Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	1,966,502	Δ1 bp	coding (447/1662 nt)	tar ←	methyl‑accepting chemotaxis protein II

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	1,966,500	0	A	.	100.0%	89.9 / NA	22	coding (449/1662 nt)	tar	methyl‑accepting chemotaxis protein II
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base . (6/16);  total (6/16)

ATATCGCGATACAGTTTTTCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCGAAATAAGCTCCAGTATTGCCATAATCTAGATAATCAATCAGTTCAGTTAACGCTGTGTAATAGTTTTTATATTTTT  >  NZ_CP009273/1966413‑1966575                                                                                        |                                                                            atatCGCGATACAGTTTTTCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCGaat                                                                           >  2:44455/1‑89 (MQ=255) atatCGCGATACAGTTTTTCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCGaat                                                                           >  2:32017/1‑89 (MQ=255) atatCGCGATACAGTTTTTCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCGaat                                                                           >  2:523313/1‑89 (MQ=255) atatCGCGATACAGTTTTTCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCGaat                                                                           <  1:32017/90‑2 (MQ=255) atatCGCGATACAGTTTTTCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCGaat                                                                           <  2:76425/90‑2 (MQ=255)   atCGCGATACAGTTTTTCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCGaataa                                                                         <  1:569181/90‑4 (MQ=255)         aTACAGTTTTTCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCa                                                                  >  1:249330/1‑90 (MQ=255)             aGTTTTTCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTAt                                                              <  2:234340/90‑1 (MQ=255)                  ttCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCa                                                         <  1:206562/90‑1 (MQ=255)                  ttCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCa                                                         <  1:51407/90‑1 (MQ=255)                  ttCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCa                                                         <  1:447640/90‑1 (MQ=255)                        gctgAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCt                                                   >  1:477591/1‑90 (MQ=255)                          tgAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAg                                                 <  1:328097/90‑1 (MQ=255)                                    cTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATaatcaatc                                       <  1:488026/90‑1 (MQ=255)                                    cTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATaatcaatc                                       <  1:520691/90‑1 (MQ=255)                                       aGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTAGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATaatcaatc                                       <  1:254299/87‑1 (MQ=255)                                       aGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTAGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATaatcaatc                                       >  2:254299/1‑87 (MQ=255)                                        gCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATAATCAAtcagtt                                   <  2:111921/90‑1 (MQ=255)                                        gCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATAATCAAtcagtt                                   <  2:237893/90‑1 (MQ=255)                                        gCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATAATCAAtcagtt                                   <  1:210961/90‑1 (MQ=255)                                        gCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATAATCAAtcagtt                                   <  2:477591/90‑1 (MQ=255)                                        gCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATAATCAAtcagtt                                   <  2:417522/90‑1 (MQ=255)                                                ttCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATAATCAATCAGTTCAGTTAAc                           <  1:214996/90‑1 (MQ=255)                                                           cattttgcattCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATAATCAATCAGTTCAGTTAACGCTGTGTAATa                <  2:95383/90‑1 (MQ=255)                                                               ttgcattCCCTGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATAATCAATCAGTTCAGTTAACGCTGTGTAATAGttt            >  1:67170/1‑90 (MQ=255)                                                                         tGGGTTGGCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATAATCAATCAGTTCAGTTAACGCTGTGTAATAGTTTTTATAttttt  >  2:324364/1‑90 (MQ=255)                                                                                gCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATAATCAATCAGTTCAGTTAACGCtg                       <  2:101353/62‑1 (MQ=255)                                                                                gCTGAGCG‑AATAAGCTCCAGTATTGCCATAATCTAGATAATCAATCAGTTCAGTTAACGCtg                       >  1:101353/1‑62 (MQ=255)                                                                                        |                                                                            ATATCGCGATACAGTTTTTCACTGCTGAGGGCGTACTGAGCAAACGCTTCGCCCATTGCATTTTGCATTCCCTGGGTTGGCTGAGCGAAATAAGCTCCAGTATTGCCATAATCTAGATAATCAATCAGTTCAGTTAACGCTGTGTAATAGTTTTTATATTTTT  >  NZ_CP009273/1966413‑1966575

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑