Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	1,712,684	T→C	intergenic (‑32/+66)	mliC ← / ← anmK	C‑type lysozyme inhibitor/anhydro‑N‑acetylmuramic acid kinase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	1,712,684	0	T	C	100.0%	41.6 / NA	13	intergenic (‑32/+66)	mliC/anmK	C‑type lysozyme inhibitor/anhydro‑N‑acetylmuramic acid kinase
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (6/7);  total (6/7)

TTCCAGCGTATCGGTTTGCATGCGCTCAACCAGCTGATTAAAGGCGCTACAGCCGGAGAGAAGGACCGGCAAAATGATAATTAACAGTTTTTTCATAGTCATATCCCGAAGACTTTCCTGGTCTGGAGGGCAATACGCCCTCCCTAACGTTCCAAGTGTAACGGCAGACGCGGTAAGAAAAATTCAGTTAACTCTGATATCACGGGTTAGCGGGGAAAATAGCCCCCAGTACCGTCTCCTGGCTTGCGCCAGTGACGGAAGGCAGATTT  >  NZ_CP009273/1712551‑1712819                                                                                                                                      |                                                                                                                                        ttCCAGCGTATCGGTTTGCATGCGCTCAACCAGCTGATTAAAGGCGCTACAGCCGGAGAGAAGGACCGGCAAAATGATAATTAACAGTTTTTTCATAGTCATATCCCGAAGACTTTCCTGGTCTGGAGGGCAACACGcc                                                                                                                                    <  2:26762/139‑1 (MQ=255) ttCCAGCGTATCGGTTTGCATGCGCTCAACCAGCTGATTAAAGGCGCTACAGCCGGAGAGAAGGACCGGCAAAATGATAATTAACAGTTTTTTCATAGTCATATCCCGAAGACTTTCCTGGTCTGGAGGGCAACACGc                                                                                                                                     <  2:277751/138‑1 (MQ=255)         tATCGGTTTGCATGCGCTCAACCAGCTGATTAAAGGCGCTACAGCCGGAGAGAAGGACCGGCAAAATGATAATTAACAGTTTTTTCATAGTCATATCCCGAAGACTTTCCTGGTCTGGAGGGCAACACGCCCTCCCTaa                                                                                                                            >  2:126624/1‑139 (MQ=255)                   cATGCGCTCAACCAGCTGATTAAAGGCGCTACAGCCGGAGAGAAGGACCGGCAAAATGATAATTAACAGTTTTTTCATAGTCATATCCCGAAGACTTTCCTGGTCTGGAGGGCAACACGCCCTCCCTAACGTTCCAAgt                                                                                                                  >  1:394848/1‑139 (MQ=255)                                 gCTGATTAAAGGCGCTACAGCCGGAGAGAAGGACCGGCAAAATGATAATTAACAGTTTTTTCATAGTCATATCCCGAAGACTTTCCTGGTCTGGAGGGCAACACGCCCTCCCTAACGTTCCAAGTGTAACGGCAGAcgc                                                                                                    <  1:126624/139‑1 (MQ=255)                                                   aGCCGGAGAGAAGGACCGGCAAAATGATAATTAACAGTTTTTTCATAGTCATATCCCGAAGACTTTCCTGGTCTGGAGGGCAACACGCCCTCCCTAACGTTCCAAGTGTAACGGCAGACGCGGTAAGAAAAATTCAGtt                                                                                  <  2:414951/139‑1 (MQ=255)                                                         agagaAGGACCGGCAAAATGATAATTAACAGTTTTTTCATAGTCATATCCCGAAGACTTTCCTGGTCTGGAGGGCAACACGCCCTCCCTAACGTTCCAAGTGTAACGGCAGACGCGGTAAGAAAAATTCAGTTAActct                                                                            <  2:391872/139‑1 (MQ=255)                                                                                      aGTTTTTTCATAGTCATATCCCGAAGACTTTCCTGGTCTGGAGGGCAACACGCCCTCCCTAACGTTCCAAGCGTAACGGCAGACGCGGTAAGAAAAATTCAGTTAACTCTGATATCACGGGTTAGCGGGGAAAATAGcc                                               <  2:316823/139‑1 (MQ=255)                                                                                               aTAGTCATATCCCGAAGACTTTCCTGGTCTGGAGGGCAACACGCCCTCCCTAACGTTCCAAGTGTAACGGCAGACGCGGTAAGAAAAATTCAGTTAACTCTGATATCACGGGTTAGCGGGGAAAATAGCCCCCAGTAcc                                      <  1:572629/139‑1 (MQ=255)                                                                                                      tatCCCGAAGACTTTCCTGGTCTGGAGGGCAACACGCCCTCCCTAACGTTCCAAGTGTAACGGCAGACGCGGTAAGAAAAATTCAGTTAACTCTGATATCACGGGTTAGCGGGGAAAATAGCCCCCAGTACCGTCTCCt                               >  1:246329/1‑139 (MQ=255)                                                                                                             aaGACTTTCCTGGTCTGGAGGGCAACACGCCCTCCCTAACGTTCCAAGTGTAACGGCAGACGCGGTAAGAAAAATTCAGTTAACTCTGATATCACGGGTTAGCGGGGAAAATAGCCCCCAGTACCGTCTCCTGGCTTgc                        >  1:12950/1‑139 (MQ=255)                                                                                                             aaGACTTTCCTGGTCTGGAGGGCAACACGCCCTCCCTAACGTTCCAAGTGTAACGGCAGACGCGGTAAGAAAAATTCAGTTAACTCTGATATCACGGGTTAGCGGGGAAAATAGCCCCCAGTACCGTCTCCTGGCTTgc                        >  1:579492/1‑139 (MQ=255)                                                                                                                                   cAACACGCCCTCCCTAACGTTCCAAGTGTAACGGCAGACGCGGTAAGAAAAATTCAGTTAACTCTGATATCACGGGTTAGCGGGGAAAATAGCCCCCAGTACCGTCTCCTGGCTTGCGCCAGTGACGGAAGGCAGAttt  >  1:52397/1‑139 (MQ=255)                                                                                                                                      |                                                                                                                                        TTCCAGCGTATCGGTTTGCATGCGCTCAACCAGCTGATTAAAGGCGCTACAGCCGGAGAGAAGGACCGGCAAAATGATAATTAACAGTTTTTTCATAGTCATATCCCGAAGACTTTCCTGGTCTGGAGGGCAATACGCCCTCCCTAACGTTCCAAGTGTAACGGCAGACGCGGTAAGAAAAATTCAGTTAACTCTGATATCACGGGTTAGCGGGGAAAATAGCCCCCAGTACCGTCTCCTGGCTTGCGCCAGTGACGGAAGGCAGATTT  >  NZ_CP009273/1712551‑1712819

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑