Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	3,994,419	T→C	intergenic (‑3/‑159)	yigE ← / → ysgD	phosphodiester glycosidase family protein/protein YsgD

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	3,994,419	0	T	C	100.0%	155.5 / NA	41	intergenic (‑3/‑159)	yigE/ysgD	phosphodiester glycosidase family protein/protein YsgD
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (20/21);  total (20/21)

TCAGCGTCGGATCTGAGAGTGCGCAATCATCAGCGGCAACAGCAAACAAGGGAAGTAAGGTGAGGGCGAGAAAAATCCGTTTGAGATTCAAGGTGATCATTCCTTTACCAATGAGTAGCTGATGCGCCATTATAGGTCCTGGATGTGGGATTTTTTTATCCTGTTAGCGACCTTGACGAGTACCAAAAAGCGCGAAGTTCAACTATTGTTCTGTGGTGTTCTGTTGCGTGTTGACGGCAAAATTTTGCTGGCGTAACATGCGCGCACG  >  NZ_CP009273/3994287‑3994554                                                                                                                                     |                                                                                                                                        tCAGCGTCGGATCTGAGAGTGCGCAATCATCAGCGGCGACAGCAAACAAGGGAAGTAAGGTGAGGGCGAGAAAAATCCGTTTGAGATTCAAGGTGATCATTCCTTTACCAATGAGTAGCTGATGCGCCATTACAGGTcc                                                                                                                                   >  1:276088/1‑139 (MQ=255)   aGCGTCGGATCTGAGAGTGCGCAATCATCAGCGGCGACAGCAAACAAGGGAAGTAAGGTGAGGGCGAGAAAAATCCGTTTGAGATTCAAGGTGATCATTCCTTTACCAATGAGTAGCTGATGCGCCATTACAGGTCCt                                                                                                                                  <  1:310623/138‑1 (MQ=255)   aGCGTCGGATCTGAGAGTGCGCAATCATCAGCGGCGACAGCAAACAAGGGAAGTAAGGTGAGGGCGAGAAAAATCCGTTTGAGATTCAAGGTGATCATTCCTTTACCAATGAGTAGCTGATGCGCCATTACAGGTCCt                                                                                                                                  >  2:310623/1‑138 (MQ=255)                agagTGCGCAATCATCAGCGGCGACAGCAAACAAGGGAAGTAAGGTGAGGGCGAGAAAAATCCGTTTGAGATTCAAGGTGATCATTCCTTTACCAATGAGTAGCTGATGCGCCATTACAGGTCCTGGATGTGGGa                                                                                                                        <  2:118992/135‑1 (MQ=255)                      cgcAATCATCAGCGGCGACAGCAAACAAGGGAAGTAAGGTGAGGGCGAGAAAAATCCGTTTGAGATTCAAGGTGATCATTCCTTTACCAATGAGTAGCTGATGCGCCATTACAGGTCCTGGATGTGGGATTTTTTTATc                                                                                                              >  1:332299/1‑139 (MQ=255)                      cgcAATCATCAGCGGCGACAGCAAACAAGGGAAGTAAGGTGAGGGCGAGAAAAATCCGTTTGAGATTCAAGGTGATCATTCCTTTACCAATGAGTAGCTGATGCGCCATTACAGGTCCTGGATGTGGGATTTTTTTATc                                                                                                              >  1:850914/1‑139 (MQ=255)                      cgcAATCATCAGCGGCGACAGCAAACAAGGGAAGTAAGGTGAGGGCGAGAAAAATCCGTTTGAGATTCAAGGTGATCATTCCTTTACCAATGAGTAGCTGATGCGCCATTACAGGTCCTGGATGTGGGATTTTTTTATc                                                                                                              <  1:454032/139‑1 (MQ=255)                             atcaGCGGCGACAGCAAACAAGGGAAGTAAGGTGAGGGCGAGAAAAATCCGTTTGAGATTCAAGGTGATCATTCCTTTACCAATGAGTAGCTGATGCGCCATTACAGGTCCTGGATGTGGGATTTTTTTATCCTGTTAg                                                                                                       <  2:308736/139‑1 (MQ=255)                                                        tAAGGTGAGGGCGAGAAAAATCCGTTTGAGATTCAAGGTGATCATTCCTTTACCAATGAGTAGCTGATGCGCCATTACAGGTCCTGGATGTGGGATTTTTTTATCCTGTTAGCGACCTTGACGAGTACCAAAAAGcgcg                                                                            <  1:19768/139‑1 (MQ=255)                                                        tAAGGTGAGGGCGAGAAAAATCCGTTTGAGATTCAAGGTGATCATTCCTTTACCAATGAGTAGCTGATGCGCCATTACAGGTCCTGGATGTGGGATTTTTTTATCCTGTTAGCGACCTTGACGAGTACCAAAAAGcgcg                                                                            <  2:88466/139‑1 (MQ=255)                                                          aGGTGAGGGCGAGAAAAATCCGTTTGAGATTCAAGGTGATCATTCCTTTACCAATGAGTAGCTGATGCGCCATTACAGGTCCTGGATGTGGGATTTTTTTATCCTGTTAGCGACCTTGACGAGTACCAAAAAGcgcg                                                                            >  2:827406/1‑137 (MQ=255)                                                               aGGGCGAGAAAAATCCGTTTGAGATTCAAGGTGATCATTCCTTTACCAATGAGTAGCTGATGCGCCATTACAGGTCCTGGATGTGGGATTTTTTTATCCTGTTAGCGACCTTGACGAGTACCAAAAAGCGCGAAGTTc                                                                      <  2:678131/138‑1 (MQ=255)                                                               aGGGCGAGAAAAATCCGTTTGAGATTCAAGGTGATCATTCCTTTACCAATGAGTAGCTGATGCGCCATTACAGGTCCTGGATGTGGGATTTTTTTATCCTGTTAGCGACCTTGACGAGTACCAAAAAGCGCGAAGTTc                                                                      <  1:410343/138‑1 (MQ=255)                                                                 ggCGAGAAAAATCCGTTTGAGATTCAAGGTGATCATTCCTTTACCAATGAGTAGCTGATGCGCCATTACAGGTCCTGGATGTGGGATTTTTTTATCCTGTTAGCGACCTTGACGAGTACCAAAAAGCGCGAAGTTCAAc                                                                   >  2:640328/1‑139 (MQ=255)                                                                 ggCGAGAAAAATCCGTTTGAGATTCAAGGTGATCATTCCTTTACCAATGAGTAGCTGATGCGCCATTACAGGTCCTGGATGTGGGATTTTTTTATCCTGTTAGCGACCTTGACGAGTACCAAAAAGCGCGAAGTTCAAc                                                                   >  2:134950/1‑139 (MQ=255)                                                                   cGAGAAAAATCCGTTTGAGATTCAAGGTGATCATTCCTTTACCAATGAGTAGCTGATGCGCCATTACAGGTCCTGGATGTGGGATTTTTTTATCCTGTTAGCGACCTTGACGAGTACCAAAAAGCGCGAAGTTCAACTa                                                                 <  2:850914/139‑1 (MQ=255)                                                                   cGAGAAAAATCCGTTTGAGATTCAAGGTGATCATTCCTTTACCAATGAGTAGCTGATGCGCCATTACAGGTCCTGGATGTGGGATTTTTTTATCCTGTTAGCGACCTTGACGAGTACCAAAAAGCGCGAAGTTCAACTa                                                                 <  1:327907/139‑1 (MQ=255)                                                                       aaaaaTCCGTTTGAGATTCAAGGTGATCATTCCTTTACCAATGAGTAGCTGATGCGCCATTACAGGTCCTGGATGTGGGATTTTTTTATCCTGTTAGCGACCTTGAc                                                                                             >  1:598887/1‑107 (MQ=255)                                                                       aaaaaTCCGTTTGAGATTCAAGGTGATCATTCCTTTACCAATGAGTAGCTGATGCGCCATTACAGGTCCTGGATGTGGGATTTTTTTATCCTGTTAGCGACCTTGAc                                                                                             <  2:598887/107‑1 (MQ=255)                                                                              cGTTTGAGATTCAAGGTGATCATTCCTTTACCAATGAGTAGCTGATGCGCCATTACAGGTCCTGGATGTGGGATTTTTTTATCCTGTTAGCGACCTTGACGAGTACCAAAAAGCGCGAAGTTCAACTATTGTTCtgtg                                                       <  2:169467/138‑1 (MQ=255)                                                                                      aTTCAAGGTGATCATTCCTTTACCAATGAGTAGCTGATGCGCCATTACAGGTCCTGGATGTGGGa                                                                                                                        <  2:672276/65‑1 (MQ=255)                                                                                      aTTCAAGGTGATCATTCCTTTACCAATGAGTAGCTGATGCGCCATTACAGGTCCTGGATGTGGGa                                                                                                                        >  1:672276/1‑65 (MQ=255)                                                                                         cAAGGTGATCATTCCTTTACCAATGAGTAGCTGATGCGCCATTACAGGTCCTGGATGTGGGATTTTTTTATCCTGTTAGCGACCTTGACGAGTACCAAAAAGCGCGAAGTTCAACTATTGTTCTGTGGTGTTCTGTTGc                                           >  2:96775/1‑139 (MQ=255)                                                                                                aTCATTCCTTTACCAATGAGTAGCTGATGCGCCATTACAGGTCCTGGATGTGGGATTTTTTTATCCTGTTAGCGACCTTGACGAGTACCAAAAAGCGCGAAGTTCAACTATTGTTCTGTGGTGTTCTGTTGCGTGTTGa                                    >  2:326447/1‑139 (MQ=255)                                                                                                        tttACCAATGAGTAGCTGATGCGCCATTACAGGTCCTGGATGTGGGATTTTTTTATCCTGTTAGCGACCTTGACGAGTACCAAAAAGCGCGAAGTTCAACTATTGTTCTGTGGTGTTCTGTTGCGTGTTGACGGCaaaa                            >  2:695740/1‑139 (MQ=255)                                                                                                          tACCAATGAGTAGCTGATGCGCCATTACAGGTCCTGGATGTGGGATTTTTTTATCCTGTTAGCGACCTTGACGAGTACCAAAAAGCGCGAAGTTCAACTATTGTTCTGTGGTGTTCTGTTGCGTGTTGACGGCAAAAtt                          >  2:501710/1‑139 (MQ=255)                                                                                                            ccAATGAGTAGCTGATGCGCCATTACAGGTCCTGGATGTGGGATTTTTTTATCCTGTTAGCGACCTTGACGAGTACCAAAAAGcgcg                                                                            >  2:613890/1‑87 (MQ=255)                                                                                                            ccAATGAGTAGCTGATGCGCCATTACAGGTCCTGGATGTGGGATTTTTTTATCCTGTTAGCGACCTTGACGAGTACCAAAAAGcgcg                                                                            <  1:613890/87‑1 (MQ=255)                                                                                                             cAATGAGTAGCTGATGCGCCATTACAGGTCCTGGATGTGGGATTTTTTTATCCTGTTAGCGACCTTGACGAGTACCAAAAAGCGCGAAGTTCAACTATTGTTCTGTGGTGTTCTGTTGCGTGTTGACGGCAAAATTTTg                       <  2:629104/139‑1 (MQ=255)                                                                                                               aTGAGTAGCTGATGCGCCATTACAGGTCCTGGATGTGGGATTTTTTTATCCTGTTAGCGACCTTGACGAGTACCAAAAAGCGCGAAGTTCAACTATTGTTCTGTGGTGTTCTGTTGCGTGTTGACGGCAAAATTTTGCt                     <  1:827406/139‑1 (MQ=255)                                                                                                                 gAGTAGCTGATGCGCCATTACAGGTCCTGGATGTGGGATTTTTTTATCCTGTTAGCGACCTTGACGAGTACCAAAAAGCGCGAAGTTCAACTATTGtt                                                            <  2:645798/98‑1 (MQ=255)                                                                                                                 gAGTAGCTGATGCGCCATTACAGGTCCTGGATGTGGGATTTTTTTATCCTGTTAGCGACCTTGACGAGTACCAAAAAGCGCGAAGTTCAACTATTGtt                                                            >  1:645798/1‑98 (MQ=255)                                                                                                                    tAGCTGATGCGCCATTACAGGTCCTGGATGTGGGATTTTTTTATCCTGTTAGCGACCTTGACGAGTACCAAAAAGCGCGAAGTTCAACTATTGTTCTGTGGTGTTCTGTTGCGTGTTGACGGCAAAATTTTGCTGGCg                 >  2:707119/1‑138 (MQ=255)                                                                                                                      gCTGATGCGCCATTACAGGTCCTGGATGTGGGATTTTTTTATCCTGTTAGCGACCTTGACGAGTACCAAAAAGCGCGAAGTTCAACTa                                                                 >  2:334452/1‑88 (MQ=255)                                                                                                                      gCTGATGCGCCATTACAGGTCCTGGATGTGGGATTTTTTTATCCTGTTAGCGACCTTGACGAGTACCAAAAAGCGCGAAGTTCAACTa                                                                 <  1:334452/88‑1 (MQ=255)                                                                                                                      gCTGATGCGCCATTACAGGTCCTGGATGTGGGATTTTTTTATCCTGTTAGCGACCTTGACGAGTACCAAAAAGCGCGAAGTTCAACTATTGTTCTGTGGTGTTCTGTTGCGTGTTGACGGCAAAATTTTGCTGGCGTaa              >  2:719884/1‑139 (MQ=255)                                                                                                                       cTGATGCGCCATTACAGGTCCTGGATGTGGGATTTTTTTATCCTGTTAGCGACCTTGACGa                                                                                           >  1:150472/1‑61 (MQ=255)                                                                                                                       cTGATGCGCCATTACAGGTCCTGGATGTGGGATTTTTTTATCCTGTTAGCGACCTTGACGa                                                                                           <  2:150472/61‑1 (MQ=255)                                                                                                                            gcgcCATTACAGGTCCTGGATGTGGGATTTTTTTATCCTGTTAGCGACCTTGACGAGTACCAAAAAGCGCGAAGTTCAACTATTGTTCTGTGGTGTTCTGTTGCGTGTTGACGGCAAAATTTTGCTGGCGTAACATgcg        >  2:584033/1‑139 (MQ=255)                                                                                                                                cATTACAGGTCCTGGATGTGGGATTTTTTTATCCTGTTAGCGACCTTGACGAGTACCAAAAAGCGCGAAGTTCAACTATTGTTCTGTGGTGTTCTGTTGCGTGTTGACGGCAAAATTTTGCTGGCGTAACATGCGCGCa    <  1:695740/139‑1 (MQ=255)                                                                                                                                  ttACAGGTCCTGGATGTGGGATTTTTTTATCCTGTTAGCGACCTTGACGAGTACCAAAAAGCGCGAAGTTCAACTATTGTTCTGTGGTGTTCTGTTGCGTGTTGACGGCAAAATTTTGCTGGCGTAACATGCGCGCACg  <  1:501710/139‑1 (MQ=255)                                                                                                                                     |                                                                                                                                        TCAGCGTCGGATCTGAGAGTGCGCAATCATCAGCGGCAACAGCAAACAAGGGAAGTAAGGTGAGGGCGAGAAAAATCCGTTTGAGATTCAAGGTGATCATTCCTTTACCAATGAGTAGCTGATGCGCCATTATAGGTCCTGGATGTGGGATTTTTTTATCCTGTTAGCGACCTTGACGAGTACCAAAAAGCGCGAAGTTCAACTATTGTTCTGTGGTGTTCTGTTGCGTGTTGACGGCAAAATTTTGCTGGCGTAACATGCGCGCACG  >  NZ_CP009273/3994287‑3994554

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑