Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	4,211,170	(T)8→7	coding (1246/2187 nt)	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	4,211,163	0	T	.	100.0%	126.8 / NA	31	coding (1253/2187 nt)	espL4	type III secretion system effector EspL4
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base . (13/18);  total (13/18)

GTTACAACATTTTTATCCTTACGTGATATCGCTAAAAATAATCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGATTTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGAATTGAAAATAGTCTCAACGATATCCGCATTACCATAATTTA  >  NZ_CP009273/4211076‑4211247                                                                                        |                                                                                     gTTACAACATTTTTATCCTTACGTGATATCGCTAAAAATAATCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGAttt                                                                                    >  2:309588/1‑90 (MQ=255)       acaTTTTTATCCTTACGTGATATCGCTAAAAATAATCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGAtttttttcg                                                                              <  2:8083/90‑3 (MQ=255)       acaTTTTTATCCTTACGTGATATCGCTAAAAATAATCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGAtttttttcg                                                                              <  2:414169/90‑3 (MQ=255)       acaTTTTTATCCTTACGTGATATCGCTAAAAATAATCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGAtttttttcg                                                                              <  1:829214/90‑3 (MQ=255)         aTTTTTATCCTTACGTGATATCGCTAAAAATAATCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGAtttttttcgag                                                                            >  1:310417/1‑86 (MQ=255)              tATCCTTACGTGATATCGCTAAAAATAATCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTaa                                                                      <  2:91498/90‑1 (MQ=255)               aTCCTTACGTGATATCGCTAAAAATAATCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAAt                                                                     >  2:241699/1‑90 (MQ=255)                tCCTTACGTGATATCGCTAAAAATAATCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATc                                                                    <  1:195046/90‑1 (MQ=255)                tCCTTACGTGATATCGCTAAAAATAATCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATc                                                                    <  1:228326/90‑1 (MQ=255)                  cTTACGTGATATCGCTAAAAATAATCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCt                                                                  <  1:419888/90‑1 (MQ=255)                  cTTACGTGATATCGCTAAAAATAATCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCt                                                                  <  1:94536/90‑1 (MQ=255)                          atatCGCTAAAAATAATCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATcc                                                          <  1:215545/90‑1 (MQ=255)                            atCGCTAAAAATAATCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCCTg                                                        >  1:266219/1‑90 (MQ=255)                            atCGCTAAAAATAATCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCCTg                                                        <  2:474450/90‑1 (MQ=255)                               gCTAAAAATAATCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCCTGttt                                                     >  1:297563/1‑90 (MQ=255)                               gCTAAAAATAATCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCCTGttt                                                     >  1:792662/1‑90 (MQ=255)                                              gAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGAATTGa                                      >  2:742634/1‑90 (MQ=255)                                                  aaCCATTTTTATCTTTTGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGAATTGAAAAt                                  <  1:329062/90‑1 (MQ=255)                                                   aCCATTTTTATCTTTTGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGAATTGAAAATa                                 <  1:563065/90‑1 (MQ=255)                                                        ttttATCTTTTGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGAATTGAAAATAGtctc                            >  1:528768/1‑90 (MQ=255)                                                           tATCTTTTGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGAATTGAAAATAGTCTCAAc                         <  1:86248/90‑1 (MQ=255)                                                                tttGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCat                                                              <  1:152671/48‑1 (MQ=255)                                                                tttGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCat                                                              >  2:152671/1‑48 (MQ=255)                                                                tttGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATcc                                                          <  1:632585/52‑1 (MQ=255)                                                                tttGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATcc                                                          >  2:632585/1‑52 (MQ=255)                                                                 ttGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATcc                                                          >  2:204000/1‑51 (MQ=255)                                                                 ttGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATcc                                                          <  1:204000/51‑1 (MQ=255)                                                                 ttGCCTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGAATTGAAAATAGTCTCAACGATATc                   >  2:666695/1‑90 (MQ=255)                                                                    ccTCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGAATTGAAAATAGTCTCAACGATATCCGc                <  1:356339/90‑1 (MQ=255)                                                                      tCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGAATTGAAAATAGTCTCAACGATATCCGCAt              <  1:807587/90‑1 (MQ=255)                                                                      tCCAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGAATTGAAAATAGTCTCAACGATATCCGCAt              <  1:309588/90‑1 (MQ=255)                                                                       ccAGAATATGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGAATTGAAAATAGTCTCAACGATATCCGCAtt             >  2:523885/1‑90 (MQ=255)                                                                            atatGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGAATTGAAAATAGTCTCAACGATATCCGCATTACCAt        <  1:219724/90‑1 (MQ=255)                                                                            atatGCATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGAATTGAAAATAGTCTCAACGATATCCGCATTACCAt        <  1:352051/90‑1 (MQ=255)                                                                                 cATGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGAATTGAAAATAGTCTCAACGATATCCGCATTACCATAAttt   >  1:243737/1‑90 (MQ=255)                                                                                  aTGAGA‑TTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGAATTGAAAATAGTCTCAACGATATCCGCATTACCATAATTta  >  2:367233/1‑90 (MQ=255)                                                                                        |                                                                                     GTTACAACATTTTTATCCTTACGTGATATCGCTAAAAATAATCCAGAAAAACCATTTTTATCTTTTGCCTCCAGAATATGCATGAGATTTTTTTTCGAGAGTAATCCTTCATATCCTGTTTCTGACAATGAATTGAAAATAGTCTCAACGATATCCGCATTACCATAATTTA  >  NZ_CP009273/4211076‑4211247

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑