Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000964	3,935,825	Δ1 bp	coding (1190/1191 nt)	rlmI ←	large subunit ribosomal RNA m5C1962 methyltransferase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000964	3,935,825	0	T	.	100.0%	105.8 / NA	23	coding (1190/1191 nt)	rlmI	large subunit ribosomal RNA m5C1962 methyltransferase
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base . (17/6);  total (17/6)

GATGTGCGTTATGAACGGGCAAGAGCGAAACAGCATTTCGAAAGGGTTGCAGGTTGATATTGTATTGAAAGCAGATCAAAAAACAGGAAAACTGACGAGAGGGACAGTGAAGGATATTTTGACGAAATCAAACTTTCATCCGCATGGCATTAAAGTCCGTCTTGAAGATGGCCGCATCGGCCGCGACCAGCAGATCGTTTCTACATAAAAAAAAGCTGCCCCTGAACAGGGCAGCTTTTTCATTTATTTTTTCTGCAGAAGGACCACTTTCAGGTAGTTGCCTTCCGGAAATGCCGAAATCGTTTTGAAATCCTCCGGCAGCGTAAATTCCTCAATGATCGTGTAGCGTTCATTTGTTTCTTTAAAGGCGGCATCAATAAAGCCTTTGAACTTCTTCATGCCAAAGGCGCTGCTGTTTGTAGAGGCAACAATGACACCCTTGTCAGCAGTGATGGCGATCGTTTCCTTCAGCAGGTTTTTATAAT  >  NC_000964/3935581‑3936065                                                                                                                                                                                                                                                     |                                                                                                                                                                                                                                                 gATGTGCGGTATGTACGGGCAAGAGCGAAACAGCATTTCGAAAGGGTTGCAGGTTGATATTGTATTGAAAGCATATCAAAAAACAGGAAAACTGACGAGAGGGACAGTGAAGGATATTTTGACGAAAGCAAACTTACGTCCGCATGGCATTAAAGTCCGTCTTGAAGATGGCCGCGTCGGCCGCGACCAGCAGATCGTTTCTACATAAAAAAAAGCTGCCCCTGAACAGGGCAGCTTTTTCATT‑Atttttt                                                                                                                                                                                                                                           <  2:1154/251‑1 (MQ=255)   tgtgCGTTATGAACGGGCAAGAGCGAAACAGCATTTCGAAAGGGTTGCAGGTTGATATTGTATTGAAAGCAGATCAAAAAACAGGAAAACTGACGAGAGGGACAGTGAAGGATATTTTGACGAAATCAAACTTTCATCCGCATGGCATTAAAGTCCGTCTTGAAGATGGCCGCATCGGCCGCGACCAGCAGATCGTTTCTACATAAAAAAAAGCTGCCCCTGAACAGGGCAGCTTTTTCATT‑ATTTTTTCt                                                                                                                                                                                                                                         >  2:194468/1‑251 (MQ=255)                    cAAGAGCGAAACAGCATTTCGAAAGGGTTGCAGGTTGATATTGTATTGAAAGCAGATCAAAAAACAGGAAAACTGACGAGAGGGACAGTGAAGGATATTTTGACGAAATCAAACTTTCATCCGCATGGCATTAAAGTCCGTCTTGAAGATGGCCGCATCGGCCGCGACCAGCAGATCGTTTCTACATAAAAAAAAGCTGCCCCTGAACAGGGCAGCTTTTTCATT‑ATTTTTTCTGCAGAAGGACCACTTTc                                                                                                                                                                                                                        <  2:149580/251‑1 (MQ=255)                               cAGCATTTCGAAAGGGTTGCAGGTTGATATTGTATTGAAAGCAGATCAAAAAACAGGAAAACTGACGAGAGGGACAGTGAAGGATATTTTGACGAAATCAAACTTTCATCCGCATGGCATTAAAGTCCGTCTTGAAGATGGCCGCATCGGCCGCGACCAGCAGATCGTTTCTACATAAAAAAAAGCTGCCCCTGAACAGGGCAGCTTTTTCATT‑ATTTTTTCTGCAGAAGGACCACTTTCAGGTAGTTGcc                                                                                                                                                                                                             >  1:290475/1‑251 (MQ=255)                                       cGAAAGGGTTGCAGGTTGATATTGTATTGAAAGCAGATCAAAAAACAGGAAAACTGACGAGAGGGACAGTGAAGGATATTTTGACGAAATCAAACTTTCATCCGCATGGCATTAAAGTCCGTCTTGAAGATGGCCGCATCGGCCGCGACCAGCAGATCGTTTCTACATAAAAAAAAGCTGCCCCTGAACAGGGCAGCTTTTTCATT‑ATTTTTTCTGCAGAAGGACCACTTTCAGGTAGTTGCCTTCCGGa                                                                                                                                                                                                      >  1:222417/1‑250 (MQ=255)                                           aGGGTTGCAGGTTGATATTGTATTGAAAGCAGATCAAAAAACAGGAAAACTGACGAGAGGGACAGTGAAGGATATTTTGACGAAATCAAACTTTCATCCGCATGGCATTAAAGTCCGTCTTGAAGATGGCCGCATCGGCCGCGACCAGCAGATCGTTTCTACATAAAAAAAAGCTGCCCCTGAACAGGGCAGCTTTTTCATT‑ATTTTTTCTGCAGAAGGACCACTTTCAGGTAGTTGCCTTCCGGAAATGc                                                                                                                                                                                                 >  2:318524/1‑251 (MQ=255)                                           aGGGTTGCAGGTTGATATTGTATTGAAAGCAGATCAAAAAACAGGAAAACTGACGAGAGGGACAGTGAAGGATATTTTGACGAAATCAAACTTTCATCCGCATGGCATTAAAGTCCGTCTTGAAGATGGCCGCATCGGCCGCGACCAGCAGATCGTTTCTACATAAAAAAAAGCTGCCCCTGAACAGGGCAGCTTTTTCATT‑ATTTTTTCTGCAGAAGGACCACTTTCAGGTAGTTGCCTTCCGGAAATGc                                                                                                                                                                                                 >  2:17296/1‑251 (MQ=255)                                                     gtagATATCGTATTGAAAGCAGATCAAACAACAGGAAAACTGACGAGAGGGACAGTGAAGGATATTTTGACGAAATCAAACTTTCATCCGCATGGCATTAAAGTCCGTCTTGACGATGGCCGCATCGGCCGCGACCAGCAGATCGTTTCTACATAAAAAAAAGCTGCCCCTGCACAGGGCAGCTTTTTCATT‑ATTTTTTCTGCAGAAGGACCACTTTCAGGTAGTTGCCTTCCGGAAATGCCGAAATCGtt                                                                                                                                                                                       >  2:216778/4‑251 (MQ=255)                                                                                                                    atTTTGACGAAATCAAACTTTCATCCGCATGGCATTAAAGTCCGTCTTGAAGATGGCCGCATCGGCCGCGACCAGCAGATCGTTTCTACATAAAAAAAAGCTGCCCCTGAACAGGGCAGCTTTTTCATT‑ATTTTTTCTGCATAAGGACCACTTTCAGGTAGTTGCCTTCCGGAAATGCCGAAATCGTTTTGAAATCCTCCGGCAGCGTAAATTCCACAATGATCGTGTAGCGTTCATTTGTTTCTTTaaa                                                                                                                         <  2:311455/250‑1 (MQ=255)                                                                                                                                         cATCCGCATGGCATTAAAGTCCGTCTTGAAGATGGCCGCATCGGCCGCGACCAGCAGATCGTTTCTACATAAAAAAAAGCTGCCCCTGAACAGGGCAGCTTTTTCATT‑ATTTTTTCTGCAGAAGGACCACTTTCAGGTAGTTGCCTTCCGGAAATGCCGAAATCGTTTTGAAATCCTCCGGCAGCGTAAATTCCTCAATGATCGTGTAGCGTTCATTTGTTTCTTTAAAGGCGGCATCAATAAAGCCTTTg                                                                                                   >  2:231615/1‑251 (MQ=255)                                                                                                                                                       tAAAGTCCGTCTTGAAGATGGCCGCATCGGCCGCGACCAGCAGATCGTTTCTACATAAAAAAAAGCTGCCCCTGAACAGGGCAGCTTTTTCATT‑ATTTTTTCTGCAGAAGGACCACTTTCAGGTAGTTGCCTTCCGGAAATGCCGAAATCGTTTTGAAATCCTCCGGCAGCGTAAATTCCTCAATGATCGTGTAGCGTTCATTTGTTTCTTTAAAGGCGGCATCAATAAAGCCTTTGAACTTCTTCATGc                                                                                      <  2:222417/250‑1 (MQ=255)                                                                                                                                                                   tGAAGATGGCCGCATCGGCCGCGACCAGCAGATCGTTTCTACATAAAAAAAAGCTGCCCCTGAACAGGGCAGGTTTTTCATT‑ATTTTTTCTGCAGAAGGACCACGTTCAGGTAGTTGCCTTCCGGAAATGCCGAAATCGTTTTGAAATCCTCCGGCAGCGTAAATTCCTCAATGATCGTGTAGCGTTCATTTGTTTCTTTAAAGTCGGCATCAATAAAGCCTTTGAACTTCTTCATGCCAAAGGCgct                                                                            <  1:75421/248‑1 (MQ=255)                                                                                                                                                                                       gcgACCAGCAGATCGTTTCTACATAAAAAAAAGCTGCCCCTGAACAGGGCAGCTTTTTCATT‑ATTTTTTCTGCAGAAGGACCACTTTCAGGTAGTTGCCTTCCGGAAATGCCGAAATCGTTTTGAAATCCTCCGGCAGCGTAAATTCCTCAATGATCGTGTAGCGTTCATTTGTTTCTTTAAAGGCGGCATCAATAAAGCCTTTGAACTTCTTCATGCCAAAGGCGCTGCTGTTTGTAGAGGCAACAATg                                                      >  2:111667/1‑250 (MQ=255)                                                                                                                                                                                        cgACCAGCAGATCGTTTCTACATAAAAAAAAGCTGCCCCTGAACAGGGCAGCTTTTTCATT‑ATTTTTTCTGCAGAAGGACCACTTTCAGGTAGTTGCCTTCCGGAAATGCCGAAATCGTTTTGAAATCCTCCGGCAGCGTAAATTCCTCAATGATCGTGTAGCGTTCATTTGTTTCTTTAAAGGCGGCATCAATAAAGCCTTTGAACTTCTTCATGCCAAAGGCGCTGCTGTTTGTAGAGGCAACAATGac                                                    >  2:218594/1‑251 (MQ=255)                                                                                                                                                                                          aCCAGCAGATCGTTTCTACATAAAAAAAAGCTGCCCCTGAACAGGGCAGCTTTTTCATT‑ATTTTTTCTGCAGAAGGACCACTTTCAGGTAGTTGCCTTCCGGAAATGCCGAAATCGTTTTGAAATCCTCCGGCAGCGTAAATTCCTCAATGATCGTGTAGCGTTCATTTGTTTCTTTAAAGGCGGCATCAATAAAGCCTTTGAACTTCTTCATGCCAAAGGCGCTGCTGTTTGTAGAGGCAACAATGacac                                                  >  2:125794/1‑251 (MQ=255)                                                                                                                                                                                                  aTCGTTTCTACATAAAAAAAAGCTGCCCCTGAACAGGGCAGCTTTTTCATT‑ATTTTTTCTGCAGAAGGACCACTTTCAGGTAGTTGCCTTCCGGAAATGCCGAAATCGTTTTGAAATCCTCCGGCAGCGTAAATTCCTCAATGATCGTGTAGCGTTCATTTGTTTCTTTAAAGGCGGCATCAATAAAGCCTTTGAACTTCTTCATGCCAAAGGCGCTGCTGTTTGTAGAGGCAACAATGACACCCTTGTca                                          <  1:194468/251‑1 (MQ=255)                                                                                                                                                                                                           aCATAAAAAAAAGCTGCCCCTGAACAGGGCAGCTTTTTCATT‑ATTTTTTCTGCAGAAGGACCACTTTCAGGTAGTTGCCTTCCGGAAATGCCGAAATCGTTTTGAAATCCTCCGGCAGCGTAAATTCCTCAATGATCGTGTAGCGTTCATTTGTTTCTTTAAAGGCGGCATCAATAAAGCCTTTGAACTTCTTCATGCCAAAGGCGCTGCTGTTTGTAGAGGCAACAATGACACCCTTGTCAGCAGTGATg                                 >  1:106954/1‑251 (MQ=255)                                                                                                                                                                                                                 aaaaaaGCTGCCCCTGAACAGTGCAGGTTTTTCATG‑AGTTTTTCTGCAGAAGGACCACTTTCATGTAGTTGCCTTCCGGAAATGGCGAATTCGTTTTGAAATCCTCCGGCAGCGTAAATTCCTCAATGATCGTGTAGCTTTCATTGTTTTCTTTAAAGGCGGCAGCAATAAAGCCTTTGAACTTCTTCATGCCAAAGGCGCTGCTGTTTGTAGAGGCAACAATGTGCCCCTTGTCAGCATTGATTGCGATc                           <  2:341257/251‑1 (MQ=255)                                                                                                                                                                                                                            cccTGAACAGGGCAGCTTTTTCATT‑ATTTTTTCTGCAGAAGGACCACTTTCAGGTAGTTGCCTTCCGGAAATGCCGAAATCGTTTTGAAATCCTCCGGCAGCGTAAATTCCTCAATGATCGTGTAGCGTTCATTTGTTTCTTTAAAGGCGGCATCAATAAAGCCTTTGAACTTCTTCATGCCAAAGGCGCTGCTGTTTGTAGAGGCAACAATGACACCCTTGTCAGCAGTGATGGCGATCGTTTCCTTc                  >  1:341637/1‑249 (MQ=255)                                                                                                                                                                                                                              cTGAACAGGGCAGCTTTTTCATT‑ATTTTTTCTGCAGAAGGACCACTTTCAGGTAGTTGCCTTCCGGAAATGCCGAAATCGTTTTGAAATCCTCCGGCAGCGTAAATTCCTCAATGATCGTGTAGCGTTCATTTGTTTCTTTAAAGGCGGCATCAATAAAGCCTTTGAACTTCTTCATGCCAAAGGCGCTGCTGTTTGTAGAGGCAACAATGACACCCTTGTCAGCAGTGATGGCGATCGTTTCCTTcagc               >  1:130802/1‑250 (MQ=255)                                                                                                                                                                                                                                gAACAGGGCAGCTTTTTCATT‑ATTTTTTCTGCAGAAGGACCACTTTCAGGTAGTTGCCTTCCGGAAATGCCGAAATCGTTTTGAAATCCTCCGGCAGCGTAAATTCCTCAATGATCGTGTAGCGTTCATTTGTTTCTTTAAAGGCGGCATCAATAAAGCCTTTGAACTTCTTCATGCCAAAGGCGCTGCTGTTTGTAGAGGCAACAATGACACCCTTGTCAGCAGTGATGGCGATCGTTTCCTTCAGCAgg            >  2:186872/1‑251 (MQ=255)                                                                                                                                                                                                                                   cAGGGCAGCTTTTTCATT‑ATTTTTTCTGCAGAAGGACCACTTTCAGGTAGTTGCCTTCCGGAAATGCCGAAATCGTTTTGAAATCCTCCGGCAGCGTAAATTCCTCAATGATCGTGTAGCGTTCATTTGTTTCTTTAAAGGCGGCATCAATAAAGCCTTTGAACTTCTTCATGCCAAAGGCGCTGCTGTTTGTAGAGGCAACAATGACACCCTTGTCAGCAGTGATGGCGATCGTTTCCTTCAGCAGGttt         >  1:95202/1‑251 (MQ=255)                                                                                                                                                                                                                                         aGCTTTTTCATT‑ATTTTTTCTGCAGAAGGACCACTTTCAGGTAGTTGCCTTCCGGAAATGCCGAAATCGTTTTGAAATCCTCCGGCAGCGTAAATTCCTCAATGATCGTGTAGCGTTCATTTGTTTCTTTAAAGGCGGCATCAATAAAGCCTTTGAACTTCTTCATGCCAAAGGCGCTGCTGTTTGTAGAGGCAACAATGACACCCTTGTCAGCAGTGATGGCGATCGTTTCCTTCAGCAGGTTTTtata    >  1:10564/1‑250 (MQ=255)                                                                                                                                                                                                                                          gCTTTTTCATT‑ATTTTTTCTGCAGAAGGACCAATTTCAGGTAGTTGCCTTCCGGAAATGCCGAAATCGTTTTGAAATCCTCCGGCAGCGTAAATTCCTCAATGATCGTGTAGCGTTCATTTGTTTCTTTAAAGGCGGCATCAATAAAGCCTTTGAACTTCTTCATGCCAAAGGCGCTGCTGTTTGTAGAGGCAACAATGACACCCTTGTCAGCAGTGATGGCGATCGTTTCCTTCAGCAGGTTTTTATAAt  >  1:159602/1‑251 (MQ=255)                                                                                                                                                                                                                                                     |                                                                                                                                                                                                                                                 GATGTGCGTTATGAACGGGCAAGAGCGAAACAGCATTTCGAAAGGGTTGCAGGTTGATATTGTATTGAAAGCAGATCAAAAAACAGGAAAACTGACGAGAGGGACAGTGAAGGATATTTTGACGAAATCAAACTTTCATCCGCATGGCATTAAAGTCCGTCTTGAAGATGGCCGCATCGGCCGCGACCAGCAGATCGTTTCTACATAAAAAAAAGCTGCCCCTGAACAGGGCAGCTTTTTCATTTATTTTTTCTGCAGAAGGACCACTTTCAGGTAGTTGCCTTCCGGAAATGCCGAAATCGTTTTGAAATCCTCCGGCAGCGTAAATTCCTCAATGATCGTGTAGCGTTCATTTGTTTCTTTAAAGGCGGCATCAATAAAGCCTTTGAACTTCTTCATGCCAAAGGCGCTGCTGTTTGTAGAGGCAACAATGACACCCTTGTCAGCAGTGATGGCGATCGTTTCCTTCAGCAGGTTTTTATAAT  >  NC_000964/3935581‑3936065

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑