Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	965,365	T→C	M174T (ATG→ACG)	ycaQ →	winged helix DNA‑binding protein YcaQ

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	965,365	0	T	C	100.0%	179.4 / NA	50	M174T (ATG→ACG)	ycaQ	winged helix DNA‑binding protein YcaQ
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (23/27);  total (23/27)

GCATATTCATGATAAGGGGCCGGTACGTTCAGCCGATTTTGAGCATCCTCGTAAAGGTGCAAGCGGCTGGTGGGAATGGAAGCCGCATAAACGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGATGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCCACCGTGTCATGCCTGACTGGGATGATGAGCGCGATCTCGTTTCGCAAACAGAAGCAGAAATCATCATGCTGGATAACAGTGCGCG  >  NZ_CP009273/965237‑965494                                                                                                                                 |                                                                                                                                  gCATATTCATGATAAGGGGCCGGTACGTTCAGCCGATTTTGAGCATCCTCGTAAAGGTGCAAGCGGCTGGTGGGAATGGAAGCCGCATAAACGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGaa                                                                                                                         <  1:228321/139‑1 (MQ=255) gCATATTCATGATAAGGGGCCGGTACGTTCAGCCGATTTTGAGCATCCTCGTAAAGGTGCAAGCGGCTGGTGGGAATGGAAGCCGCATAAACGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGaa                                                                                                                         >  1:760126/1‑139 (MQ=255)   atatTCATGATAAGGGGCCGGTACGTTCAGCCGATTTTGAGCATCCTCGTAAAGGTGCAAGCGGCTGGTGGGAATGGAAGCCGCATAAACGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACg                                                                                                                       >  1:102723/1‑139 (MQ=255)   atatTCATGATAAGGGGCCGGTACGTTCAGCCGATTTTGAGCATCCTCGTAAAGGTGCAAGCGGCTGGTGGGAATGGAAGCCGCATAAACGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACg                                                                                                                       >  1:806348/1‑139 (MQ=255)              aaGGGGCCGGTACGTTCAGCCGATTTTGAGCATCCTCGTAAAGGTGCAAGCGGCTGGTGGGAATGGAAGCCGCATAAACGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTc                                                                                                             >  1:827682/1‑138 (MQ=255)               aGGGGCCGGTACGTTCAGCCGATTTTGAGCATCCTCGTAAAGGTGCAAGCGGCTGGTGGGAATGGAAGCCGCATAAACGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCa                                                                                                           <  2:827682/139‑1 (MQ=255)                ggggCCGGTACGTTCAGCCGATTTTGAGCATCCTCGTAAAGGTGCAAGCGGCTGGTGGGAATGGAAGCCGCATAAACGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAg                                                                                                          >  2:177028/1‑139 (MQ=255)                ggggCCGGTACGTTCAGCCGATTTTGAGCATCCTCGTAAAGGTGCAAGCGGCTGGTGGGAATGGAAGCCGCATAAACGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAg                                                                                                          >  1:361862/1‑139 (MQ=255)                   gCCGGTACGTTCAGCCGATTTTGAGCATCCTCGTAAAGGTGCAAGCGGCTGGTGGGAATGGAAGCCGCATAAACGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAgcgc                                                                                                       >  1:141151/1‑139 (MQ=255)                   gCCGGTACGTTCAGCCGATTTTGAGCATCCTCGTAAAGGTGCAAGCGGCTGGTGGGAATGGAAGCCGCATAAACGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAgcgc                                                                                                       >  2:578810/1‑139 (MQ=255)                   gCCGGTACGTTCAGCCGATTTTGAGCATCCTCGTAAAGGTGCAAGCGGCTGGTGGGAATGGAAGCCGCATAAACGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAgcgc                                                                                                       >  2:318910/1‑139 (MQ=255)                     cGGTACGTTCAGCCGATTTTGAGCATCCTCGTAAAGGTGCAAGCGGCTGGTGGGAATGGAAGCCGCATAAACGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGt                                                                                                     >  1:4510/1‑139 (MQ=255)                     cGGTACGTTCAGCCGATTTTGAGCATCCTCGTAAAGGTGCAAGCGGCTGGTGGGAATGGAAGCCGCATAAACGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGt                                                                                                     >  2:902/1‑139 (MQ=255)                     cGGTACGTTCAGCCGATTTTGAGCATCCTCGTAAAGGTGCAAGCGGCTGGTGGGAATGGAAGCCGCATAAACGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGt                                                                                                     >  2:259708/1‑139 (MQ=255)                      ggTACGTTCAGCCGATTTTGAGCATCCTCGTAAAGGTGCAAGCGGCTGGTGGGAATGGAAGCCGCATAAACGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGtt                                                                                                    <  2:580714/139‑1 (MQ=255)                       gTACGTTCAGCCGATTTTGAGCATCCTCGTAAAGGTGCAAGCGGCTGGTGGGAATGGAAGCCGCATAAACGGCATCTGGCAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGtt                                                                                                    >  2:149716/1‑138 (MQ=255)                        tACGTTCAGCCGATTTTGAGCATCCTCGTAAAGGTGCAAGCGGCTGGTGGGAATGGAAGCCGCATAAACGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGTTTa                                                                                                  <  1:420730/139‑1 (MQ=255)                        tACGTTCAGCCGATTTTGAGCATCCTCGTAAAGGTGCAAGCGGCTGGTGGGAATGGAAGCCGCATAAACGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGTTTa                                                                                                  <  2:760126/139‑1 (MQ=255)                                 ccGATTTTGAGCATCCTCGTAAAGGTGCAAGCGGCTGGTGGGAATGGAAGCCGCATAAACGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAAc                                                                                         >  2:745577/1‑139 (MQ=255)                                 ccGATGTTGAGCATCCTCGTAAAGGTGCAAGCGGCTGGTGGGAATGGAAGCCGCATAAACGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAAc                                                                                         <  2:288926/139‑1 (MQ=255)                                     ttttGAGCATCCTCGTAAAGGTGCAAGCGGCTGGTGGGAATGGAATCCGCATAAACGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCCAc                                                                                     <  1:169713/139‑1 (MQ=255)                                     ttttGAGCATCCTCGTAAAGGTGCAAGCGGCTGGTGGGAATGGAAGCCGCATAAACGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCCAc                                                                                     <  2:106856/139‑1 (MQ=255)                                     ttttGAGCATCCTCGTAAAGGTGCAAGCGGCTGGTGGGAATGGAAGCCGCATAAACGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCCAc                                                                                     <  2:651594/139‑1 (MQ=255)                                     ttttGAGCATCCTCGTAAAGGTGCAAGCGGCTGGTGGGAATGGAAGCCGCATAAACGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCCAc                                                                                     <  1:286704/139‑1 (MQ=255)                                     ttttGAGCATCCTCGTAAAGGTGCAAGCGGCTGGTGGGAATGGAAGCCGCATAAACGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCCAc                                                                                     <  2:433280/139‑1 (MQ=255)                                              tCCTCGTAAAGGTGCAAGCGGCTGGTGGGAATGGAAGCCGCATAAACGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCCACCGTGTCATg                                                                            <  2:23889/139‑1 (MQ=255)                                               ccTCGTAAAGGTGCAAGCGGCTGGTGGGAATGGAAGCCGCATAAACGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCCACCGTGTCATGc                                                                           >  2:95600/1‑139 (MQ=255)                                                cTCGTAAAGGTGCAAGCGGCTGGTGGGAATGGAAGCCGCATAAACGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCCACCGTGTCATGc                                                                           <  2:553423/138‑1 (MQ=255)                                                   gTAAAGGTGCAAGCGGCTGGTGGGAATGGAAGCCGCATAAACGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCCACCGTGTCATGCCTGa                                                                       <  1:181041/139‑1 (MQ=255)                                                      aaGGTGCAAGCGGCTGGTGGGAATGGAAGCCGCATAAACGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCCACCGTGTCATGCCTGACt                                                                     <  2:806348/138‑1 (MQ=255)                                                      aaGGTGCAAGCGGCTGGTGGGAATGGAAGCCGCATAAACGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCCACCGTGTCATGCCTGACt                                                                     <  2:522342/138‑1 (MQ=255)                                                         gTGCAAGCGGCTGGTGGGAATGGAAGCCGCATAAACGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCCACCGTGTCATGCCTGACTGGga                                                                 >  2:253195/1‑139 (MQ=255)                                                            cAAGCGGCTGGTGGGAATGGAAGCCGCATAAACGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCCACCGTGTCATGCCTGACTGGgatg                                                               <  2:443996/138‑1 (MQ=255)                                                                cGGCTGGTGGGAATGGAAGCCGCATAAACGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCCACCGTGTCATGCCTGACTGGGATGATGAg                                                          <  1:902/139‑1 (MQ=255)                                                                            aTGGAAGCCGCATAAACGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCCACCGTGTCATGCCTGACTGGGATGATGAGCGCGATCTCGtt                                              >  2:583926/1‑139 (MQ=255)                                                                             tGGAAGCCGCATAAACGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGTTTa                                                                                                  >  1:200543/1‑86 (MQ=255)                                                                             tGGAAGCCGCATAAACGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGTTTa                                                                                                  <  2:200543/86‑1 (MQ=255)                                                                                aaGCCGCATAAACGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCCACCGTGTCATGCCTGACTGGGATGATGAGCGCGATCTCGTTTCg                                           >  2:679606/1‑138 (MQ=255)                                                                                aaGCCGCATAAACGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCCACCGTGTCATGCCTGACTGGGATGATGAGCGCGATCTCGTTTCg                                           >  2:107226/1‑138 (MQ=255)                                                                                 aGCCGCATAAACGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCCACCGTGTCATGCCTGACTGGGATGATGAGCGCGATCTCGTTTCGCa                                         <  1:745577/139‑1 (MQ=255)                                                                                                     gAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCCACCGTGTCATGCCTGACTGGGATGATGAGCGCGATCTCGTTTCGCAAACAGAAGCAGAAAtcatca                     <  2:102723/139‑1 (MQ=255)                                                                                                     gAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCCACCGTGTCATGCCTGACTGGGATGATGAGCGCGATCTCGTTTCGCAAACAGAAGCAGAAAtcatca                     <  1:230746/139‑1 (MQ=255)                                                                                                     gAAGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCCACCGTGTCATGCCTGACTGGGATGATGAGCGCGATCTCGTTTCGCAAACAGAAGCAGAAAtcatca                     <  1:95600/139‑1 (MQ=255)                                                                                                       aGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCCACCGTGTCATGCCTGACTGGGATGATGAGCGCGATCTCGTTTCGCAAACAGAAGCAGAAATCATCATg                   <  2:568204/139‑1 (MQ=255)                                                                                                       aGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCCACCGTGTCATGCCTGACTGGGATGATGAGCGCGATCTCGTTTCGCAAACAGAAGCAGAAATCATCATg                   <  1:15125/139‑1 (MQ=255)                                                                                                       aGGTTTATTTACTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCCACCGTGTCATGCCTGACTGGGATGATGAGCGCGATCTCGTTTCGCAAACAGAAGCAGAAATCATCATg                   >  1:736707/1‑139 (MQ=255)                                                                                                             atttaCTGCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCCACCGTGTCATGCCTGACTGGGATGATGAGCGCGATCTCGTTTCGCAAACAGAAGCAGAAATCATCATGCTGGa              >  2:508581/1‑138 (MQ=255)                                                                                                                    gCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCCACCGTGTCATGCCTGACTGGGATGATGAGCGCGATCTCGTTTCGCAAACAGAAGCAGAAATCATCATGCTGGa              <  2:298829/131‑1 (MQ=255)                                                                                                                    gCCGGAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCCACCGTGTCATGCCTGACTGGGATGATGAGCGCGATCTCGTTTCGCAAACAGAAGCAGAAATCATCATGCTGGa              >  1:298829/1‑131 (MQ=255)                                                                                                                        gAAAGGTGACGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCCACCGTGTCATGCCTGACTGGGATGATGAGCGCGATCTCGTTTCGCAAACAGAAGCAGAAATCATCATGCTGGATAACAGTGcgcg  <  1:197621/139‑1 (MQ=255)                                                                                                                                 |                                                                                                                                  GCATATTCATGATAAGGGGCCGGTACGTTCAGCCGATTTTGAGCATCCTCGTAAAGGTGCAAGCGGCTGGTGGGAATGGAAGCCGCATAAACGGCATCTGGAAGGTTTATTTACTGCCGGAAAGGTGATGGTGATTGAACGGCGCAACTTCCAGCGCGTTTATGATTTAACCCACCGTGTCATGCCTGACTGGGATGATGAGCGCGATCTCGTTTCGCAAACAGAAGCAGAAATCATCATGCTGGATAACAGTGCGCG  >  NZ_CP009273/965237‑965494

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑