Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	4,180,586	(A)7→6	intergenic (+333/+77)	yjaZ → / ← thiH	heat‑shock protein C/2‑iminoacetate synthase ThiH

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	4,180,580	0	A	.	100.0%	161.8 / NA	38	intergenic (+327/+83)	yjaZ/thiH	heat‑shock protein C/2‑iminoacetate synthase ThiH
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base . (14/24);  total (14/24)

TTGCATTACGGAATTTTTAAGAAAGGCAGGGCGAAACGAGGAAGAAGCTTTTCGCCCTGGACAACATTCCTGCTGACGGCACTACCATAAAAAAACACAACGCTTTCAACAACCTTGCGTTTTTCATCTTCCGTAGCGGCTCGGAATAAATTTACGTTCTTACATTCCG  >  NZ_CP009273/4180492‑4180660                                                                                         |                                                                                 ttGCATTACGGAATTTTTAAGAAAGGCAGGGCGAAACGAGGAAGAAGCTTTTCGCCCTGGACAACATTCCTGCTGACGGCACTACCATaa                                                                                 >  2:164486/1‑90 (MQ=255) ttGCATTACGGAATTTTTAAGAAAGGCAGGGCGAAACGAGGAAGAAGCTTTTCGCCCTGGACAACATTCCTGCTGACGGCACTACCATaa                                                                                 >  1:261716/1‑90 (MQ=255) ttGCATTACGGAATTTTTAAGAAAGGCAGGGCGAAACGAGGAAGAAGCTTTTCGCCCTGGACAACATTCCTGCTGACGGCACTACCATaa                                                                                 >  2:124780/1‑90 (MQ=255) ttGCATTACGGAATTTTTAAGAAAGGCAGGGCGAAACGAGGAAGAAGCTTTTCGCCCTGGACAACATTCCTGCTGACGGCACTACCATaa                                                                                 >  1:847408/1‑90 (MQ=255) ttGCATTACGGAATTTTTAAGAAAGGCAGGGCGAAACGAGGAAGAAGCTTTTCGCCCTGGACAACATTCCTGCTGACGGCACTACCATaa                                                                                 >  1:502437/1‑90 (MQ=255) ttGCATTACGGAATTTTTAAGAAAGGCAGGGCGAAACGAGGAAGAAGCTTTTCGCCCTGGACAACATTCCTGCTGACGGCACTACCATaa                                                                                 >  2:559825/1‑90 (MQ=255) ttGCATTACGGAATTTTTAAGAAAGGCAGGGCGAAACGAGGAAGAAGCTTTTCGCCCTGGACAAAATTCCTGCTGACGGCACTACCATaa                                                                                 >  1:981217/1‑90 (MQ=255)   gCATTACGGAATTTTTAAGAAAGGCAGGGCGAAACGAGGAAGAAGCTTTTCGCCCTGGACAACATTCCTGCTGACGGCACTACCATaaaa                                                                               <  1:970286/90‑1 (MQ=255)          ggAATTTTTAAGAAAGGCAGGGCGAAACGAGGAAGAAGCTTTTCGCCCTGGACAACATTCCTGCTGACGGCACTACCAT‑AAAAAACACaa                                                                       <  1:124780/90‑1 (MQ=255)          ggAATTTTTAAGAAAGGCAGGGCGAAACGAGGAAGAAGCTTTTCGCCCTGGACAACATTCCTGCTGACGGCACTACCAT‑AAAAAACACaa                                                                       <  2:806385/90‑1 (MQ=255)          ggAATTTTTAAGAAAGGCAGGGCGAAACGAGGAAGAAGCTTTTCGCCCTGGACAACATTCCTGCTGACGGCACTACCAT‑AAAAAACACaa                                                                       <  1:530702/90‑1 (MQ=255)             aTTTTTAAGAAAGGCAGGGCGAAACGAGGAAGAAGCTTTTCGCCCTGGACAACATTCCTGCTGACGGCACTACCAT‑AAAAAACACAACGc                                                                    <  2:803213/90‑1 (MQ=255)             aTTTTTAAGAAAGGCAGGGCGAAACGAGGAAGAAGCTTTTCGCCCTGGACAACATTCCTGCTGACGGCACTACCAT‑AAAAAACACAACGc                                                                    <  1:387315/90‑1 (MQ=255)             aTTTTTAAGAAAGGCAGGGCGAAACGAGGAAGAAGCTTTTCGCCCTGGACAACATTCCTGCTGACGGCACTACCAT‑AAAAAACACAACGc                                                                    <  1:304122/90‑1 (MQ=255)               ttttAAGAAAGGCAGGGCGAAACGAGGAAGAAGCTTTTCGCCCTGGACAACATTCCTGCTGACGGCACTACCAT‑AAAAAACACAACGCtt                                                                  <  2:847408/90‑1 (MQ=255)               ttttAAGAAAGGCAGGGCGAAACGAGGAAGAAGCTTTTCGCCCTGGACAACATTCCTGCTGACGGCACTACCAT‑AAAAAACACAACGCtt                                                                  <  2:364255/90‑1 (MQ=255)                    aGAAAGGCAGGGCGAAACGAGGAAGAAGCTTTTCGCCCTGGACAACATTCCTGCTGACGGCACTACCAT‑AAAAAACACAACGCTTTcaac                                                             <  1:588448/90‑1 (MQ=255)                    aGAAAGGCAGGGCGAAACGAGGAAGAAGCTTTTCGCCCTGGACAACATTCCTGCTGACGGCACTACCAT‑AAAAAACACAACGCTTTcaac                                                             <  2:367239/90‑1 (MQ=255)                             gggCGAAACGAGGAAGAAGCTTTTCGCCCTGGACAACATTCCTGCTGACGGCACTACCAT‑AAAAAACACAACGCTTTCAACAACCTTGCg                                                    >  1:384090/1‑90 (MQ=255)                                     cGAGGAAGAAGCTTTTCGCCCTGGACAACATTCCTGCTGACGGCACTACCAT‑AAAAAACACAACGCTTTCAACAACCTTGCGTTTTTCAt                                            <  2:384090/90‑1 (MQ=255)                                       aGGAAGAAGCTTTTCGCCCTGGACAACATTCCTGCTGACGGCACTACCAT‑AAAAAACACAACGCTTTCAACAACCTTGCGTTTTTCATCt                                          >  2:876460/1‑90 (MQ=255)                                             aagCTTTTCGCCCTGGACAACATTCCTGCTGACGGCACTACCAT‑AAAAAACACAACGCTTTCAACAACCTTGCGTTTTTCATCTTCCGTa                                    >  1:946098/1‑90 (MQ=255)                                                    tCGCCCTGGACAACATTCCTGCTGACGGCACTACCAT‑AAAAAACACAACGCTTTCAACAACCTTGCGTTTTTCATCTTCCGTAGCGGCTc                             <  2:169335/90‑1 (MQ=255)                                                    tCGCCCTGGACAACATTCCTGCTGACGGCACTACCAT‑AAAAAACACAACGCTTTCAACAACCTTGCGTTTTTCATCTTCCGTAGCGGCTc                             <  2:543052/90‑1 (MQ=255)                                                          tGGACAACATTCCTGCTGACCGCACTACCAT‑AAAAAACACAACGCTTTCAACAACCTTGCGTTTTTCATCTTCCGTAGCGGCTCGGAATa                       <  2:441928/90‑1 (MQ=255)                                                           ggACAACATTCCTGCTGACGGCACTACCAT‑AAAAAACACAACGCTTTCAACAACCTTGCGTTTTTCATCTTCCGTAGCGGCTCGGAATaa                      >  2:891366/1‑90 (MQ=255)                                                                acaTTCCTGCTGACGGCACTACCAT‑AAAAAACACAACGc                                                                    <  2:794767/39‑1 (MQ=38)                                                                acaTTCCTGCTGACGGCACTACCAT‑AAAAAACACAACGc                                                                    >  1:794767/1‑39 (MQ=38)                                                                acaTTCCTGCTGACGGCACTACCAT‑AAAAAACACAACGCTTTCAACAACCTTGCGTTTTTCATCTTCCGTAGCGGCTCGGAATAAATTTa                 >  1:623254/1‑90 (MQ=255)                                                                 caTTCCTGCTGACGGCACTACCAT‑AAAAAACACAACGCTTTCAACAACCTTGCGTTTTTCATCTTCCGTAGCGGCTCGGAATAAATTTAc                <  1:891366/90‑1 (MQ=255)                                                                   ttCCTGCTGACGGCACTACCAT‑AAAAAACACAACGCTTTCAACAACCTTGCGTTTTTCATCTTCCGTAGCGGCTCGGAATAAATTTACGt              <  1:74652/90‑1 (MQ=255)                                                                     ccTGCTGACGGCACTACCAT‑AAAAAACACAACGCTTTcaac                                                             <  2:84108/41‑1 (MQ=39)                                                                     ccTGCTGACGGCACTACCAT‑AAAAAACACAACGCTTTcaac                                                             >  1:84108/1‑41 (MQ=39)                                                                     ccTGCTGACGGCACTACCAT‑AAAAAACACAACGCTTTCAACAACCTTGCGTTTTTCATCTTCCGTAGCGGCTCGGAATAAATTTACGTTc            >  2:971858/1‑90 (MQ=255)                                                                        gctgACGGCACTACCAT‑AAAAAACACAACGCTTTCAACAACCTTGCGTTTTTCATCTTCCGTAGCGGCTCGGAATAAATTTACGTTCTTa         >  2:465975/1‑90 (MQ=255)                                                                           gACGGCACTACCAT‑AAAAAACACAACGCTTTCAACAACCTTGCGTTTTTCATCTTCCGTAGCGGCTCGGAATAAATTTACGTTCTTACAt      >  2:838225/1‑90 (MQ=255)                                                                           gACGGCACTACCAT‑AAAAAACACAACGCTTTCAACAACCTTGCGTTTTTCATCTTCCGTAGCGGCTCGGAATAAATTTACGTTCTTACAt      >  1:738767/1‑90 (MQ=255)                                                                           gACGGCACTACCAT‑AAAAAACACAACGCTTTCAACAACCTTGCGTTTTTCATCTTCCGTAGCGGCTCGGAATAAAATTACGCTCCTACac      >  2:754358/1‑89 (MQ=255)                                                                            aCGGCACTACCAT‑AAAAAACACAACGCTTTCAACAACCTTGCGTTTTTCATCTTCCGTAGCGGCTCGGAATAAATTTACGt              <  2:24281/81‑1 (MQ=255)                                                                            aCGGCACTACCAT‑AAAAAACACAACGCTTTCAACAACCTTGCGTTTTTCATCTTCCGTAGCGGCTCGGAATAAATTTACGt              >  1:24281/1‑81 (MQ=255)                                                                             cGGCACTACCAT‑AAAAAACACAACGCTTTCAACAACCTTGCGTTTTTCATCTTCCGTAGCGGCTCGGAATAAATTTACGTTCTTACATTc    <  2:611931/90‑1 (MQ=255)                                                                             cGGCACTACCAT‑AAAAAACACAACGCTTTCAACAACCTTGCGTTTTTCATCTTCCGTAGCGGCTCGGAATAAATTTACGTTCTTACATTc    <  2:799043/90‑1 (MQ=255)                                                                             cGGCACTACCAT‑AAAAAACACAACGCTTTCAACAACCTTGCGTTTTTCATCTTCCGTAGCGGCTCGGAATAAATTTACGTTCTTACATTc    <  2:576099/90‑1 (MQ=255)                                                                             cGGCACTACCAT‑AAAAAACACAACGCTTTCAACAACCTTGCGTTTTTCATCTTCCGTAGCGGCTCGGAATAAATTTACGTTCTTACATTc    <  1:64217/90‑1 (MQ=255)                                                                             cGGCACTACCAT‑AAAAAACACAACGCTTTCAACAACCTTGCGTTTTTCATCTTCCGTAGCGGCTCGGAATAAATTTACGTTCTTACATTc    >  1:283584/1‑90 (MQ=255)                                                                               gCACTACCAT‑AAAAAACACAACGCTTTCAACAACCTTGCGTTTTTCATCTTCCGTAGCGGCTCGGAATAAATTTACGTTCTTACATTCCg  <  2:694503/90‑1 (MQ=255)                                                                                         |                                                                                 TTGCATTACGGAATTTTTAAGAAAGGCAGGGCGAAACGAGGAAGAAGCTTTTCGCCCTGGACAACATTCCTGCTGACGGCACTACCATAAAAAAACACAACGCTTTCAACAACCTTGCGTTTTTCATCTTCCGTAGCGGCTCGGAATAAATTTACGTTCTTACATTCCG  >  NZ_CP009273/4180492‑4180660

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑