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

TATGCTGCCGACGGATCTGCTGCTTAATATGGGATCGTCTCATGGCCTTGCCATGGTGTTCTCTATGTTGCTGGCGGCGATTATCTGGAACCTGGGTACCTGGTACTTTGGTTTACCTGCATCCAGCTCTCATACGCTGATTGGCGCGATCATCGGGATTG  >  NZ_CP009273/3631235‑3631395                                                                          |                                                                                        ggcggcggtattcaactttttgggtgttttgctgggtggtctgagtgttgcctatgccattgtgcatatgctgGCGGCGATTATCTGGaa                                                                         <  2:495705‑M2/17‑1 (MQ=255)   cggcggtattcaactttttgggtgttttgctgggtggtctgagtgttgcctatgccattgtgcatatgctgGCGGCGATTATCTGGa                                                                          >  2:52629‑M2/72‑87 (MQ=255)   cggcggtattcaactttttgggtgttttgctgggtggtctgagtgttgcctatgccattgtgcatatgctgGCGGCGATTATCTGGa                                                                          <  1:52629‑M2/16‑1 (MQ=255)    ggcgggattcaactttttgggtgttttgctggggggtctgagggttgcctatgccattttgcatatgctgGCGGCGGTTATCTGGAACCt                                                                      >  1:452797‑M2/71‑90 (MQ=255)     gcggtattcaactttttgggtgttttgctgggtggtctgagtgttgcctatgccattgtgcatatgctgGCGGCGATTATCTGGAACCTg                                                                     >  2:384745‑M2/70‑90 (MQ=255)       ggtattcaactttttgggtgttttgctgggtggtctgagtgttgcctatgccattgtgcatatgctgGCGGCGATTATCTGGAACCTggg                                                                   <  2:405531‑M2/23‑1 (MQ=255)            tcaactttttgggtgttttgctgggtggtctgagtgttgcctatgccattgtgcatatgctgGCGGCGATTATCTGGAACCTGGGTACCt                                                              <  2:229440‑M2/28‑1 (MQ=255)                  ttttgggtgttttgctgggtggtctgagtgttgcctatgccattgtgcatatgctgGCGGCGATTATCTGGAACCTGGGTACCTGGTACt                                                        >  2:544050‑M2/57‑90 (MQ=255)                  ttttgggtgttttgctgggtggtctgagtgttgcctatgccattgtgcatatgctgGCGGCGATTATCTGGAACCTGGGTACCTGGTACt                                                        >  1:404657‑M2/57‑90 (MQ=255)                   tttgggtgttttgctgggtggtctgagtgttgcctatgccattgtgcatatgctgGCGGCGATTATCTGGAACCTGGGTACCTGGTACtt                                                       <  1:544050‑M2/35‑1 (MQ=255)                         tgttttgctgggtggtctgagtgttgcctatgccattgtgcatatgctgGCGGCGATTATCTGGAACCTGGGTACCTGGTACTTTGGttt                                                 >  2:79714‑M2/50‑90 (MQ=255)                         tgttttgctgggtggtctgagtgttgcctatgccattgtgcatatgctgGCGGCGATTATCTGGAACCTGGGTACCTGGTACTTTGGttt                                                 <  1:367902‑M2/41‑1 (MQ=255)                         tgttttgctgggtggtctgagtgttgcctatgccattgtgcatatgctgGCGGCGATTATCTGGAACCTGGGTACCTGGTACTTTGGttt                                                 <  1:564449‑M2/41‑1 (MQ=255)                            tttgctgggtggtctgagtgttgcctatgccattgtgcatatgctgGCGGCGATTATCTGGAACCTGGGTACCTGGTACTTTGGTTTAcc                                              >  1:449709‑M2/47‑90 (MQ=255)                                 tgggtggtctgagtgttgcctatgccattgtgcatatgctgGCGGCGATTATCTGGAACCTGGGTACCTGGTACTTTGGTTTACCTGCAt                                         <  1:384745‑M2/49‑1 (MQ=255)                                  gggtggtctgagtgttgcctatgccattgtgcatatgctgGCGGCGATTATCTGGAACCTGGGTACCTGGTACTTTGGTTTACCTGCATc                                        >  1:233559‑M2/41‑90 (MQ=255)                                      ggtctgagtgttgcctatgccattgtgcatatgctgGCGGCGATTATCTGGAACCTGGGTACCTGGTACTTTGGTTTACCTGCATCCAGc                                    <  2:452797‑M2/54‑1 (MQ=255)                                       gtctgagtgttgcctatgccattgtgcatatgctgGCGGCGATTATCTGGAACCTGGGTACCTGGTACTTTGGTTTACCTGCATCCAGct                                   >  1:533683‑M2/36‑90 (MQ=255)                                           gagtgttgcctatgccattgtgcatatgctgGCGGCGATTATCTGGAACCTGGGTACCTGGTACTTTGGTTTACCTGCATCCAGCTCTCa                               <  2:468962‑M2/59‑1 (MQ=255)                                                ttgcctatgccattgtgcatatgctgGCGGCGATTATCTGGAACCTGGGTACCTGGTACTTTGGTTTACCTGCATCCAGCTCTCATACGc                          >  1:292149‑M2/27‑90 (MQ=255)                                                 tgcctatgccattgtgcatatgctgGCGGCGATTATCTGGAACCTGGGTACCTGGTACTTTGGTTTACCTGCATCCAGCTCTCATACGCt                         >  2:58608‑M2/26‑90 (MQ=255)                                                 tgccaatgccattgtgcatatgctgGCGGCGATTATCTGGAACCTGGGTACCTGGTACTTTGGTTTACCTGCATCCAGCTCTCATACGCt                         >  1:352584‑M2/26‑90 (MQ=255)                                                 tGCCATGGTGTTCTCTATGTTGCTGGCGGCGATTATCTGGAACCTGGGTACCTGGTACTTTGGTTTACCTGCATCCAGCTCTCATACGCt                         >  1:55417/1‑90 (MQ=255)                                                    ctatgccattgtgcatatgctgGCGGCGATTATCTGGAACCTGGGTACCTGGTACTTTGGTTTACCTGCATCCAGCTCTCATACGCTGAt                      <  1:453665‑M2/68‑1 (MQ=255)                                                            ttgtgcatatgctgGCGGCGATTATCTGGAACCTGGGTACCTGGTACTTTGGTTTACCTGCATCCAGCTCTCATACGCTGATTGGCGCGa              >  1:478298‑M2/15‑90 (MQ=255)                                                              gtgcatatgctgGCGGCGATTATCTGGAACCTGGGTACCTGGTACTTTGGTTTACCTGCATCCAGCTCTCATACGCTGATTGGCGCGatc            >  1:450707‑M2/13‑90 (MQ=255)                                                                gcatatgctgGCGGCGATTATCTGGAACCTGGGTACCTGGTACTTTGGTTTACCTGCATCCAGCTCTCATACGCTGATTGGCGCGatcat          >  1:542995‑M2/11‑90 (MQ=255)                                                                 catatgctgGCGGCGATTATCTGGAACCTGGGTACCTGGTACTTTGGTTTACCTGCATCCAGCTCTCATACGCTGATTGGCGCGatcatc         <  2:292149‑M2/81‑1 (MQ=255)                                                                 catatgctgGCGGCGATTATCTGGAACCTGGGTACCTGGTACTTTGGTTTACCTGCATCCAGCTCTCATACGCTGATTGGCGCGatcatc         <  2:449709‑M2/81‑1 (MQ=255)                                                                      gctgGCGGCGATTATCTGGAACCTGGGTACCTGGTACTTTGGTTTACCTGCATCCAGCTCTCATACGCTGATTGGCGCGATCATCGGGAt    <  2:404657‑M2/86‑1 (MQ=255)                                                                      gctgGCGGCGATTATCTGGAACCTGGGTACCTGGTACTTTGGTTTACCTGCATCCAGCTCTCATACGCTGATTGGCGCGATCATCGGGAt    <  2:166751‑M2/86‑1 (MQ=255)                                                                      gctgGCGGCGATTATCTGGAACCTGGGTACCTGGTACTTTGGTTTACCTGCATCCAGCTCTCATACGCTGATTGGCGCGATCATCGGGAt    <  1:162860‑M2/86‑1 (MQ=255)                                                                        tgGCGGCGATTATCTGGAACCTGGGTACCTGGTACTTTGGTTTACCTGCATCCAGc                                    <  2:318351‑M2/54‑1 (MQ=255)                                                                        tgGCGGCGATTATCTGGAACCTGGGTACCTGGTACTTTGGTTTACCTGCATCCAGc                                    >  1:318351‑M2/3‑56 (MQ=255)                                                                        tgGCGGCGATTATCTGGAACCTGGGTACCTGGTACTTTGGTTTACCTGCATCCAGCTCTCATACGCTGATTGGCGCGATCATCGGGATTg  >  2:180281‑M2/3‑90 (MQ=255)                                                                        tgGCGGCGATTATCTGGAACCTGGGTACCTGGTACTTTGGTTTACCTGCATCCAGCTCTCATACGCTGATTGGCGCGATCATCGGGATTg  >  1:298321‑M2/3‑90 (MQ=255)                                                                        tgGCGGCGATTATCTGGAACCTGGGTACCTGGTACTTTGGTTTACCTGCATCCAGCTCTCATACGCTGATTGGCGCGATCATCGGGATTg  >  2:105045‑M2/3‑90 (MQ=255)                                                                        tgGCGGCGATTATCTGGAACCTGGGTACCTGGTACTTTGGTTTACCTGCATCCAGCTCTCATACGCTGATTGGCGCGATCATCGGGATTg  >  1:48083‑M2/3‑90 (MQ=255)                                                                          |                                                                                        TATGCTGCCGACGGATCTGCTGCTTAATATGGGATCGTCTCATGGCCTTGCCATGGTGTTCTCTATGTTGCTGGCGGCGATTATCTGGAACCTGGGTACCTGGTACTTTGGTTTACCTGCATCCAGCTCTCATACGCTGATTGGCGCGATCATCGGGATTG  >  NZ_CP009273/3631235‑3631395

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑