Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	4,130,531	A→G	I540T (ATC→ACC)	ptsP ←	phosphoenolpyruvate‑‑protein phosphotransferase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	4,130,531	0	A	G	100.0%	109.9 / NA	29	I540T (ATC→ACC)	ptsP	phosphoenolpyruvate‑‑protein phosphotransferase
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (16/13);  total (16/13)

AGCGTTATCGCGATCCACCGCCAGCAGATACTGCGTCAGGTCATTACTACCAATACTAAAGAAATCAATCTCTTCGCAGCATTGATCGATGATGAACATCACCGACGGCACTTCCAGCATGATGCCGAGCTGGATTTTCTCATCAAACGGAATGTGTTCGTTACGTAGTTGCTGTTTGGCTTCCGCCAGTTTTTCTTTCACCCATAAGATCTCTTCCATTGAGGAGATCATCGGGATCATGATTTTCAGGCTGCC  >  NZ_CP009273/4130410‑4130664                                                                                                                          |                                                                                                                                      aGCGTTATCGCGATCCACCGCCAGCAGATACTGCGTCAGGTCATTACTACCAATACTAAAGAAATCAATCTCTTCGCAGCATTGATCGATGATGAACATCACCGACGGCACTTCCAGCATGGTGCCGAGCTGGATTTtc                                                                                                                      >  2:457760/1‑139 (MQ=255)       aTCGCGATCCACCGCCAGCAGATACTGCGTCAGGTCATTACTACCAATACTAAAGAAATCAATCTCTTCGCAGCATTGATCGATGATGAACATCACCGACGGCACTTCCAGCATGGTGCCGAGCTGGATTTTCtcatc                                                                                                                 >  1:161338/1‑138 (MQ=255)       aTCGCGATCCACCGCCAGCAGATACTGCGTCAGGTCATTACTACCAATACTAAAGAAATCAATCTCTTCGCAGCATTGATCGATGATGAACATCACCGACGGCACTTCCAGCATGGTGCCGAGCTGGATTTTCtcatc                                                                                                                 >  2:499408/1‑138 (MQ=255)                                  cGTCAGGTCATTACTACCAATACTAAAGAAATCAATCTCTTCGCAGCATTGATCGATGATGAACATCACCGACGGCACTTCCAGCATGGTGCCGAGCTGGATTTTCTCATCAAACGGAATGTGTTCGTTACGTAGt                                                                                        >  2:12519/1‑136 (MQ=255)                                  cGTCAGGTCATTACTACCAATACTAAAGAAATCAATCTCTTCGCAGCATTGATCGATGATGAACATCACCGACGGCACTTCCAGCATGGTGCCGAGCTGGATTTTCTCATCAAACGGAATGTGTTCGTTACGTAGt                                                                                        <  1:12519/136‑1 (MQ=255)                                  cGTCAGGTCATTACTACCAATACTAAAGAAATCAATCTCTTCGCAGCATTGATCGATGATGAACATCACCGACGGCACTTCCAGCATGGTGCCGAGCTGGATTTTCTCATCAAACGGAATGTGTTCGTTACGTAGTTGc                                                                                     >  2:472399/1‑139 (MQ=255)                                             tactacCAATACTAAAGAAATCAATCTCTTCGCAGCATTGATCGATGATGAACATCACCGACGGCACTTCCAGCATGGTGCCGAGCTGGATTTTCTCATCAAACGGAATGTGTTCGTTACGTAGTTGCTGTTTGGCTTc                                                                          >  2:342704/1‑139 (MQ=255)                                                         tAAAGAAATCAATCTCTTCGCAGCATTGATCGATGATGAACATCACCGACGGCACTTCCAGCATGGTGCCGAGCTGGATTTTCTCATCAAACGGAAtgt                                                                                                      >  1:220719/1‑99 (MQ=255)                                                         tAAAGAAATCAATCTCTTCGCAGCATTGATCGATGATGAACATCACCGACGGCACTTCCAGCATGGTGCCGAGCTGGATTTTCTCATCAAACGGAAtgt                                                                                                      <  2:220719/99‑1 (MQ=255)                                                            aGAAATCAATCTCTTCGCAGCATTGATCGATGATGAACATCACCGACGGCACTTCCAGCATGGTGCCGAGCTGGATTTTCTCATCAAACGGAATGTGTTCGTTACGTAGTTGCTGTTTGGCTTCCGCCAGTTtttcttt                                                           <  2:105704/139‑1 (MQ=255)                                                              aaaTCAATCTCTTCGCAGCATTGATCGAGGATGAACAGTACCGACGGCACTTCCAGCATGGTGCCGAGCTGGATTTTCTTATCAAACGGAATGTGTTCGTTACGTAGTTGCTGTTTGGCTTCCGCCAGTTTTTCTTTCa                                                         <  2:70810/139‑1 (MQ=255)                                                                atcaatcTCTTCGCAGCATTGATCGATGATGAACATCACCGACGGCACTTCCAGCATGGTGCCGAGCTGGATTTTCTCATCAAACGGAATGTGTTCGTTACGTAGTTGCTGTTTGGCTTCCGCCAGTTTTTCTTTCAcc                                                       >  1:425013/1‑139 (MQ=255)                                                                   aatcTCTTCGCAGCATTGATCGATGATGAACATCACCGACGGCACTTCCAGCATGGTGCCGAGCTGGATTTTCTCATCAAACGGAATGTGTTCGTTACGTAGTTGCTGTTTGGCTTCCGCCAGTTTTTCTTTCACCCAt                                                    <  2:113706/139‑1 (MQ=255)                                                                   aatcTCTTCGCAGCATTGATCGATGATGAACATCACCGACGGCACTTCCAGCATGGTGCCGAGCTGGATTTTCTCATCAAACGGAATGTGTTCGTTACGTAGTTGCTGTTTGGCTTCCGCCAGTTTTTCTTTCACCCAt                                                    <  1:457760/139‑1 (MQ=255)                                                                         ttCGCAGCATTGATCGATGATGAACATCACCGACGGCACTTCCAGCATGGTGCCGAGCTGGATTTTCTCATCAAACGGAATGTGTTCGTTACGTAGTTGCTGTTTGGCTTCCGCCAGTTTTTCTTTCACCCATAAg                                                 <  2:635096/136‑1 (MQ=255)                                                                           cGCAGCATTGATCGATGATGAACATCACCGACGGCACTTCCAGCATGGTGCCGAGCTGGATTTTCTCATCAAACGGAATGTGTTCGTTACGTAGTTGCTGTTTGGCTTCCGCCAGTTTTTCTTTCACCCATAAGAt                                               <  2:556347/136‑1 (MQ=255)                                                                                   tGATCGATGATGAACATCACCGACGGCACTTCCAGCATGGTGCCGAGCTGGATTTTCTCATCAAACGGAATGTGTTCGTTACGTAGTTGCTGTTTGGCTTCCGCCAGTTTTTCTTTCACCCATAAGATCTCTTCCAtt                                     >  1:218722/1‑138 (MQ=255)                                                                                     aTCGATGATGAACATCACCGACGGCACTTCCAGCATGGTGCCGAGCTGGATTTTCTCATCAAACGGAATGTGTTCGt                                                                                                <  1:563799/77‑1 (MQ=255)                                                                                     aTCGATGATGAACATCACCGACGGCACTTCCAGCATGGTGCCGAGCTGGATTTTCTCATCAAACGGAATGTGTTCGt                                                                                                >  2:563799/1‑77 (MQ=255)                                                                                     aTCGATGATGAACATCACCGACGGCACTTCCAGCATGGTGCCGAGCTGGATTTTCTCATCAAACGGAATGTGTTCGTTACGTAGTTGCTGTTTGGCTTCCGCCAGTTTTTCTTTCACCCATAAGATCTCTTCCATTgag                                  >  1:605624/1‑139 (MQ=255)                                                                                     aTCGATGATGAACATCACCGACGGCACTTCCAGCATGGTGCCGAGCTGGATTTTCTCATCAAACGGAATGTGTTCGTTACGTAGTTGCTGTTTGGCTTCCGCCAGTTTTTCTTTCACCCATAAGATCTCTTCCATTgag                                  <  1:342704/139‑1 (MQ=255)                                                                                     aTCGATGATGAACATCACCGACGGCACTTCCAGCATGGTGCCGAGCTGGATTTTCTCATCAAACGGAATGTGTTCGTTACGTAGTTGCTGTTTGGCTTCCGCCAGTTTTTCTTTCACCCATAAGATCTCTTCCATTgag                                  >  2:635962/1‑139 (MQ=255)                                                                                          tgatgaACATCACCGACGGCACTTCCAGCATGGTGCCGAGCTGGATTTTCTCATCAAACGGAATGTGTTCGTTACGTAGTTGCTGTTTGGCTTCCGCCAGTTTTTCTTTCACCCAt                                                    <  1:589354/116‑1 (MQ=255)                                                                                          tgatgaACATCACCGACGGCACTTCCAGCATGGTGCCGAGCTGGATTTTCTCATCAAACGGAATGTGTTCGTTACGTAGTTGCTGTTTGGCTTCCGCCAGTTTTTCTTTCACCCAt                                                    >  2:589354/1‑116 (MQ=255)                                                                                                    cACCGACGGCACTTCCAGCATGGTGCCGAGCTGGATTTTCTCATCAAACGGAATGTGTTCGTTACGTAGTTGCTGTTTGGCTTCCGCCAGTTTTTCTTTCACCCATAAGATCTCTTCCATTGAGGAGATCATCGGGAt                    >  2:53603/1‑138 (MQ=255)                                                                                                         aCGGCACTTCCAGCATGGTGCCGAGCTGGATTTTCTCATCAAACGGAATGTGTTCGTTACGTAGTTGCTGTTTGGCTTCCGCCAGTTTTTCTTTCACCCATAAGATCTCTTCCATTGAGGAGATCATCGGGATCATGAt              >  2:13931/1‑139 (MQ=255)                                                                                                           ggCACTTCCAGCATGGTGCCGAGCTGGATTTTCTCATCAAACGGAATGTGTTCGTTACGTAGTTGCTGTTTGGCTTCCGCCAGTTTTTCTTTCACCCATAAGATCTCTTCCATTGAGGAGATCATCGGGATCATGAttt            >  1:374365/1‑139 (MQ=255)                                                                                                                  ccAGCATGGTGCCGAGCTGGATTTTCTCATCAAACGGAATGTGTTCGTTACGTAGTTGCTGTTTGGCTTCCGCCAGTTTTTCTTTCACCCATAAGATCTCTTCCATTGAGGAGATCATCGGGATCATGATTTTCAGGc      <  1:499408/138‑1 (MQ=255)                                                                                                                     gCATGGTGCCGAGCTGGATTTTCTCATCAAACGGAATGTGTTCGTTACGTAGTTGCTGTTTGGCTTCCGCCAGTTTTTCTTTCACCCATAAGATCTCTTCCATTGAGGAGATCATCGGGATCATGATTTTCAGGCTGcc  <  2:374365/139‑1 (MQ=255)                                                                                                                          |                                                                                                                                      AGCGTTATCGCGATCCACCGCCAGCAGATACTGCGTCAGGTCATTACTACCAATACTAAAGAAATCAATCTCTTCGCAGCATTGATCGATGATGAACATCACCGACGGCACTTCCAGCATGATGCCGAGCTGGATTTTCTCATCAAACGGAATGTGTTCGTTACGTAGTTGCTGTTTGGCTTCCGCCAGTTTTTCTTTCACCCATAAGATCTCTTCCATTGAGGAGATCATCGGGATCATGATTTTCAGGCTGCC  >  NZ_CP009273/4130410‑4130664

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑