Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	2,492,743	(A)5→4	coding (594/1698 nt)	ypdA →	two‑component system sensor histidine kinase YpdA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	2,492,739	0	A	.	100.0%	112.8 / NA	27	coding (590/1698 nt)	ypdA	two‑component system sensor histidine kinase YpdA
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base . (17/10);  total (17/10)

ATCGTCTCTAAAATCGGCATTCCAATGATCCTCGGTAGCGTCTGTATCGGCTTTATTGTGCTTCTGGTGCAAAGCGTTGAGGGCGAAAAAGAGGCCAGCGCCGCGCGGCAGGCCAAGCTGGCGCTGGATATCGCCAACAAAACGCTACCGCTGTTTCGCCATGTCAATAGC  >  NZ_CP009273/2492654‑2492824                                                                                      |                                                                                      atCGTCTCTAAAATCGGCATTCCAATGATCCTCGGTAGCGTCTGTATCGGCTTTATTGTGCTTCTGGTGCAAAGCGTTGAGGGCGaaaag                                                                                   <  2:674645/90‑2 (MQ=255)               cGGCATTCCAATGATCCTCGGTAGCGTCTGTATCGGCTTTATTGTGCTTCTGGTGCAAAGCGTTGAGGGCG‑AAAAGAGGCCAGCGCcgcg                                                                    >  1:17279/1‑90 (MQ=255)               cGGCATTCCAATGATCCTCGGTAGCGTCTGTATCGGCTTTATTGTGCTTCTGGTGCAAAGCGTTGAGGGCG‑AAAAGAGGCCAGCGCcgcg                                                                    >  1:75194/1‑90 (MQ=255)                   aTTCCAATGATCCTCGGTAGCGTCTGTATCGGCTTTATTGTGCTTCTGGTGCAAAGCGTTGAGGGCG‑AAAAGAGGCCAGCGCCGCGCGGc                                                                <  2:609530/90‑1 (MQ=255)                   aTTCCAATGATCCTCGGTAGCGTCTGTATCGGCTTTATTGTGCTTCTGGTGCAAAGCGTTGAGGGCG‑AAAAGAGGCCAGCGCCGCGCGGc                                                                <  1:548928/90‑1 (MQ=255)                    ttCCAATGATCCTCGGTAGCGTCTGTATCGGCTTTATTGTGCTTCTGGTGCAAAGCGTTGAGGGCG‑AAAAGAGGCCAGCGCCGCGCGGCa                                                               >  2:61335/1‑90 (MQ=255)                         aTGATCCTCGGTAGCGTCTGTATCGGCTTTATTGTGCTTCTGGTGCAAAGCGTTGAGGGCG‑AAAAGAGGCCAGCGCCGCGCGGCAGGCCa                                                          <  1:723795/90‑1 (MQ=255)                             tCCTCGGTAGCGTCTGTATCGGCTTTATTGTGCTTCTGGTGCAAAGCGTTGAGGGCG‑AAAAGAGGCCAGCGCCGCGCGGCAGGCCAAGCt                                                      <  2:98104/90‑1 (MQ=255)                                  ggTAGCGTCTGTATCGGCTTTATTGTGCTTCTGGTGCAAAGCGTTGAGGGCG‑AAAAGAGGCCAGCGCCGCGCGGCAGGCCAAGCTGgcgc                                                 <  2:600373/90‑1 (MQ=255)                                        gTCTGTATCGGCTTTATTGTGCTTCTGGTGCAAAGCGTTGAGGGCG‑AAAAGAGGCCAGCGCCGCGCGGCAGGCCAAGCTGGCGCTGGata                                           >  2:27626/1‑90 (MQ=255)                                        gTCTGTATCGGCTTTATTGTGCTTCTGGTGCAAAGCGTTGAGGGCG‑AAAAGAGGCCAGCGCCGCGCGGCAGGCCAAGCTGGCGCTGGata                                           >  2:156455/1‑90 (MQ=255)                                                 ggCTTTATTGTGCTTCTGGTGCAAAGCGTTGAGGGCG‑AAAAGAGGCCAGCGCCGCGCGGCAGGCCAAGCTGGCGCTGGATATCGCcaaca                                  >  1:389937/1‑90 (MQ=255)                                                  gCTTTATTGTGCTTCTGGTGCAAAGCGTTGAGGGCG‑AAAAGAGGCCAGCGCCGCGCGGCAGGCCAAGCTGGCGCTGGATATCGCcaacaa                                 >  2:469073/1‑90 (MQ=255)                                                  gCTTTATTGTGCTTCTGGTGCAAAGCGTTGAGGGCG‑AAAAGAGGCCAGCGCCGCGCGGCAGGCCAAGCTGGCGCTGGATATCGCcaacaa                                 >  2:660864/1‑90 (MQ=255)                                                     ttATTGTGCTTCTGGTGCAAAGCGTTGAGGGCG‑AAAAGAGGCCAGCGCCGCGCGGCAGGCCAAGCTGGCGCTGGATATCGCCAACAAAAc                              <  1:860851/90‑1 (MQ=255)                                                            gCTTCTGGTGCAAAGCGTTGAGGGCG‑AAAAGAGGCCAGCGCCGCGCGGCAGGCCAAGCTGGCGCTGGATATCGCCAACAAAACGCTACCg                       >  1:613423/1‑90 (MQ=255)                                                            gCTTCTGGTGCAAAGCGTTGAGGGCG‑AAAAGAGGCCAGCGCCGCGCGGCAGGCCAAGCTGGCGCTGGATATCGCCAACAAAACGCTACCg                       >  2:57296/1‑90 (MQ=255)                                                             cTTCTGGTGCAAAGCGTTGAGGGCG‑AAAAGAGGCCAGCGCCGCGCGGCAGGCCAAGCTGGTGCTGGATATCGCCAACAAAACGCTACCGc                      <  1:520673/90‑1 (MQ=255)                                                               tCTGGTGCAAAGCGTTGAGGGCG‑AAAAGAGGCCAGCGCCGCGCGGCAGGCCAAGCTGGCGCTGGATATCGCCAACAAAACGCTACCGCTg                    >  1:659749/1‑90 (MQ=255)                                                               tCTGGTGCAAAGCGTTGAGGGCG‑AAAAGAGGCCAGCGCCGCGCGGCAGGCCAAGCTGGCGCTGGATATCGCCAACAAAACGCTACCGCTg                    >  2:413200/1‑90 (MQ=255)                                                               tCTGGTGCAAAGCGTTGAGGGCG‑AAAAGAGGCCAGCGCCGCGCGGCAGGCCAAGCTGGCGCTGGATATCGCCAACAAAACGCTACCGCTg                    >  1:473312/1‑90 (MQ=255)                                                                    tGCAAAGCGTTGAGGGCG‑AAAAGAGGCCAGCGCCGCGCGGCAGGCCAAGCTGGCGCTGGATATCGCCAACAAAACGCTACCGCTGTTTCg               >  1:208842/1‑90 (MQ=255)                                                                       aaaGCGTTGAGGGCG‑AAAAGAGGCCAGCGCCGCGCGGCAGGCCAAGCTGGCGCTGGATATCGCCAACAAAACGCTACCGCTGTTTCGCCa            <  1:436410/90‑1 (MQ=255)                                                                       aaaGCGTTGAGGGCG‑AAAAGAGGCCAGCGCCGCGCGGCAGGCCAAGCTGGCGCTGGATATCGCCAACAAAACGCTACCGCTGTTTCGCCa            >  1:142947/1‑90 (MQ=255)                                                                           cGTTGAGGGCG‑AAAAGAGGCCAGCGCCGCGCGGCAGGCCAAGCTGGCGCTGGATATCGCCAACAAAACGCTACCGCTGTTTCGCCATGTc        <  1:660864/90‑1 (MQ=255)                                                                            gTTGAGGGCG‑AAAAGAGGCCAGCGCCGCGCGGCAGGCCAAGCTGGCGCTGGATATCGCCAACAAAACGCTACCGCTGTTTCGCCATGTCa       <  2:100389/90‑1 (MQ=255)                                                                                 gggCG‑AAAAGAGGCCAGCGCCGCGCGGCAGGCCAAGCTGGCGCTGGATATCGCCAACAAAACGCTACCGCTGTTTCGCCATGTCAATAGc  >  1:692354/1‑90 (MQ=255)                                                                                 gggCG‑AAAAGAGGCCAGCGCCGCGCGGCAGGCCAAGCTGGCGCTGGATATCGCCAACAAAACGCTACCGCTGTTTCGCCATGTCAATAGc  >  1:307801/1‑90 (MQ=255)                                                                                      |                                                                                      ATCGTCTCTAAAATCGGCATTCCAATGATCCTCGGTAGCGTCTGTATCGGCTTTATTGTGCTTCTGGTGCAAAGCGTTGAGGGCGAAAAAGAGGCCAGCGCCGCGCGGCAGGCCAAGCTGGCGCTGGATATCGCCAACAAAACGCTACCGCTGTTTCGCCATGTCAATAGC  >  NZ_CP009273/2492654‑2492824

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 23 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑