Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	3,452,746	G→T	G350V (GGC→GTC)	gspE →	type II secretion system ATPase GspE

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	3,452,746	0	G	T	100.0%	160.0 / NA	41	G350V (GGC→GTC)	gspE	type II secretion system ATPase GspE
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base T (24/17);  total (24/17)

CGCGCCATACTTCGCCAGGACCCGGATGTCGTCATGGTGGGGGAAATTCGTGATACAGAAACCGCGCAGATTGCGGTTCAGGCCTCGCTCACCGGCCATCTGGTACTCTCAACACTCCACACTAACAGTGCATCAGGCGCAGTGACCCGGCTCCGCGACATGGGCGTCGAATCATTCCTGCTTTCGTCTTCCCTGGCAGGGATTATCGCGCAACGTCTGGTTCGTCGCCTGTGTCCGCAATGCCGACAATTCACGCCCGTATCACCCCAAC  >  NZ_CP009273/3452610‑3452880                                                                                                                                         |                                                                                                                                       cgcgcCATACTTCGCCAGGACCCGGATGTCGTCATGGTGGGGGAAATTCGTGATACAGAAACCGCGCAGATTGCGGTTCAGGCCTCGCTCACCGGCCATCTGGTACTCTCAACACTCCACACTAACAGTGCATCAGtcg                                                                                                                                      <  1:433265/139‑1 (MQ=255)                       cGGATGTCGTCATGGTGGGGGAAATTCGTGATACAGAAACCGCGCAGATTGCGGTTCAGGCCTCGCTCACCGGCCATCTGGTACTCTCAACACTCCACACTAACAGTGCATCAGTCGCAGTGACCCGGCTCCGCGACAt                                                                                                                >  1:143173/1‑139 (MQ=255)                         gATGTCGTCATGGTGGGGGAAATTCGTGATACAGAAACCGCGCAGATTGCGGTTCAGGCCTCGCTCACCGGCCATCTGGTACTCTCAACACTCCACACTAACAGTGCATCAGTCGCAGTGACCCGGCTCCGCGACATgg                                                                                                              <  2:478075/139‑1 (MQ=255)                             tcgtcATGGTGGGGGAAATTCGTGATACAGAAACCGCGCAGATTGCGGTTCAGGCCTCGCTCACCGGCCATCTGGTACTCTCAACACTCCACACTAACAGTGCATCAGTCGCAGTGACCCGGCTCCGCGACATGGGCGt                                                                                                          <  1:810340/139‑1 (MQ=255)                                  aTGGTGGGGGAAATTCGTGATACAGAAACCGCGCAGATTGCGGTTCAGGCCTCGCTCACCGGCCATCTGGTACTCTCAACACTCCACACTAACAGTGCATCAGTCGCAGTGACCCGGCTCCGCGACATGGGCGTCGAAt                                                                                                     <  2:182223/139‑1 (MQ=255)                                                                gcgcAGATTGCGGTTCAGGCCTCGCTCACCGGCCATCTGGTACTCTCAACACTCCACACTAACAGTGCATCAGTCGCAGTGACCCGGCTCCGCGACATGGGCGTCGAATCATTCCTGCTTTCGTCTTCCCTGGCAGGGa                                                                       >  1:140783/1‑139 (MQ=255)                                                                 cgcAGATTGCGGTTCAGGCCTCGCTCACCGGCCATCTGGTACTCTCAACACTCCACACTAACAGTGCATCAGTCGCAGTGACCCg                                                                                                                            >  1:579376/1‑85 (MQ=255)                                                                 cgcAGATTGCGGTTCAGGCCTCGCTCACCGGCCATCTGGTACTCTCAACACTCCACACTAACAGTGCATCAGTCGCAGTGACCCg                                                                                                                            <  2:579376/85‑1 (MQ=255)                                                                  gcAGATTGCGGTTCAGGCCTCGCTCACCGGCCATCTGGTACTCTCAACACTCCACACTAACAGTGCATCAGTCGCAGTGACCCGGCTCCGCGACATGGGCGTCGAATCATTCCTGCTTTCGTCTTCCCTGGCAGGGAt                                                                      >  2:469670/1‑138 (MQ=255)                                                                   cAGATTGCGGTTCAGGCCTCGCTCACCGGCCATCTGGTACTCTCAACACTCCACACTAACAGTGCATCAGTCGCAGTGACCCGGCTCCGCGACATGGGCGTCGAATCATTCCTGCTTTCGTCTTCCCTGGCAGGGATTa                                                                    <  2:262885/139‑1 (MQ=255)                                                                          cGGTTCAGGCCTCGCTCACCGGCCATCTGGTACTCTCAACACTCCACACTAACAGTGCATCAGTCGCAGTGACCCGGCTCCGCGACATGGGCGTCGAATCATTCCTGCTTTCGTCTTCCCTGGCAGGGATTATCgcgc                                                              <  2:348117/138‑1 (MQ=255)                                                                           ggTTCAGGCCTCGCTCACCGGCCATCTGGTACTCTCAACACTCCACACTAACAGTGCATCAGTCGCAGTGACCCGGCTCCGCGACATGGGCGTCGAATCATTCCTGCTTTCGTCTTCCCTGGCAGGGATTATCGCGCaa                                                            >  2:168159/1‑139 (MQ=255)                                                                                aGGCCTCGCTCACCGGCCATCTGGTACTCTCAACACTCCACACTAACAGTGCATCAGTCGCAGTGACCCGGCTCCGCGACATGGGCGTCGAATCATTCCTGCTTTCGTCTTCCCTGGCAGGGATTATCGCGCAACGTCt                                                       >  2:511429/1‑139 (MQ=255)                                                                                       gCTCACCGGCCATCTGGTACTCTCAACACTCCACACTAACAGTGCATCAGTCGCAGTGACCCGGCTCCGCGACATGGGCGTCGAATCATTCCTGCTTTCGTCTTCCCTGGCAGGGATTATCGCGCAACGTCTGGTtcgt                                                >  2:680872/1‑139 (MQ=255)                                                                                       gCTCACCGGCCATCTGGTACTCTCAACACTCCACACTAACAGTGCATCAGTCGCAGTGACCCGGCTCCGCGACATGGGCGTCGAATCATTCCTGCTTTCGTCTTCCCTGGCAGGGATTATCGCGCAACGTCTGGTtcgt                                                >  1:727622/1‑139 (MQ=255)                                                                                       gCTCACCGGCCATCTGGTACTCTCAACACTCCACACTAACAGTGCATCAGTCGCAGTGACCCGGCTCCGCGACATGGGCGTCGAATCATTCCTGCTTTCGTCTTCCCTGGCAGGGATTATCGCGCAACGTCTGGTtcgt                                                >  2:284154/1‑139 (MQ=255)                                                                                       gCTCACCGGCCATCTGGTACTCTCAACACTCCACACTAACAGTGCATCAGTCGCAGTGACCCGGCTCCGCGACATGGGCGTCGAATCATTCCTGCTTTCGTCTTCCCTGGCAGGGATTATCGCGCAACGTCTGGTtcg                                                 <  1:469670/138‑1 (MQ=255)                                                                                                       gTACTCTCAACACTCCACACTAACAGTGCATCAGTCGCAGTGACCCGGCTCCGCGACATGGGCGTCGAATCATTCCTGCTTTCGTCTTCCCTGGCAGGGATTATCGCGCAACGTCTGGTTCGTCGCCTGTGTCCGCa                                  <  2:140783/137‑1 (MQ=255)                                                                                                             tcAACACTCCACACTAACAGTGCATCAGTCGCAGTGACCCGGCTCCGCGACATGGGCGTCGAATCATTCCTGCTTTCGTCTTCCCTGGCAGGGATTATCgcgc                                                              >  1:449457/1‑103 (MQ=255)                                                                                                             tcAACACTCCACACTAACAGTGCATCAGTCGCAGTGACCCGGCTCCGCGACATGGGCGTCGAATCATTCCTGCTTTCGTCTTCCCTGGCAGGGATTATCgcgc                                                              <  2:449457/103‑1 (MQ=255)                                                                                                             tcAACACTCCACACTAACAGTGCATCAGTCGCAGTGACCCGGCTCCGCGACATGGGCGTCGAATCATTCCTGCTTTCGTCTTCCCTGGCAGGGATTATCGCGCAACGTCTGGTTCGTCGCCtgt                                         <  2:468149/124‑1 (MQ=255)                                                                                                             tcAACACTCCACACTAACAGTGCATCAGTCGCAGTGACCCGGCTCCGCGACATGGGCGTCGAATCATTCCTGCTTTCGTCTTCCCTGGCAGGGATTATCGCGCAACGTCTGGTTCGTCGCCtgt                                         >  1:468149/1‑124 (MQ=255)                                                                                                               aaCACTCCACACTAACAGTGCATCAGTCGCAGTGACCCGGCTCCGCGACATGGGCGTCGAATCATTCCTGCTTTCGTCTTCCCTGGCAGGGATTATCGCGCAACGTCTGGTTCGTCGCCTGTGTCCGCAATGCCGa                           <  1:168159/136‑1 (MQ=255)                                                                                                                    tCCACACTAACAGTGCATCAGTCGCAGTGGCCCGGCTCCGCGACATGGGCGTCGAATCATTCCTGCTTTCGTCTTCCCTGGCAGGGATTATCGCGCAACGTCTGGTTCGTCGCCTGTGTCCGCAATGCCGa                           <  1:455855/131‑1 (MQ=255)                                                                                                                    tCCACACTAACAGTGCATCAGTCGCAGTGACCCGGCTCCGCGACATGGGCGTCGAATCATTCCTGCTTTCg                                                                                       <  2:419612/71‑1 (MQ=255)                                                                                                                    tCCACACTAACAGTGCATCAGTCGCAGTGACCCGGCTCCGCGACATGGGCGTCGAATCATTCCTGCTTTCg                                                                                       >  1:419612/1‑71 (MQ=255)                                                                                                                    tCCACACTAACAGTGCATCAGTCGCAGTGACCCGGCTCCGCGACATGGGCGTCGAATCATTCCTGCTTTCGTCTTCCCTGGCAGGGATTATCGCGCAACGTCTGGTTCGTCGCCTGTGTCCGCAATGCCGa                           >  2:455855/1‑131 (MQ=255)                                                                                                                         acTAACAGTGCATCAGTCGCAGTGACCCGGCTCCGCGACATGGGCGTCGAATCATTCCTGCTTTCGTCTTCCCTGGCAGGGATTATCGCGCAACGTCTGGTTCGTCGCCTGTGTCCGCAATGCCGACAATTCACGCCCg              >  1:449041/1‑139 (MQ=255)                                                                                                                             aCAGTGCATCCGTCGCAGTGACCCCGCTCCGCGACATGGGCGTCGAATCATCCCTGCTTTCGTCTTCCCTGGCAGGGATTATCGCGCAACGTCTGGTTCGTCGCCTGTGTCCGCAATGCCGACAATTCACGCCCGTa            <  1:248729/137‑1 (MQ=255)                                                                                                                             aCAGTGCATCAGTCGCAGTGACCCGGCTCCGCGACATGGGCGTCGAATCATTCCTGCTTTCGTCTTCCCTGGCAGGGATTATCGCGCAACGTCTGGTTCGTCGCCTGTGTCCGCAATGCCGACAATTCACGCCCGTa            <  1:284154/137‑1 (MQ=255)                                                                                                                             aCAGTGCATCAGTCGCAGTGACCCGGCTCCGCGACATGGGCGTCGAATCATTCCTGCTTTCGTCTTCCCTGGCAGGGATTATCGCGCAACGTCTGGTTCGTCGCCTGTGTCCGCAATGCCGACAATTCACGCCCGTa            <  1:245834/137‑1 (MQ=255)                                                                                                                              cAGTGCATCAGTCGCAGTGACCCGGCTCCGCGACATGGGCGTCGAATCATTCCTGCTTTCGTCTTCCCTGGCAGGGATTATCGCGCAACGTCTGGTTCGTCGCCTGTGTCCGCAATGCCGACAATTCACGCCCGTATCa         >  2:396630/1‑139 (MQ=255)                                                                                                                              cAGTGCATCAGTCGCAGTGACCCGGCTCCGCGACATGGGCGTCGAATCATTCCTGCTTTCGTCTTCCCTGGCAGGGATTATCGCGCAACGTCTGGTTCGTCGCCTGTGTCCGCAATGCCGACAATTCACGCCCGTATCa         >  2:32419/1‑139 (MQ=255)                                                                                                                              cAGTGCATCAGTCGCAGTGACCCGGCTCCGCGACATGGGCGTCGAATCATTCCTGCTTTCGTCTTCCCTGGCAGGGATTATCGCGCAACGTCTGGTTCGTCGCCTGTGTCCGCAATGCCGACAATTCACGCCCGTATCa         >  1:3664/1‑139 (MQ=255)                                                                                                                                gTGCATCAGTCGCAGTGACCCGGCTCCGCGACATGGGCGTCGAATCATTCCTGCTTTCGTCTTCCCTGGCAGGGATTATCGCGCAACGTCTGGTTCGTCGCCTGTGTCCGCAATGCCGACAATTCACGCCCGTATCAcc       >  2:343714/1‑139 (MQ=255)                                                                                                                                gTGCATCAGTCGCAGTGACCCGGCTCCGCGACATGGGCGTCGAATCATTCCTGCTTTCGTCTTCCCTGGCAGGGATTATCGCGCAACGTCTGGTTCGTCGCCTGTGTCCGCAATGCCGACAATTCACGCCCGTATCAcc       >  1:170264/1‑139 (MQ=255)                                                                                                                                   cATCAGTCGCAGTGACCCGGCTCCGCGACATGGGCGTCGAATCATTCCTGCTTTCGTCTTCCCTGGCAGGGATTATCGCGCAACGTCTGGTTCGTCGCCTGTGTCCGCAAt                                >  2:100704/1‑111 (MQ=255)                                                                                                                                   cATCAGTCGCAGTGACCCGGCTCCGCGACATGGGCGTCGAATCATTCCTGCTTTCGTCTTCCCTGGCAGGGATTATCGCGCAACGTCTGGTTCGTCGCCTGTGTCCGCAAt                                <  1:100704/111‑1 (MQ=255)                                                                                                                                   cATCAGTCGCAGTGACCCGGCTCCGCGACATGGGCGTCGAATCATTCCTGCTTTCGTCTTCCCTGGCAGGGATTATCGCGCAACGTCTGGTTCGTCGCCTGTGTCCGCAATGCCGACAATTCACGCCCGTATCAcccc     >  1:38383/1‑138 (MQ=255)                                                                                                                                   cATCAGTCGCAGTGACCCGGCTCCGCGACATGGGCGTCGAATCATTCCTGCTTTCGTCTTCCCTGGCAGGGATTATCGCGCAACGTCTGGTTCGTCGCCTGTGTCCGCAATGCCGACAATTCACGCCCGTATCAcccc     >  2:839571/1‑138 (MQ=255)                                                                                                                                     tCAGTCGCAGTGACCCGGCTCCGCGACATGGGCGTCGAATCATTCCTGCTTTCGTCTTCCCTGGCAGGGATTATCGCGCAACGTCTGGTTCGTCGCCTGTGTCCGCAATGCCGACAATTCACGCCCGTATCACCCcaa   >  1:431497/1‑138 (MQ=255)                                                                                                                                     tCAGTCGCAGTGACCCGGCTCCGCGACATGGGCGTCGAATCATTCCTGCTTTCGTCTTCCCTGGCAGGGATTATCGCGCAACGTCTGGTTCGTCGCCTGTGTCCGCAATGCCGACAATTCACGCCCGAATCACCCcaac  >  2:520246/1‑139 (MQ=255)                                                                                                                                         |                                                                                                                                       CGCGCCATACTTCGCCAGGACCCGGATGTCGTCATGGTGGGGGAAATTCGTGATACAGAAACCGCGCAGATTGCGGTTCAGGCCTCGCTCACCGGCCATCTGGTACTCTCAACACTCCACACTAACAGTGCATCAGGCGCAGTGACCCGGCTCCGCGACATGGGCGTCGAATCATTCCTGCTTTCGTCTTCCCTGGCAGGGATTATCGCGCAACGTCTGGTTCGTCGCCTGTGTCCGCAATGCCGACAATTCACGCCCGTATCACCCCAAC  >  NZ_CP009273/3452610‑3452880

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑