Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
MC JC	NZ_CP009273	3,512,038	Δ42 bp	coding (345‑386/522 nt)	aroK ←	shikimate kinase AroK

Missing coverage evidence...
			seq id	start	end	size	←reads	reads→	gene	description
*	*	÷	NZ_CP009273	3512038	3512079	42	53 [0]	[0] 53	aroK	shikimate kinase AroK

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NZ_CP009273	= 3512037	0 (0.000)	50 (1.010)	33/154	0.2	100%	coding (387/522 nt)	aroK	shikimate kinase AroK
	?	NZ_CP009273	3512080 =	0 (0.000)					coding (344/522 nt)	aroK	shikimate kinase AroK

CATACAGCGGATTGCGTTCATTGGCCAACGCTTCCAGAACTTCACGCGGCGGTGTTTCAACGTGCAGCAACGGGCGTTTTTTATCACGCTGCGTGCGTGCAAGTTGCTTTTCGATGGTCGTTTCAAGATAAACGACAACGCCACGAGCGGAAAGACGGTTACGCGTTTCACGGGAT  >  NZ_CP009273/3511991‑3512166                                                                                          |                                                                                       cgctttgatcatcagtacgaatggtcacgtcggcaatctcttcatacagcggattgcgttcattggccaacgcttccagaacttcacgct                                                                                        <  2:1286479‑M2/1‑1 (MQ=255)  gctttgatcatcagtacgaatggtcacgtcggcaatctcttcatacagcggattgcgttcattggccaacgcttccagaacttcacgctg                                                                                       <  1:1102375‑M2/2‑1 (MQ=255)  gctttgatcatcagtacgaatggtcacgtcggcaatctcttcatacagcggattgcgttcattggccaacgcttccagaacttcacgctg                                                                                       >  2:106178‑M2/89‑90 (MQ=255)     ttgatcatcagtacgaatggtcacgtcggcaatctcttcatacagcggattgcgttcattggccaacgcttccagaacttcacgctgcgt                                                                                    >  2:460791‑M2/86‑90 (MQ=255)               gtacgaatggtcacgtcggcaatctcttcatacagcggattgcgttcattggccaacgcttccagaacttcacgcTgcgtgcgt                                                                                >  2:1421103‑M2/76‑84 (MQ=255)               gtacgaatggtcacgtcggcaatctcttcatacagcggattgcgttcattggccaacgcttccagaacttcacgcTgcgtgcgt                                                                                <  1:1421103‑M2/9‑1 (MQ=255)               gtacgaatggtcacgtcggcaatctcttcatacagcggattgcgttcattggccaacgcttccagaacttcacgcTGCGTGCGTGCAAGt                                                                          >  2:581298‑M2/76‑90 (MQ=255)               gtacgaatggtcacgtcggcaatctcttcatacagcggattgcgttcattggccaacgcttccagaacttcacgcTGCGTGCGTGCAAGt                                                                          >  1:1251705‑M2/76‑90 (MQ=255)                 acgaatggtcacgtcggcaatctcttcatacagcggattgcgttcattggccaacgcttccagaacttcacgcTGCGTGCGTGCAAGTTg                                                                        >  2:1488596‑M2/74‑90 (MQ=255)                    aatggtcacgtcggcaatctcttcatacagcggattgcgttcattggccaacgcttccagaacttcacgcTGCGTGCGTGCAAGTTGCtt                                                                     >  2:745206‑M2/71‑90 (MQ=255)                    aatggtcacgtcggcaatctcttcatacagcggattgcgttcattggccaacgcttccagaacttcacgcTGCGTGCGTGCAAGTTGCtt                                                                     >  1:974924‑M2/71‑90 (MQ=255)                    aatggtcacgtcggcaatctcttcatacagcggattgcgttcattggccaacgcttccagaacttcacgcTGCGTGCGTGCAAGTTGCtt                                                                     >  1:665058‑M2/71‑90 (MQ=255)                      tggtcacgtcggcaatctcttcatacagcggattgcgttcattggccaacgcttccagaacttcacgcTGCGTGCGTGCAAGTTGCtttt                                                                   >  1:532134‑M2/69‑90 (MQ=255)                       ggtcacgtcggcaatctcttcatacagcggattgcgttcattggccaacgcttccagaacttcacgcTGCGTGCGTGCAAGTTGCTTTTc                                                                  >  1:805485‑M2/68‑90 (MQ=255)                         tcacgtcggcaatctcttcatacagcggattgcgttcattggccaacgcttccagaacttcacgcTGCGTGCGTGCAAGTTGc                                                                       <  1:281408‑M2/18‑1 (MQ=255)                         tcacgtcggcaatctcttcatacagcggattgcgttcattggccaacgcttccagaacttcacgcTGCGTGCGTGCAAGTTGc                                                                       >  2:281408‑M2/66‑83 (MQ=255)                         tcacgtcggcaatctcttcatacagcggattgcgttcattggccaacgcttccagaacttcacgcTGCGTGCGTGCAAGTTGCTTTTCGa                                                                >  2:1031098‑M2/66‑90 (MQ=255)                             gtcggcaatctcttcatacagcggattgcgttcattggccaacgcttccagaacttcacgcTGCGTGCGTGCAAGTTGCTTTTCGATGGt                                                            >  1:777644‑M2/62‑90 (MQ=255)                              tcggcaatctcttcatacagcggattgcgttcattggccaacgcttccagaacttcacgcTGCGTGCGTGCAAGTTGCTTTTCGATGGTc                                                           <  2:285202‑M2/30‑1 (MQ=255)                              tcggcaatctcttcatacagcggattgcgttcattggccaacgcttccagaacttcacgcTGCGTGCGTGCAAGTTGCTTTTCGATGGTc                                                           <  2:1582888‑M2/30‑1 (MQ=255)                                ggcaatctcttcatacagcggattgcgttcattggccaacgcttccagaacttcacgcTGCGTGCGTGCAAGTTGCTTTTCGATGGTCGt                                                         >  1:1438876‑M2/59‑90 (MQ=255)                                  caatctcttcatacagcggattgcgttcattggccaacgcttccagaacttcacgcTGCGTGCGTGCAAGTTGCTTTTCGATGGTCGttt                                                       <  1:847835‑M2/34‑1 (MQ=255)                                     tctcttcatacagcggattgcgttcattggccaacgcttccagaacttcacgcTGCGTGCGTGCAAGTTGCTTTTCGATGGTCGTTTCaa                                                    <  1:106178‑M2/37‑1 (MQ=255)                                      ctcttcatacagcggattgcgttcattggccaacgcttccagaacttcacgcTGCGTGCGTGCAAGTTGCTTTTCGATGGTCGTTTCAAg                                                   >  1:1233327‑M2/53‑90 (MQ=255)                                      ctcttcatacagcggattgcgttcattggccaacgcttccagaacttcacgcTGCGTGCGTGCAAGTTGCTTTTCGATGGTCGTTTCAAg                                                   >  2:14830‑M2/53‑90 (MQ=255)                                                agcggattgcgttcattggccaacgcttccagaacttcacgcTGCGTGCGTGCAAGTTGCTTTTCGATGGTCGTTTCAAGATAAACGACa                                         >  1:707297‑M2/43‑90 (MQ=255)                                                 gcggattgcgttcattggccaacgcttccagaacttcacgcTGCGTGCGTGCAAGTTGCTTTTCGATGGTCGTTTCAAGATAAACGACaa                                        >  1:629439‑M2/42‑90 (MQ=255)                                                 gcggattgcgttcattggccaacgcttccagaacttcacgcTGCGTGCGTGCAAGTTGCTTTTCGATGGTCGTTTCAAGATAAACGACaa                                        >  1:1177006‑M2/42‑90 (MQ=255)                                                 gcggattgcgttcattggccaacgcttccagaacttcacgcTGCGTGCGTGCAAGTTGCTTTTCGATGGTCGTTTCAAGATAAACGACaa                                        >  2:722841‑M2/42‑90 (MQ=255)                                                  cggattgcgttcattggccaacgcttccagaacttcacgcTGCGTGCGTGCAAGTTGCTTTTCGATGGTCGTTTCAAGATAAACGACAAc                                       >  1:130282‑M2/41‑90 (MQ=255)                                                  cggattgcgttcattggccaacgcttccagaacttcacgcTGCGTGCGTGCAAGTTGCTTTTCGATGGTCGTTTCAAGATAAACGACAAc                                       >  2:533959‑M2/41‑90 (MQ=255)                                                    gattgcgttcattggccaacgcttccagaacttcacgcTGCGTGCGTGCAAGTTGCTTTTCGATGGTCGTTTCAAGATaa                                               >  1:1381940‑M2/39‑80 (MQ=255)                                                    gattgcgttcattggccaacgcttccagaacttcacgcTGCGTGCGTGCAAGTTGCTTTTCGATGGTCGTTTCAAGATaa                                               <  2:1381940‑M2/42‑1 (MQ=255)                                                      ttgcgttcattggccaacgcttccagaacttcacgcTGCGTGCGTGCAAGTTGCTTTTCGATGGTCGTTTCaa                                                    <  1:1020623‑M2/37‑1 (MQ=255)                                                      ttgcgttcattggccaacgcttccagaacttcacgcTGCGTGCGTGCAAGTTGCTTTTCGATGGTCGTTTCaa                                                    >  2:1020623‑M2/37‑73 (MQ=255)                                                      ttgcgttcattggccaacgcttccagaacttcacgcTGCGTGCGTGCAAGTTGCTTTTCGATGGTCGTTTCAAGATAAACGACAACGcc                                    >  2:133072‑M2/37‑89 (MQ=255)                                                      ttgcgttcattggccaacgcttccagaacttcacgcTGCGTGCGTGCAAGTTGCTTTTCGATGGTCGTTTCAAGATAAACGACAACGcc                                    <  1:133072‑M2/53‑1 (MQ=255)                                                      ttgcgttcattggccaacgcttccagaacttcacgcTGCGTGCGTGCAAGTTGCTTTTCGATGGTCGTTTCAAGATAAACGACAACGCCa                                   >  2:1533439‑M2/37‑90 (MQ=255)                                                      ttgcgttcattggccaacgcttccagaacttcacgcTGCGTGCGTGCAAGTTGCTTTTCGATGGTCGTTTCAAGATAAACGACAACGCCa                                   >  2:506038‑M2/37‑90 (MQ=255)                                                        gcgttcattggccaacgcttccagaacttcacgcTGCGTGCGTGCAAGTTGCTTTTCGATGGTCGTTTCAAGATAAACGACAACGCCACg                                 <  2:1235951‑M2/56‑1 (MQ=255)                                                         cgttcattggccaacgcttccagaacttcacgcTGCGTGCGTGCAAGTTGCTTTTCGATGGTCGTTTCAAGATAAACGACAACGCCACGa                                <  2:532134‑M2/57‑1 (MQ=255)                                                           ttcattggccaacgcttccagaacttcacgcTGCGTGCGTGCAAGTTGCTTTTCGATGGTCGTTTCAAGATAAACGACAACGCCACGAGc                              >  1:1102063‑M2/32‑90 (MQ=255)                                                           ttcattggccaacgcttccagaacttcacgcTGCGTGCGTGCAAGTTGCTTTTCGATGGTCGTTTCAAGATAAACGACAACGCCACGAGc                              >  1:1165829‑M2/32‑90 (MQ=255)                                                                      acgcttccagaacttcacgcTGCGTGCGTGCAAGTTGCTTTTCGATGGTCGTTTCAAGATAAACGACAACGCCACGAGCGGAAAGACGGt                   >  2:1473645‑M2/21‑90 (MQ=255)                                                                      acgcttccagaacttcacgcTGCGTGCGTGCAAGTTGCTTTTCGATGGTCGTTTCAAGATAAACGACAACGCCACGAGCGGAAAGACGGt                   >  2:453463‑M2/21‑90 (MQ=255)                                                                       cgcttccagaacttcacgcTGCGTGCGTGCAAGTTGCTTTTCGATGGTCGTTTCAAGATAAACGACAACGCCACGAGCGGAAAGACGGtt                  >  1:1141522‑M2/20‑90 (MQ=255)                                                                           tccagaacttcacgcTGCGTGCGTGCAAGTTGCTTTTCGATGGTCGTTTCAAGATAAACGACAACGCCACGAGCGGAAAGACGGTTAcgc              <  1:533959‑M2/75‑1 (MQ=255)                                                                                aacttcacgcTGCGTGCGTGCAAGTTGCTTTTCGATGGTCGTTTCAAGATAAACGACAACGCCACGAGCGGAAAGACGGTTACGCGTTTc         <  1:1016528‑M2/80‑1 (MQ=255)                                                                                  cttcacgcTGCGTGCGTGCAAGTTGCTTTTCGATGGTCGTTTCAAGATAAACGACAACGCCACGAGCGGAAAGACGGTTACGCGTTTCAc       <  2:502670‑M2/82‑1 (MQ=255)                                                                                  cttcacgcTGCGTGCGTGCAAGTTGCTTTTCGATGGTCGTTTCAAGATAAACGACAACGCCACGAGCGGAAAGACGGTTACGCGTTTCAc       <  2:745980‑M2/82‑1 (MQ=255)                                                                                       cgcTGCGTGCGTGCAAGTTGCTTTTCGATGGTCGTTTCAAGATAAACGACAACGCCACGAGCGGAAAGACGGTTACGCGTTTCACGGGAt  <  2:176323‑M2/87‑1 (MQ=255)                                                                                         cTGCGTGCGTGCAAGTTGCTTTTCGATGGTCGTTTCAAGATAAACGACAACGCCACGAGCGGAAAGACGGTTACGCGTTTCAc       >  1:126107‑M2/2‑83 (MQ=255)                                                                                         cTGCGTGCGTGCAAGTTGCTTTTCGATGGTCGTTTCAAGATAAACGACAACGCCACGAGCGGAAAGACGGTTACGCGTTTCAc       <  2:126107‑M2/82‑1 (MQ=255)                                                                                          |                                                                                       CATACAGCGGATTGCGTTCATTGGCCAACGCTTCCAGAACTTCACGCGGCGGTGTTTCAACGTGCAGCAACGGGCGTTTTTTATCACGCTGCGTGCGTGCAAGTTGCTTTTCGATGGTCGTTTCAAGATAAACGACAACGCCACGAGCGGAAAGACGGTTACGCGTTTCACGGGAT  >  NZ_CP009273/3511991‑3512166

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑