Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	4,416,405	A→G	intergenic (+31/+40)	rplI → / ← yjfZ	50S ribosomal protein L9/DUF2686 family protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	4,416,405	0	A	G	100.0%	98.3 / NA	28	intergenic (+31/+40)	rplI/yjfZ	50S ribosomal protein L9/DUF2686 family protein
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (14/14);  total (14/14)

TTCCAGGTTCACAGCGAAGTATTCGCGAAAGTGATCGTAAACGTAGTAGCTGAATAATTCGTTATTCAACGAGACGTAAAAACGCCGACCATTGGTCGGCGTTTTGCTTTCTATTTTTCGTCAGGTATTAGTTTCGCAAGTAGATCCATTCACCATTCTCTTGTGTCCATAAG  >  NZ_CP009273/4416318‑4416490                                                                                        |                                                                                      ttCCAGGTTCACAGCGAAGTATTCGCGAAAGTGATCGTAAACGTAGTAGCTGAATAATTCGTTATTCAACGAGACGTAAAAACGCCGGcc                                                                                     >  2:462195/1‑90 (MQ=255)                        cgcgAAAGTGATCGTAAACGTAGTAGCTGAATAATTCGTTATTCAACGAGACGTAAAAACGCCGGCCATTGGTCGGCGTTTTGCTTTCTa                                                              >  1:56855/1‑90 (MQ=255)                        cgcgAAAGTGATCGTAAACGTAGTAGCTGAATAATTCGTTATTCAACGAGACGTAAAAACGCCGGCCATTGGTCGGCGTTTTGCTTTCTa                                                              >  1:57221/1‑90 (MQ=255)                             aaGTGATCGTAAACGTAGTAGCTGAATAATTCGTTATTCAACGAGACGTAAAAACGCCGGCCATTGGTCGGCGTTTTGTTTTCTAttttt                                                         >  1:299623/1‑90 (MQ=255)                             aaGTGATCGTAAACGTAGTAGCTGAATAATTCGTTATTCAACGAGACGTAAAAACGCCGGCCATTGGTCGGCGTTTTGCtt                                                                  >  1:306734/1‑81 (MQ=255)                             aaGTGATCGTAAACGTAGTAGCTGAATAATTCGTTATTCAACGAGACGTAAAAACGCCGGCCATTGGTCGGCGTTTTGCtt                                                                  <  2:306734/81‑1 (MQ=255)                             aaGTGATCGTAAACGTAGTAGCTGAATAATTCGTTATTCAACGAGACGTAAAAACGCCGGCCATTGGTCGGCGTTTTGCTTTCTAttttt                                                         >  2:449604/1‑90 (MQ=255)                                 gATCGTAAACGTAGTAGCTGAATAATTCGTTATTCAACGAGACGTAAAAACGCCGGCCATTGGTCGGCGTTTTGCTTTCTATTTTTCGTc                                                     <  2:153180/90‑1 (MQ=255)                                  aTCGTAAACGTAGTAGCTGAATAATTCGTTATTCAACGAGACGTAAAAACGCCGGCCATTGGTCGGCGTTTTGCTTTCTATTTTTCGTCa                                                    <  1:449604/90‑1 (MQ=255)                                      tAAACGTAGTAGCTGAATAATTCGTTATTCAACGAGACGTAAAAACGCCGGCCATTGGTCGGCGTTTTGCt                                                                   >  2:197127/1‑71 (MQ=255)                                      tAAACGTAGTAGCTGAATAATTCGTTATTCAACGAGACGTAAAAACGCCGGCCATTGGTCGGCGTTTTGCt                                                                   <  1:197127/71‑1 (MQ=255)                                              gtagCTGAATAATTCGTTATTCAACGAGACGTAAAAACGCCGGCCATTGGTCGGCGTTTTGCTTTCTATTTTTCGTCAGGTATTAGTTTc                                        >  1:517883/1‑90 (MQ=255)                                               tagCTGAATAATTCGTTATTCAACGAGACGTAAAAACGCCGGCCATTGGTCGGCGTTTTGCTTTCTATTTTTCGTCAGGTATTAGTTTCg                                       <  2:158477/90‑1 (MQ=255)                                                    gAATAATTCGTTATTCAACGAGACGTAAAAACGCCGGCCATTGGTCGGCGTTTTGCTTTCTATTTTTCGTCAGGTATTAGTTTCGCAAGt                                  <  2:208961/90‑1 (MQ=255)                                                    gAATAATTCGTTATTCAACGAGACGTAAAAACGCCGGCCATTGGTCGGCGTTTTGCTTTCTATTTTTCGTCAGGTATTAGTTTCGCAAGt                                  >  2:292268/1‑90 (MQ=255)                                                    gAATAATTCGTTATTCAACGAGACGTAAAAACGCCGGCCATTGGTCGGCGTTTTGCTTTCTATTTTTCGTCAGGTATTAGTTTCGCAAGt                                  <  2:517883/90‑1 (MQ=255)                                                      ataatTCGTTATTCAACGAGACGTAAAAACGCCGGCCATTGGTCGGCGTTTTGCTTTCTATTTTTCGTCAGGTATTAGTTTCGCAAGTAg                                >  2:410242/1‑90 (MQ=255)                                                      ataatTCGTTATTCAACGAGACGTAAAAACGCCGGCCATTGGTCGGCGTTTTGCTTTCTATTTTTCGTCAGGTATTAGTTTCGCAAGTAg                                <  1:394113/90‑1 (MQ=255)                                                              ttATTCAACGAGACGTAAAAACGCCGGCCATTGGTCGGCGTTTTGCTTTCTATTTTTCGTCAGGTATTAGTTTCGCAAGTAGATCCATTc                        >  1:87697/1‑90 (MQ=255)                                                              ttATTCAACGAGACGTAAAAACGCCGGCCATTGGTCGGCGTTTTGCTTTCTATTTTTCGTCAGGTATTAGTTTCGCAAGTAGATCCATTc                        >  2:338501/1‑90 (MQ=255)                                                              ttATTCAACGAGACGTAAAAACGCCGGCCATTGGTCGGCGTTTTGCTTTCTATTTTTCGTCAGGTATTAGTTTCGCAAGTAGATCCATTc                        <  2:452969/90‑1 (MQ=255)                                                              ttATTCAACGAGACGTAAAAACGCCGGCCATTGGTCGGCGTTTTGCTTTCTATTTTTCGTCAGGTATTAGTTTCGCAAGTAGATCCATTc                        <  2:558552/90‑1 (MQ=255)                                                              ttATTCAACGAAACGTAAAACCGCCGGCCATTGGTCGGCGTTTTTTTTTCTATTTTTCGTCAGGTATTAGTTTCGCAAGTAGATCCATTc                        <  1:509572/90‑1 (MQ=255)                                                                aTTCAACGAGACGTAAAAACGCCGGCCATTGGTCGGCGTTTTGCTTTCTATTTTTCGTCAGGTATTAGTTTCGCAAGTAGATCCATTCAc                      <  1:338501/90‑1 (MQ=255)                                                                        agaCGTAAAAACGCCGGCCATTGGTCGGCGTTTTGCTTTCTATTTTTCGTCAGGTATTAGTTTCGCAAGTAGATCCATTCACCATTctct              >  1:477330/1‑90 (MQ=255)                                                                                 accGCCGGCCATTGGTCCGCGTTTTGCTTTCTATTTTTCGTCAGGTATTAGTTTCGCAAGTAGATCCATTCACCATTCTCTTGTGTCCAt     <  2:299623/88‑1 (MQ=255)                                                                                 aaCGCCGGCCATTGGTCGGCGTTCTGCTTTCTATTTTTCGTCAGGTATTAGTTTCGCAAGTAGATCCATTCACCATTCTCTTGTGTCCAt     <  1:485412/90‑1 (MQ=255)                                                                                    gCCGGCCATTGGTCGGCGTTTTGCTTTCTATTTTTCGTCAGGTATTAGTTTCGCAAGTAGATCCATTCACCATTCTCTTGTGTCCATAAg  >  2:344062/1‑90 (MQ=255)                                                                                        |                                                                                      TTCCAGGTTCACAGCGAAGTATTCGCGAAAGTGATCGTAAACGTAGTAGCTGAATAATTCGTTATTCAACGAGACGTAAAAACGCCGACCATTGGTCGGCGTTTTGCTTTCTATTTTTCGTCAGGTATTAGTTTCGCAAGTAGATCCATTCACCATTCTCTTGTGTCCATAAG  >  NZ_CP009273/4416318‑4416490

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑