Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
MC JC	NZ_CP009273	3,631,242	Δ66 bp	coding (241‑306/1500 nt)	pitA →	inorganic phosphate transporter PitA

Missing coverage evidence...
			seq id	start	end	size	←reads	reads→	gene	description
*	*	÷	NZ_CP009273	3631242	3631307	66	38 [1]	[1] 38	pitA	inorganic phosphate transporter PitA

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NZ_CP009273	= 3631241	1 (0.050)	28 (1.510)	24/154	0.0	96.7%	coding (240/1500 nt)	pitA	inorganic phosphate transporter PitA
	?	NZ_CP009273	3631308 =	1 (0.050)					coding (307/1500 nt)	pitA	inorganic phosphate transporter PitA

CGCCGTGGTTATGGCGGCGGTATTCAACTTTTTGGGTGTTTTGCTGGGTGGTCTGAGTGTTGCCTATGCCATTGTGCATATGCTGCCGACGGATCTGCTGCTTAATATGGGATCGTCTCATGGCCTTGCCATGGTGTTCTCTATGTTGCTGGCGGCGATTATCTGGAACCTGG  >  NZ_CP009273/3631157‑3631329                                                                                     |                                                                                         cGCCGTGGTTATGGCGGCGGGATTTAACTTTTTTGGGGTTTTTCTGGGGGGGCTGAGGGTTGCCTATGCCCTTGTGCATATGCTGGCggc                                                                                     >  1:404946/1‑88 (MQ=255)             ggcggcGGTATTCAACTTTTTGGGTGTTTTGCTGGGTGGTCTGAGTGTTGCCTATGCCATTGTGCATATGCTGgcggcgattatctggaa                                                                         <  2:495705‑M1/90‑18 (MQ=255)               cggcggTATTCAACTTTTTGGGTGTTTTGCTGGGTGGTCTGAGTGTTGCCTATGCCATTGTGCATATGCTGgcggcgattatctgga                                                                          >  2:52629‑M1/1‑71 (MQ=255)               cggcggTATTCAACTTTTTGGGTGTTTTGCTGGGTGGTCTGAGTGTTGCCTATGCCATTGTGCATATGCTGgcggcgattatctgga                                                                          <  1:52629‑M1/87‑17 (MQ=255)                ggcggGATTCAACTTTTTGGGTGTTTTGCTGGGGGGTCTGAGGGTTGCCTATGCCATTTTGCATATGCTGgcggcggttatctggaacct                                                                      >  1:452797‑M1/1‑70 (MQ=255)                 gcggTATTCAACTTTTTGGGTGTTTTGCTGGGTGGTCTGAGTGTTGCCTATGCCATTGTGCATATGCTGgcggcgattatctggaacctg                                                                     >  2:384745‑M1/1‑69 (MQ=255)                   ggTATTCAACTTTTTGGGTGTTTTGCTGGGTGGTCTGAGTGTTGCCTATGCCATTGTGCATATGCTGgcggcgattatctggaacctggg                                                                   <  2:405531‑M1/90‑24 (MQ=255)                        tCAACTTTTTGGGTGTTTTGCTGGGTGGTCTGAGTGTTGCCTATGCCATTGTGCATATGCTGgcggcgattatctggaacctgggtacct                                                              <  2:229440‑M1/90‑29 (MQ=255)                              ttttGGGTGTTTTGCTGGGTGGTCTGAGTGTTGCCTATGCCATTGTGCATATGCTGgcggcgattatctggaacctgggtacctggtact                                                        >  2:544050‑M1/1‑56 (MQ=255)                              ttttGGGTGTTTTGCTGGGTGGTCTGAGTGTTGCCTATGCCATTGTGCATATGCTGgcggcgattatctggaacctgggtacctggtact                                                        >  1:404657‑M1/1‑56 (MQ=255)                               tttGGGTGTTTTGCTGGGTGGTCTGAGTGTTGCCTATGCCATTGTGCATATGCTGgcggcgattatctggaacctgggtacctggtactt                                                       <  1:544050‑M1/90‑36 (MQ=255)                                     tgtTTTGCTGGGTGGTCTGAGTGTTGCCTATGCCATTGTGCATATGCTGgcggcgattatctggaacctgggtacctggtactttggttt                                                 >  2:79714‑M1/1‑49 (MQ=255)                                     tgtTTTGCTGGGTGGTCTGAGTGTTGCCTATGCCATTGTGCATATGCTGgcggcgattatctggaacctgggtacctggtactttggttt                                                 <  1:564449‑M1/90‑42 (MQ=255)                                     tgtTTTGCTGGGTGGTCTGAGTGTTGCCTATGCCATTGTGCATATGCTGgcggcgattatctggaacctgggtacctggtactttggttt                                                 <  1:367902‑M1/90‑42 (MQ=255)                                        tttGCTGGGTGGTCTGAGTGTTGCCTATGCCATTGTGCATATGCTGgcggcgattatctggaacctgggtacctggtactttggtttacc                                              >  1:449709‑M1/1‑46 (MQ=255)                                             tGGGTGGTCTGAGTGTTGCCTATGCCATTGTGCATATGCTGgcggcgattatctggaacctgggtacctggtactttggtttacctgcat                                         <  1:384745‑M1/90‑50 (MQ=255)                                              gggTGGTCTGAGTGTTGCCTATGCCATTGTGCATATGCTGgcggcgattatctggaacctgggtacctggtactttggtttacctgcatc                                        >  1:233559‑M1/1‑40 (MQ=255)                                                  ggtCTGAGTGTTGCCTATGCCATTGTGCATATGCTGgcggcgattatctggaacctgggtacctggtactttggtttacctgcatccagc                                    <  2:452797‑M1/90‑55 (MQ=255)                                                   gtCTGAGTGTTGCCTATGCCATTGTGCATATGCTGgcggcgattatctggaacctgggtacctggtactttggtttacctgcatccagct                                   >  1:533683‑M1/1‑35 (MQ=255)                                                       gAGTGTTGCCTATGCCATTGTGCATATGCTGgcggcgattatctggaacctgggtacctggtactttggtttacctgcatccagctctca                               <  2:468962‑M1/90‑60 (MQ=255)                                                            ttGCCTATGCCATTGTGCATATGCTGgcggcgattatctggaacctgggtacctggtactttggtttacctgcatccagctctcatacgc                          >  1:292149‑M1/1‑26 (MQ=255)                                                             tGCCTATGCCATTGTGCATATGCTGgcggcgattatctggaacctgggtacctggtactttggtttacctgcatccagctctcatacgct                         >  2:58608‑M1/1‑25 (MQ=255)                                                             tGCCAATGCCATTGTGCATATGCTGgcggcgattatctggaacctgggtacctggtactttggtttacctgcatccagctctcatacgct                         >  1:352584‑M1/1‑25 (MQ=255)                                                                cTATGCCATTGTGCATATGCTGgcggcgattatctggaacctgggtacctggtactttggtttacctgcatccagctctcatacgctgat                      <  1:453665‑M1/90‑69 (MQ=255)                                                                        ttGTGCATATGCTGgcggcgattatctggaacctgggtacctggtactttggtttacctgcatccagctctcatacgctgattggcgcga              >  1:478298‑M1/1‑14 (MQ=255)                                                                          gtgCATATGCTGgcggcgattatctggaacctgggtacctggtactttggtttacctgcatccagctctcatacgctgattggcgcgatc            >  1:450707‑M1/1‑12 (MQ=255)                                                                            gCATATGCTGgcggcgattatctggaacctgggtacctggtactttggtttacctgcatccagctctcatacgctgattggcgcgatcat          >  1:542995‑M1/1‑10 (MQ=255)                                                                             cATATGCTGgcggcgattatctggaacctgggtacctggtactttggtttacctgcatccagctctcatacgctgattggcgcgatcatc         <  2:292149‑M1/90‑82 (MQ=255)                                                                             cATATGCTGgcggcgattatctggaacctgggtacctggtactttggtttacctgcatccagctctcatacgctgattggcgcgatcatc         <  2:449709‑M1/90‑82 (MQ=255)                                                                                  gCTGgcggcgattatctggaacctgggtacctggtactttggtttacctgcatccagctctcatacgctgattggcgcgatcatcgggat    <  2:404657‑M1/90‑87 (MQ=255)                                                                                  gCTGgcggcgattatctggaacctgggtacctggtactttggtttacctgcatccagctctcatacgctgattggcgcgatcatcgggat    <  2:166751‑M1/90‑87 (MQ=255)                                                                                  gCTGgcggcgattatctggaacctgggtacctggtactttggtttacctgcatccagctctcatacgctgattggcgcgatcatcgggat    <  1:162860‑M1/90‑87 (MQ=255)                                                                                    tGgcggcgattatctggaacctgggtacctggtactttggtttacctgcatccagctctcatacgctgattggcgcgatcatcgggattg  >  2:180281‑M1/1‑2 (MQ=255)                                                                                    tGgcggcgattatctggaacctgggtacctggtactttggtttacctgcatccagctctcatacgctgattggcgcgatcatcgggattg  >  1:298321‑M1/1‑2 (MQ=255)                                                                                    tGgcggcgattatctggaacctgggtacctggtactttggtttacctgcatccagctctcatacgctgattggcgcgatcatcgggattg  >  2:105045‑M1/1‑2 (MQ=255)                                                                                    tGgcggcgattatctggaacctgggtacctggtactttggtttacctgcatccagctctcatacgctgattggcgcgatcatcgggattg  >  1:48083‑M1/1‑2 (MQ=255)                                                                                    tGgcggcgattatctggaacctgggtacctggtactttggtttacctgcatccagc                                    >  1:318351‑M1/1‑2 (MQ=255)                                                                                    tGgcggcgattatctggaacctgggtacctggtactttggtttacctgcatccagc                                    <  2:318351‑M1/56‑55 (MQ=255)                                                                                     |                                                                                         CGCCGTGGTTATGGCGGCGGTATTCAACTTTTTGGGTGTTTTGCTGGGTGGTCTGAGTGTTGCCTATGCCATTGTGCATATGCTGCCGACGGATCTGCTGCTTAATATGGGATCGTCTCATGGCCTTGCCATGGTGTTCTCTATGTTGCTGGCGGCGATTATCTGGAACCTGG  >  NZ_CP009273/3631157‑3631329

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑