Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	4,211,733	T→C	E228G (GAA→GGA)	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	4,211,733	0	T	C	100.0%	34.8 / NA	11	E228G (GAA→GGA)	espL4	type III secretion system effector EspL4
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (7/4);  total (7/4)

TCAGTTGTGTTCTTTATTCTTAGCCGGACCGTCAAAGCATGGTTATCCACCAGTAATATGGCTGCCATAACACTGATGCCATTTGATTCCATCTTGTCAAAATATGCTTTCATAACTAGCCCGAAATCACCGCAGGCAGCAACGCAACGCCCCTCAGGACGGCT  >  NZ_CP009273/4211646‑4211809                                                                                        |                                                                             tCAGTTGTGTTCTTTATTCTTAGCCGGACCGTCAAAGCATGGTTATCCACCAGTAATATGGCTGCCATAACACTGATGCCATTTGATccc                                                                            >  1:214016/1‑90 (MQ=255)              ttATTCTTAGCCGGACCGTCAAAGCATGGTTATCCACCAGTAATATGGCTGCCATAACACTGATGCCATTTGATCCCATCTTGTCAAAat                                                               >  2:445523/1‑90 (MQ=255)                  tCTTAGCCGGACCGTCAAAGCATGGTTATCCACCAGTAATATGGCTGCCATAACACTGATGCCATTTGATCCCATCTTGTCAAAATATGc                                                           <  1:386233/90‑1 (MQ=255)                                         ggTTATCCCCCAGTAATATGGCTGCCATAACACTGATGCCATTTGATCCCATCTTGTCAAAATATGCTTTCATAACTAGCCCGAAATccc                                    <  2:236941/90‑3 (MQ=255)                                               ccaccaGTAATATGGCTGCCATAACACTGATGCCATTTGATCCCATCTTGTCAAAATATGCTTTCATAACTAGCCCGAAATCACCgcagg                              >  1:319229/1‑90 (MQ=255)                                                           tGGCTGCCATAACACTGATGCCATTTGATCCCATCTTGTCAAAATATGCTTTCATAACTAGCCCGAAATCCCCGCAGGCAgcaacgcaac                  <  2:486544/90‑1 (MQ=255)                                                           tGGCTGCCATAACACTGATGCCATTTGATCCCATCTTGTCAAAATATGCTTTCATAACTAGCCCGAAATCACCGCAGGCAgcaacgcaac                  <  2:214016/90‑1 (MQ=255)                                                            ggCTGCCATAACACTGATGCCATTTGATCCCATCTTGTCAAAATATGCTTTCATAACTAGCCCGAAATCACCGCAGGCAGcaacgcaacg                 >  1:44088/1‑90 (MQ=255)                                                               tGCCATAACACTGATGCCATTTGATCCCATCTTGTCAAAATATGCTTTCATAACTAGCCCGAAATCACCGCAGGCAGCAACGCAACGccc              >  1:349282/1‑90 (MQ=255)                                                               tGCCATAACACTGATGCCATTTGATCCCATCTTGTCAAAATATGCTTTCATAACTAGCCCGAAATCACCGCAGGCAGCAACGCAACGccc              >  2:327748/1‑90 (MQ=255)                                                                          tGATGCCATTTGATCCCATCTTGTCAAAATATGCTTTCATAACTAGCCCGAAATCACCGCAGGCAGCAACGCAACGCCCCTCAGGACGGc   >  2:291036/1‑90 (MQ=255)                                                                           gATGCCATTTGATCCCATCTTGTCAAAATATGCTTTCATAACTAGCCCGAAATCACCGCAGGCAGCAACGCAACGCCCCTCAGGACGGCt  >  2:15192/1‑90 (MQ=255)                                                                                        |                                                                             TCAGTTGTGTTCTTTATTCTTAGCCGGACCGTCAAAGCATGGTTATCCACCAGTAATATGGCTGCCATAACACTGATGCCATTTGATTCCATCTTGTCAAAATATGCTTTCATAACTAGCCCGAAATCACCGCAGGCAGCAACGCAACGCCCCTCAGGACGGCT  >  NZ_CP009273/4211646‑4211809

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑