Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	1,002,200	T→G	100%	M173R (ATG→AGG)	mecA2 →	competence negative regulator MecA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	1,002,200	0	T	G	100.0%	65.2 / NA	20	M173R (ATG→AGG)	mecA2	competence negative regulator MecA
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base G (3/17);  total (3/17)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

CTAAACGTCAAAAGTCTTCAGCACGTAAAAATACAAGAACAATCATTGTGAAATTTAACGATTTAGAAGATGTTATTAATTATGCATATCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATATGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCATTAATGATAGTTACAGTCAATTGCTTGAATTTGCTTATCCAACAGACAGAACAGAAGTTTATTTAAATGACTATGCT  >  CP000730/1002068‑1002336                                                                                                                                     |                                                                                                                                         cTAAACGTCAAAAGTCTTCAGCACGTAAAAATACAAGAACAATCATTGTGAAATTTAACGATTTAGAAGATGTTATTAATTATGCATATCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATg                                                                                                                                  <  1:98608/141‑1 (MQ=255)      cGTCAAAGGTCCTCAGCACGTAAAAATACAAGAACAATCATTGTGAAATTTAACGATTTAGAAGATGTTAGTAATGATGCATATCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACt                                                                                                                             <  1:58224/141‑1 (MQ=255)            aaGTCTTCAGCACGTAAAAATACAAGAACAATCATTGTGAAATTTAACGATTTAGAAGATGTTATTAATTATGCATATCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACttattat                                                                                                                       <  2:173278/141‑1 (MQ=255)             agacTTCAGCACGTAAAAAAACAAGAAGAATCATTGTGAAATTTAACTATTTAGAAGATGTTATTAATTATGCATATCATAGCAATCCAATAACTACATAGTTTGAAGATTTGTTATATAGGGTTGATGGTACttattatt                                                                                                                      <  2:11350/138‑1 (MQ=255)                   cAGCACGTAAAAATACAAGAACAATCATTGTGAAATTTAACGATTTAGAAGATGTTATTAATTATGCATATCATAGCAATCCAATAACTACAGAGTTTGAAGGTTTGTTATATAGGGTTGATGGTACTTATTATTATGCTg                                                                                                                >  1:8130/1‑141 (MQ=255)                   cAGCACGTAAAAATACAAGAACAATCATTGTGAAATTTAACGATTTAGAAGATGTTATTAATTATGCATATCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTg                                                                                                                >  1:157415/1‑141 (MQ=255)                                 aCAAGAACAATCATTGTGAAATTTAACGATTTAGAAGATGTTATTAATTCTGCATCACATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGt                                                                                                  <  1:181114/141‑1 (MQ=255)                                          aTCATTGTGAAATTTAACGATTTAGAAGATGTTATTAATTATGCATATCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGAt                                                                                         <  1:215838/141‑1 (MQ=255)                                                  gAAATTTAACGATTTAGAAGATGTTATTAATTATGCATATCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGt                                                                                 <  2:202862/141‑1 (MQ=255)                                                      tttAACGATTTAGAAGATGTTATTAATTATGCATATCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCAtt                                                                             <  2:234188/141‑1 (MQ=255)                                                          aCGATTTAGAAGATTTTATTAATTATGCATATCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCATTAATg                                                                         <  1:191554/141‑1 (MQ=255)                                                               ttAGAAGATGTTATTAATTATGCATATCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCATTAATGATAGt                                                                    <  2:164549/141‑1 (MQ=255)                                                               ttAGAAGATGTTATTAATTATGCATATCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCATTAATGATAGt                                                                    <  1:78154/141‑1 (MQ=255)                                                                  gaagaTGTTATTAATTATGCATATCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCATTAATGATAGTTAc                                                                 <  2:206189/141‑1 (MQ=255)                                                                            ttaattaTGCATTTCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGTGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCATTAATGATAGTTACAGTCAATTGc                                                       <  2:39965/141‑1 (MQ=255)                                                                             taattaTGCATATCATCGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCATTAATGATAGTTACAGTCAATTGCt                                                      <  1:62555/141‑1 (MQ=255)                                                                                  aTGCATATCACAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCATTAATGATAGTTACAGTCAATTGCTTGAAt                                                 <  1:221066/141‑1 (MQ=255)                                                                                          tattgCAATCCAATAACTACAGGGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCATTAATGATAGTTACAGTCAATTGCTTGAATTTGCTTAt                                         <  2:177834/137‑1 (MQ=255)                                                                                                             cAGAGTTTGAAGATTTGTTATATAGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCATTAATGATAGTTACAGTCAATTGCTTGAATTTGCTTATCCAACAGACAGAACAGAAg                      >  1:209825/1‑141 (MQ=255)                                                                                                                               tatataGGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCATTAATGATAGTTACAGTCAATTGCTTGAATTTGCTTATCCAACAGACAGAACAGAAGTTTATTTAAATGACTATg    <  2:28700/141‑1 (MQ=255)                                                                                                                                 tatagGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCATTAATGATAGTTACAGTCAATTGCTTGAATTTGCTTATCCAACAGACAGAACAGAAGTTTATTTAAATGACTATGCt  >  2:7709/1‑141 (MQ=255)                                                                                                                                     |                                                                                                                                         CTAAACGTCAAAAGTCTTCAGCACGTAAAAATACAAGAACAATCATTGTGAAATTTAACGATTTAGAAGATGTTATTAATTATGCATATCATAGCAATCCAATAACTACAGAGTTTGAAGATTTGTTATATATGGTTGATGGTACTTATTATTATGCTGTATATTTTGATAGTCATGTTGATCAAGAAGTCATTAATGATAGTTACAGTCAATTGCTTGAATTTGCTTATCCAACAGACAGAACAGAAGTTTATTTAAATGACTATGCT  >  CP000730/1002068‑1002336

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑