Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	4,210,609	T→G	T603P (ACG→CCG)	espL4 ←	type III secretion system effector EspL4

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	4,210,609	0	T	G	100.0%	120.1 / NA	31	T603P (ACG→CCG)	espL4	type III secretion system effector EspL4
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base G (16/15);  total (16/15)

TCAGATAAAGCAAGATAAACCGTCTCTACAACATTTTGTTGTTTATGCTGTATCGCTGAAAACAAACCGGGATATTCATTAGAATTATTTGCCAGGAGGAGGGGCTTCATATTTTTTTTATCGAATTTAAACGTATTAAACAGAGTGGGTAATGCGTTAAAAATAGTATTAATAACGTTCATGTGTCCGCGCTGCATGGCCATAAACAAACCCGTGTCGCGCGCAAGACTTTTAGCGGTCAGAAGATCTACAATATCGGAAGCTGAAA  >  NZ_CP009273/4210476‑4210743                                                                                                                                      |                                                                                                                                       tCAGATAAAGCAAGATAAACCGTCTCTACAACATTTTGTTGTTTATGCTGTATCGCTGAAAACAAACCGGGATATTCATTAGAATTATTTGCCAGGAGGAGGGGCTTCATATTTTTTTTATCGAATTTAAACGGATTa                                                                                                                                    >  1:356628/1‑138 (MQ=255)   aGATAAAGCAAGATAAACCGTCTCTACAACATTTTGTTGTTTATGCTGTATCGCTGAAAACAAACCGGGATATTCATTAGAATTATTTGCCAGGAGGAGGGGCTTCATATTTTTTTTATCGAATTTAAACGGATTAAAc                                                                                                                                 <  1:28437/139‑1 (MQ=255)     aTAAAGCAAGATAAACCGTCTCTACAACATTTTGTTGTTTATGCTGTATCGCTGAAAACAAACCGGGATATTCATTAGAATTATTTGCCAGGAGGAGGGGCTTCATATTTTTTTTATCGAATTTAAACGGATTAAACag                                                                                                                               <  2:285654/139‑1 (MQ=255)      tAAAGCAAGATAAACCGTCTCTACAACATTTTGTTGTTTATGCTGTATCGCTGAAAACAAACCGGGATATTCATTAGAATTATTTGCCAGGAGGAGGGGCTTCATATTTTTTTTATCGAATTTAAACGGATTAAACaga                                                                                                                              <  2:523295/139‑1 (MQ=255)      tAAAGCAAGATAAACCGTCTCTACAACATTTTGTTGTTTATGCTGTATCGCTGAAAACAAACCGGGATATTCATTAGAATTATTTGCCAGGAGGAGGGGCTTCATATTTTTTTTATCGAATTTAAACGGATTAAACaga                                                                                                                              <  1:458862/139‑1 (MQ=255)           cAAGATAAACCGTCTCTACAACATTTTGTTGTTTATGCTGTATCGCTGAAAACAAACCGGGATATTCATTAGAATTATTTGCCAGGAGGAGGGGCTTCATATTTTTTTTATCGAATTTAAACGGATTAAACaga                                                                                                                              >  1:361958/1‑134 (MQ=255)           cAAGATAAACCGTCTCTACAACATTTTGTTGTTTATGCTGTATCGCTGAAAACAAACCGGGATATTCATTAGAATTATTTGCCAGGAGGAGGGGCTTCATATTTTTTTTATCGAATTTAAACGGATTAAACaga                                                                                                                              <  2:449637/134‑1 (MQ=255)           cAAGATAAACCGTCTCTACAACATTTTGTTGTTTATGCTGTATCGCTGAAAACAAACCGGGATATTCATTAGAATTATTTGCCAGGAGGAGGGGCTTCATATTTTTTTTATCGAATTTAAACGGATTAAACaga                                                                                                                              >  1:449637/1‑134 (MQ=255)           cAAGATAAACCGTCTCTACAACATTTTGTTGTTTATGCTGTATCGCTGAAAACAAACCGGGATATTCATTAGAATTATTTGCCAGGAGGAGGGGCTTCATATTTTTTTTATCGAATTTAAACGGATTAAACaga                                                                                                                              <  2:361958/134‑1 (MQ=255)               aTAAACCGTCTCTACAACATTTTGTTGTTTATGCTGTATCGCTGAAAACAAACCGGGATATTCATTAGAATTATTTGCCAGGAGGAGGGGCTTCATATTTTTTTTATCGAATTTAAACGGATTAAACAGAGTGGGTAAt                                                                                                                     >  2:396449/1‑139 (MQ=255)               aTAAAACGTCTCTACAAAATTTTGTTGTTTAGGACGTGACGCTGAAAACGAACCGGGATATTCATTAGAATGATTTGCCAGGAGGAGGGGCTTCATATTTTTTTTATCGAGTTTAAACGGATTAAACAGAGTGGGTaag                                                                                                                     >  2:21571/1‑138 (MQ=255)                         tctACAACATTTTGTTGTTTATGCTGTATCGCTGAAAACAAACCGGGATATTCATTAGAATTATTTGCCAGGAGGAGGGGCTTCATATTTTTTTTATCGAATTTAAACGGATTAAACAGAGTGGGTAATGCGTTaaaaa                                                                                                           >  2:552176/1‑139 (MQ=255)                                  ttttGTTGTTTATGCTGTATCGCTGAAAACAAACCGGGATATTCATTAGAATTATTTGCCAGGAGGAGGGGCTTCATATTTTTTTTATCGAATTTAAACGGATTAAACAGAGTGGGTAATGCGTTAAAAATAGTATtaa                                                                                                  <  1:396449/139‑1 (MQ=255)                                                 tGTATCGCTGAAAACAAACCGGGATATTCATTAGAATTATTTGCCAGGAGGAGGGGCTTCATATTTTTTTTATCGAATTTAAACGGATTAAACAGAGTGGGTAATGCGTTAAAAATAGTATTAATAACGTTCATGTGTc                                                                                   >  1:595403/1‑139 (MQ=255)                                                    aTCGCTGAAAACAAACCGGGATATTCATTAGAATTATTTGCCAGGAGGAGGGGCTTCATATTTTTTTTATCGAATTTAAACGGATTAAACAGAGTGGGTAATGCGTTAAAAATAGTATTAATAACGTTCATGTGTCcgc                                                                                >  2:252349/1‑139 (MQ=255)                                                           aaaaCAAACCGGGATATTCATTAGAATTATTTGCCAGGAGGAGGGGCTTCATATTTTTTTTATCGAATTTAAACGGATTAAACAGAGTGGGTAATGCGTTAAAAATAGTATTAATAACGTTCATGTGTCCGCGCTGCa                                                                          <  2:306203/138‑1 (MQ=255)                                                           aaaaCAAACCGGGATATTCATTAGAATTATTTGCCAGGAGGAGGGGCTTCATATTTTTTTTATCGAATTTAAACGGATTAAACAGAGTGGGTAATGCGTTAAAAATAGTATTAATAACGTTCATGTGTCCGCGCTGCAt                                                                         >  2:559488/1‑139 (MQ=255)                                                             aacaaacCGGGATATTCATTAGAATTATTTGCCAGGAGGAGGGGCTTCATATTTTTTTTATCGAATTTAAACGGATTAAACaga                                                                                                                              >  2:318200/1‑84 (MQ=255)                                                             aacaaacCGGGATATTCATTAGAATTATTTGCCAGGAGGAGGGGCTTCATATTTTTTTTATCGAATTTAAACGGATTAAACaga                                                                                                                              <  1:318200/84‑1 (MQ=255)                                                                    cGGGATATTCATTAGAATTATTTGCCAGGAGGAGGGGCTTCATATTTTTTTTATCGAATTTAAACGGATTAAACAGAGTGGGTAATGCGTTAAAAATAGTATTAATAACGTTCATGTGTCCGCGCTGCATGGCCATaaa                                                                <  1:565620/139‑1 (MQ=255)                                                                                tAGAATTATTTGCCAGGAGGAGGGGCTTCATATTTTTTTTATCGAATTTAAACGGATTAAACAGAGTGGGTAATGCGTTAAAAATAGTATTAATAACGTTCATGTGTCCGCGCTGCATGGCCATAAACAAACCCGTGTc                                                    >  1:98088/1‑139 (MQ=255)                                                                                        tttGCCAGGAGGAGGGGCTTCATATTTTTTTTATCGAATTTAAACGGATTAAACAGAGTGGGTAATGCGTTAAAAATAGTATTAATAACGTTCATGTGTCCGCGCTGCATGGCCATAAACAAACCCGTGTCgcgcgc                                              >  1:468180/1‑137 (MQ=255)                                                                                                      gggCTTCATATTTTTTTTATCGAATTTAAACGGATTAAACAGAGTGGGTAATGCGTTAAAAATAGTATTAATAACGTTCATGTGTCCGCGCTGCATGGCCATAAACAAACCCGTGTCGCGCGCAAGACTTTTAGCGGt                               >  2:484522/1‑138 (MQ=255)                                                                                                      gggCTTCATATTTTTTTTATCGAATTTAAACGGATTAAACAGAGTGGGTAATGCGTTAAAAATAGTATTAATAACGTTCATGTGTCCGCGCTGCATGGCCATAAACAAACCCGTGTCGCGCGCAAGACTTTTAGCGGTc                              <  2:468180/139‑1 (MQ=255)                                                                                                        gCTTCATATTTTTTTTATCGAATTTAAACGGATTAAACAGAGTGGGTAATGCGTTAAAAATAGTATTAATAACGTTCATGTGTCCGCGCTGCATGGCCATAAACAAACCCGTGTCGCGCGCAAGACTTTTAGCGGTCag                            <  1:552176/139‑1 (MQ=255)                                                                                                           tCATATTTTTTTTATCGAATTTAAACGGATTAAACAGAGTGGGTAATGCGTTAAAAATAGTATTAATAACGTTCATGTGTCCGCGCTGCATGGCCATAAACAAACCCGTGTCGCGCGCAAGACTTTTAGCGGTCag                            >  1:512309/1‑136 (MQ=255)                                                                                                            cATATTTTTTTTATCGAATTTAAACGGATTAAACAGAGTGGGTAATGCGTTAAAAATAGTATTAATAACGTTCATGTGTCCGCGCTGCATGGCCATAAACAAACCCGTGTCGCGCGCAAGACTTTTAGCGGTCagaag                         <  2:595403/138‑1 (MQ=255)                                                                                                             atatTTTTTTTATCGAATTTAAACGGATTAAACAGAGTGGGTAATGCGTTAAAAATAGTATTAATAACGTTCATGTGTCCGCGCTGCATGGCCATaaa                                                                <  1:205698/98‑1 (MQ=255)                                                                                                             atatTTTTTTTATCGAATTTAAACGGATTAAACAGAGTGGGTAATGCGTTAAAAATAGTATTAATAACGTTCATGTGTCCGCGCTGCATGGCCATaaa                                                                >  2:205698/1‑98 (MQ=255)                                                                                                                         tCGAATTTAAACGGATTAAACAGAGTGGGTAATGCGTTAAAAATAGTATTAATAACGTTCATGTGTCCGCGCTGCATGGCCATAAACAAACCCGTGTCGCGCGCAAGACTTTTAGCGGTCAGAAGATCTACAATATCg            >  2:326832/1‑138 (MQ=255)                                                                                                                                  aaCGGATTAAACAGAGTGGGTAATGCGTTAAAAATAGTATTAATAACGTTCATGTGTCCGCGCTGCATGGCCATAAACAAACCCGTGTCGCGCGCAAGACTTTTAGCGGTCAGAAGATCTACAATATCGGAAGCTGaaa  <  2:356628/139‑1 (MQ=255)                                                                                                                                      |                                                                                                                                       TCAGATAAAGCAAGATAAACCGTCTCTACAACATTTTGTTGTTTATGCTGTATCGCTGAAAACAAACCGGGATATTCATTAGAATTATTTGCCAGGAGGAGGGGCTTCATATTTTTTTTATCGAATTTAAACGTATTAAACAGAGTGGGTAATGCGTTAAAAATAGTATTAATAACGTTCATGTGTCCGCGCTGCATGGCCATAAACAAACCCGTGTCGCGCGCAAGACTTTTAGCGGTCAGAAGATCTACAATATCGGAAGCTGAAA  >  NZ_CP009273/4210476‑4210743

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: ‑