                                     <  1:116724/149‑1 (MQ=255)                                                                           tccgcgccgGCGGTATTGGTGACCATAATTGGCGCAGCAATATTACTCACCAGACGAACCGCATCTTCATTAGGTCGCGAGATAGCAAGGATCATCAGCATATGCACCATTTCAGCGACGAACATTACGGCAACGGCAGTAATGGGGtg                                                                 >  2:675933/2‑148 (MQ=255)                                                                                gccgACGGTAGTTGTGACCATCATGGGCGCAGCAATATTACTCACCAGACGCACCGCATCTTCATTAGGTCGGGCGATCGCAAGGATGATCAGCATTTGCACCATTTCAGCGACGAACGTGACGGCACCGGCGGTAATGGGGTTAAAGa                                                            <  2:692996/149‑1 (MQ=255)                                                                                  cgACGGTACTGGTGACCATCATTGGCGCAGCAATATTACTCACCAGACGCACTGCATCTTCATTAGGTCGGGCGATCGCAAGGATGATCAGCATTTGCACCATTTCAGCGACGAACGTGACGGCACCGGCGGTAATGGGGTTAAAGACt                                                          <  2:1019139/149‑1 (MQ=255)                                                                                    gcGGTATTGGTGACCATCATTGGCGCAGCAATATTACTCACCAGACGCACCGCATCTTCATTAGGTCGGGCGATCGCAAGGATGATCAGCATTTGCACCATTTCAGCGACGAACGTGACGGCACCGGCGGTAATGGGGTTAAAGACttt                                                        <  2:195416/148‑1 (MQ=255)                                                                                       gTATTGGTGACCATCATTGGCGCAGCAATATTACTCACCAGACGCACCGCATCTTCATTAGGTCGGGCGATCGCAAGGATGATCAGCATTTGCACCATTTCAGCGACGAACGTGACGGCACCGGCGGTAATGGGGTTAAAGACTTTATc                                                     <  2:931641/149‑1 (MQ=255)                                                                                        tATTGGTGACCATCATTGGCGCAGCAATATTACTCACCAGACGCACCGCATCTTCATTAGGTCGGGCGATCGCAAGGATGATCAGCATTTGCACCATTTCAGCGACGAACGTGACGGCACCGGCGGTAATGGGGTTAAAGACTTTATCa                                                    >  1:476322/1‑149 (MQ=255)                                                                                        gaTTGGTGACCATCATTGGCGCAGCAATATTACTCACCAGACGCACCGCATCTTCATTAGGTCGGGCGATCGCAAGGATGATCAGCATTTGCACCATTTCAGCGACGAACGTGACGGCACCGGCGGTAATGGGGTTAAAGACTTTATCa                                                    <  1:876816/148‑1 (MQ=255)                                                                                            ggTGACCATCATTGGCGCAGCAATATTACTCACCAGACGCACCGCATCTTCATTAGGTCGGGCGATCGCAAGGATGATCAGCATTTGCACCATTTCAGCGACGAACGTGACGGCACCGGCGGTAATGGGGTTAAAGACTTTATCAGTgc                                                >  2:603746/1‑149 (MQ=255)                                                                                              tGACCATCATTGGCGCAGCAATATTACTCACCAGACGCACCGCATCTTCATTAGGTCGGGCGATCGCAAGGATGATCAGCATTTGCACCATTTCAGCGACGAACGTGACGGCACCGGCGGTAATGGGGTTAAAGACTTTATCAGTgcgc                                              <  1:221604/149‑1 (MQ=255)                                                                                                    tgatTGGCGCAGCAATATTACTCACCAGACGCACCGCATCTTCATTAGGTCGGGCGATCGCAAGGATGATCAGCATTTGCACCATTTCAGCGACGAACGTGACGGCACCGGCGGTAATGGGGTTAAAGACTTTATCAGTGCGCCCgcgg                                        >  2:11154/3‑149 (MQ=255)                                                                                                            gcagcaATATTACTCACCAGACGCACCGCATCTTCATTAGGTCGGGCGATCGCAAGGATGATCAGCATTTGCACCATTTCAGCGACGAACGTGACGGCACCGGCGGTAATGGGGTTAAAGACTTTATCAGTGCGCCCGCGGCGGATCAg                                <  1:831968/149‑1 (MQ=255)                                                                                                                caATATTACTCACCAGACGCACCGCATCTTCATTAGGTCGGGCGATCGCAAGGATGATCAGCATTTGCACCATTTCAGCGACGAACGTGACGGCACCGGCGGTAAGGAGGTTAAAGACTTTAGCCGTGCGCCCGCCGCGGGTCAGGATg                            >  2:709978/1‑149 (MQ=255)                                                                                                                  atatTACTCACCAGACGCACCGCATCTTCATTAGGTCGGGCGATCGCAAGGATGATCAGCATTTGCACCATTTCAGCGACGAACGTGACGGCACCGGCGGTAATGGGGTTAAAGACTTTATCAGTGCGCCCGCGGCGGATCAGGATGCt                          <  2:382011/149‑1 (MQ=255)                                                                                                                        cTCACCAGACGCACCGCAACTTCATTAGGTCGGGCGCTCGCAAGGATGATCCGCATTTGCACCATTTCAGCGACGAACGTGCCGGCACCGGCGGTAAGGGGGTTAAAGACTTTCTCAGTGCGCCCGCGCCGGACCACGATGCCGTGTAc                    >  2:126096/1‑149 (MQ=255)                                                                                                                         tCACCAGACGCACCGCATCTTCATTAGGTCGGGCGATCGCAAGGATGATCAGCATTTGCACCATTTCAGCGACGAACGTGACGGCACCGGCGGTAATGGGGTTAAAGACTTTATCCGTGCGCCCGCGGCGGATCAGGATGCTGGGTAcc                   >  2:870065/1‑149 (MQ=255)                                                                                                                         tCACCAGACGCACCGCATCTTCATTAGGTCGGGCGATCGCAAGGATGATCAGCATTTGCACCATTTCAGCGACGAACGTGACGACACCGGCGGTAATGGAGCTAAAGACTTTATCAGTACGCCCCCGGCGAAGCAGAATACtgtggtac                   >  2:298954/1‑145 (MQ=255)                                                                                                                          catcAGACGCACCGCATCTTCATTAGGTCGGGCGATCGCAAGGATGATCAGCATTTGCACCATTTCAGCGACGAACGTGACGGCACCGGCGGTAATGGGGTTAAAGACTTTATCAGTGCGCCCGCGGCGGATCAGGATGCTGTGTACCa                  <  1:267978/146‑1 (MQ=255)                                                                                                                          cACCAGACGCACCGCATCTTCATTAGGTCGGGCGATCGCAAGGATGATCAGCATTTGCACCATTTCAGCGACGAACGTGACGGCACCGGCGGTAATGGGGTTAAAGACTTTATCAGTGCGCCCGCGGCGGATCAGGATGCTGTGTACCa                  <  2:13166/149‑1 (MQ=255)                                                                                                                           aCCAGACGCACCGGATCTTCATTAGGTCTGGCGATCGCAAGGATGATCAGCATTTGCACCATTTCAGCGACGAACGTGACGGCACCGGCGGTAATGGGGTTAAAGACTTTATCAGTGCGCCCGCGGCGGATCAGGAAGCTATTTAccgg                 <  2:11491/149‑3 (MQ=255)                                                                                                                           aCCAGACGCACCGCATCTTCATTAGGTCGGGCGATCGCAAGGATGATCAGCATTTGCACCATTTCAGCGACGAACGTGACGGCACCGGCGGTAATGAGGTTAAAGACTTTATCAGTGCGCCCGCGGCGGATCAGGAGGCTGTGTACCAg                 >  2:15538/1‑149 (MQ=255)                                                                                                                             cAGACGCACCGCATCTTCATTAGGTCGGGCGATCGCAAGGATGATCAGCATTTGCACCATTTCAGCGACGAACGTGACGGCACCGGCGGTAATGGGGTTAAAGACTTTATCAGTGCGCCCGCGGCGGATCAGGATGCTGTGTACCAGGc               <  1:31446/149‑1 (MQ=255)                                                                                                                                   cACCGCATCTTCATTAGGTCGGGCGATCGCAAGGATGATCAGCATTTGCACCATTTCAGCGACGAACGTGACGGCACCGGCGGTAATGGGGTTAAAGACTTTATCAGTGCGCCCGCGGCGGATCAGGATGCTGTGTACCAGGCCACCGa         <  1:603746/149‑1 (MQ=255)                                                                                                                                   cACCGCATCTTCATTAGGTCGGGCGATCGCAAGGATGATCAGCATTTGCACCATTTCAGCGACGAACGTGACGGCACCGGCGGTAATGGGGTTAAAGACTTTATCAGTGCGCCCGCGGCGGATCAGGATGCTGTGTACCAGGCCACCGa         <  1:11154/149‑1 (MQ=255)                                                                                                                                          tCTTCATTAGGTCGGGCGATCGCAAGGATGATCAGCATTTGCACCATTTCAGCGACGAACGTGACGGCACCGGCGGTAATGGGGTTAAAGACTTTATCAGTGCGCCCGCGGCGGATCAGGATGCTGTGTACCAGGCCACCGAGTAATcc  >  1:400882/1‑149 (MQ=255)                                                                                                                                                 |                                                                                                                                              GCGCAGTGGCAGAAAAAGCCGAAGTGTATTTTTCAAACATCGCGCGTTTATCGAGCAATATACGCATAAACAGCGCCGCGCCGACGGTATTGGTGACCATCATTGGCGCAGCAATATTACTCACCAGACGCACCGCATCTTCATAAGGTCGGGCGATCGCAAGGATGATCAGCATTTGCACCATTTCAGCGACGAACGTGACGGCACCGGCGGTAATGGGGTTAAAGACTTTATCAGTGCGCCCGCGGCGGATCAGGATGCTGTGTACCAGGCCACCGAGTAATCC  >  NC_000913_3_vch_tpiA/2214008‑2214293

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: ‑