Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	3,575,877	(A)6→5	coding (655/1179 nt)	hcp →	Hcp1 family type VI secretion system effector

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	3,575,872	0	A	.	100.0%	83.6 / NA	21	coding (650/1179 nt)	hcp	Hcp1 family type VI secretion system effector
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base . (8/13);  total (8/13)

ATGGGAACATTGAAGGATTCAGAGATACTGCGGAAAAACTGGGTGGAGATGCAATAAAAGGCTATGATCAAATACTAAATGAAAAAACAGCGGGCATAGCGATAGCAACAGCATCTATTCTTTTAACAAAGCGTTCTAATGTTGATACATATACAGAAATA  >  NZ_CP009273/3575791‑3575951                                                                                  |                                                                                aTGGGAACATTGAAGGATTCAGAGATACTGCGGAAAAACTGGGTGGAGATGCAATAAAAGGCTATGATCAAATACTAAATGaaaaacagc                                                                         >  2:26140/1‑86 (MQ=255)   gggAACATTGAAGGATTCAGAGATACTGCGGAAAAACTGGGTGGAGATGCAATAAAAGGCTATGATCAAATACTAAATGaaaaacag                                                                          <  1:214013/87‑4 (MQ=255)   gggAACATTGAAGGATTCAGAGATACTGCGGAAAAACTGGGTGGAGATGCAATAAAAGGCTATGATCAAATACTAAATGaaaaacag                                                                          >  2:214013/1‑84 (MQ=255)      aaCATTGAAGGATTCAGAGATACTGCGGAAAAACTGGGTGGAGATGCAATAAAAGGCTATGATCAAATACTAAATG‑AAAAACAGCGGGCa                                                                   >  2:385653/1‑90 (MQ=255)         aTTGAAGGATTCAGAGATACTGCGGAAAAACTGGGTGGAGATGCAATAAAAGGCTATGATCAAATACTAAATG‑AAAAACAGCGGGCATAg                                                                >  2:373698/1‑90 (MQ=255)         aTTGAAGGATTCAGAGATACTGCGGAAAAACTGGGTGGAGATGCAATAAAAGGCTATGATCAAATACTAAATG‑AAAAACAGCGGGCATAg                                                                >  1:297562/1‑90 (MQ=255)                    cAGAGATACTGCGGAAAAACTGGGTGGAGATGCAATAAAAGGCTATGATCAAATACTAAATG‑AAAAACAGCGGGCATAGCGATAGCAACa                                                     >  2:14941/1‑90 (MQ=255)                    cAGAGATACTGCGGAAAAACTGGGTGGAGATGCAATAAAAGGCTATGATCAAATACTAAATG‑AAAAACAGCGGGCATAGCGATAGCAACa                                                     <  2:97714/90‑1 (MQ=255)                    cAGAGATACTGCGGAAAAACTGGGTGGAGATGCAATAAAAGGCTATGATCAAATACTAAATG‑AAAAACAGCGGGCATAGCGATAGCAACa                                                     <  1:357008/90‑1 (MQ=255)                         aTACTGCGGAAAAACTGGGTGGAGATGCAATAAAAGGCTATGATCAAACACTAAATG‑AAAAACAGCGGGCATAGCGATAGCAACAGCATc                                                >  2:367903/1‑90 (MQ=255)                           aCTGCGGAAAAACTGGGTGGAGATGCAATAAAAGGCTATGATCAAATACTAAATG‑AAAAACAGCGGGCATAGCGATAGCAACAGCATCTa                                              <  1:385653/90‑1 (MQ=255)                            ttGCGGAAAAACTGGGTGGAGATGCAATAAAAGGCTATGATCAAATACTAAATG‑AAAAACAGCGGGCATAGCGATAGCAACAGCATCTAt                                             >  1:227989/2‑90 (MQ=255)                                   aaaaCTGGGTGGAGATGCAATAAAAGGCTATGATCAAATACTAAATG‑AAAAACAGCGGGCATAGCGATAGCAACAGCATCTATTCTTTTa                                      >  1:195012/1‑90 (MQ=255)                                       cTGGGTGGAGATGCAATAAAAGGCTATGATCAAATACTAAATG‑AAAAACAGCGGGCATAGCGATAGCAACAGCATCTATTCTTTTAACaa                                  <  2:195012/90‑1 (MQ=255)                                        tGGGTGGAGATGCAATAAAAGGCTATGATCAAATACTAAATG‑AAAAACAGCGGGCATAGCGATAGCAACAGCATCTATTCTTTTAACaaa                                 <  1:193309/90‑1 (MQ=255)                                         gggTGGAGATGCAATAAAAGGCTATGATCAAATACTAAATG‑AAAAACAGCGGGCATAGCGATAGCAACAGCATCTATTCTTTTAACAAAg                                <  2:440874/90‑1 (MQ=255)                                              gagaTGCAATAAAAGGCTATGATCAAATACTAAATG‑AAAAACAGCGGGCATAGCGATAGCAACAGCATCTATTCTTTTAACAAAGCGTTc                           <  2:439838/90‑1 (MQ=255)                                                gaTGCAATAAAAGGCTATGATCAAATACTAAATG‑AAAAACAGCGGGCATAGCGATAGCAACAGCATCTATTCTTTTAACAAAGCGTTCTa                         <  1:366030/90‑1 (MQ=255)                                                  tGCAATAAAAGGCTATGATCAAATACTAAATG‑AAAAACAGCGGGCATAGCGATAGCAACAGCATCTATTCTTTTAACAAAGCGTTCTAAt                       <  1:199627/90‑1 (MQ=255)                                                      aTAAAAGGCTATGATCAAATACTAAATG‑AAAAACAGCGGGCATAGCGATAGCAACAGCATCTATTCTTTTAACAAAGCGTTCTAATGTTg                   <  1:167264/90‑1 (MQ=255)                                                        aaaaGGCTATGATCAAATACTAAATG‑AAAAACAGCGGGCATAGCGATAGCAACAGCATCTATTCTTTTAACAAAGCGTTCTAATGTTGAt                 <  1:26140/90‑1 (MQ=255)                                                           aGGCTATGATCAAATACTAAATG‑AAAAACAGCGGGCATAGCGATAGCAACAGCATCTATTCTTTTAACAAAGCGTTCTAATGTTGATACa              <  1:112396/90‑1 (MQ=255)                                                                aTGATCAAATACTAAATG‑AAAAACAGCGGGCATAGCGATAGCAACAGCATCTATTCTTTTAACAAAGCGTTCTAATGTTGATACATATAc         <  2:375722/90‑1 (MQ=255)                                                                       aaTACTAAATG‑AAAAACAGCGGGCATAGCGATAGCAACAGCATCTATTCTTTTAACAAAGCGTTCTAATGTTGATACATATACAGaaata  >  2:207504/1‑90 (MQ=255)                                                                                  |                                                                                ATGGGAACATTGAAGGATTCAGAGATACTGCGGAAAAACTGGGTGGAGATGCAATAAAAGGCTATGATCAAATACTAAATGAAAAAACAGCGGGCATAGCGATAGCAACAGCATCTATTCTTTTAACAAAGCGTTCTAATGTTGATACATATACAGAAATA  >  NZ_CP009273/3575791‑3575951

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑