Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,766,859	(T)7→8	coding (942/1074 nt)	rnlA →	CP4‑57 prophage; RNase LS, toxin of the RnlAB toxin‑antitoxin system

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,766,852	1	.	T	100.0%	57.4 / NA	17	T312I (ACT→ATT)	rnlA	CP4‑57 prophage; RNase LS, toxin of the RnlAB toxin‑antitoxin system
Reads supporting (aligned to +/- strand):  ref base . (0/0);  new base T (9/8);  total (9/8)

ATTACATTCTGAAACCGCAATTTGCAGCTACTCTTAGACCGGAACAGATTAACATCATCAGCACAGCCTATAC‑TTTTTTTAATGTGGAACGTCATTCTCTGTTCCACATGGAAACTGTGGTCGATGCCAGCCGTATGAT  >  NC_000913/2766780‑2766918                                                                          |                                                                   aTTACATTCTGAAACCGCAATTTGCAGCTACTCTTAGACCGGAACAGATTAACATCATCAGCACAGCCTATAC‑tttttt                                                              <  2:445621/79‑1 (MQ=255)        tCTGAAACCGCAATTTGCAGCTACTCTTAGACCGGAACAGATTAACATCATCAGCACAGCCTATACTTTTTTTTAAtgtg                                                       >  2:445645/1‑80 (MQ=255)            aaaCCGCAATTTGCAGCTACTCTTAGACCGGAACAGATTAACATCATCAGCACAGCCTATACTTTTTTTTAATGTGGaa                                                    <  2:445622/79‑1 (MQ=255)               ccGCAATTTGCAGCTACTCTTAGACCGGAACAGATTAACATCATCAGCACAGCTTATACTTTTTTTTAATGTGGAACGTCa                                               >  1:445644/1‑81 (MQ=255)                cGCAATTTGCAGCTACTCTTAGACCGGAACAGATTAACATCATCAGCACAGCCTATACTTTTTTTTAATGTGGAACGTCAt                                              <  2:445623/81‑1 (MQ=255)                 gCAATTTGCAGCTACTCTTAGACCGGAACAGATTAACATCATCAGCACAGCCTATACTTTTTTTTAATGTGGAACGTCAtt                                             >  2:445640/1‑81 (MQ=255)                     tttGCAGCTACTCTTAGACCGGAACAGATTAACATCATCAGCACAGCCTATACTTTTTTTTAATGTGGAACGTCATTctct                                         <  1:445624/81‑1 (MQ=255)                       tGCAGCTACTCTTAGACCGGAACAGATTAACATCATCAGCACAGCCTATACTTTTTTTTAATGTGGAACGTCATTCTCTGt                                       >  1:445642/1‑81 (MQ=255)                              aCTCTTAGACCGGAACAGATTAACATCATCAGCACAGCCTATACTTTTTTTTAATGTGGAACGTCATTCTCTGTTCCACAt                                >  2:445663/1‑81 (MQ=255)                               ctctTAGACCGGAACAGATTAACATCATCAGCACAGCCTATACTTTTTTTTAATGTGGAACGTCATTCTCTGTTCCACAt                                <  1:445625/80‑1 (MQ=255)                                  ttAGACCGGAACAGATTAACATCATCAGCACAGCCTATACTTTTTTTTAATGTGGAACGTCATTCTCTGTTCCACATGGa                             >  1:445641/1‑80 (MQ=255)                                       ccGGAACAGATTAACATCATCAGCACAGCCTATACTTTTTTTTAATGTGGAACGTCATTCTCTGTTCCACATGGAAACtgt                       <  1:445626/81‑1 (MQ=255)                                         ggAACAGATTAACATCATCAGCACAGCCTATACTTTTTTTTAATGTGGATCGTCATTCTCTGTTCCACATGGAAACTGTgg                     >  2:445659/1‑81 (MQ=255)                                             cAGATTAACATCATCAGCACAGCCTATACTTTTTTTTAATGTGGAACGTCATTCTCTGTTCCACATGGAAACTGTGGTCGa                 <  1:445627/81‑1 (MQ=255)                                                   aaCATCATCAGCACAGCCTATACTTTTTTTTAATGTGGAACGTCATTCTCTGTTCCACATGGAAACTGTGGTCGATGCCa            <  2:445628/80‑1 (MQ=255)                                                     catcatCAGCACAGCCTATACTTTTTTTTAATGTGGAACGTCATTCTCTGTTCCACATGGAAACTGTGGTCGATGCCAGcc         <  1:445629/81‑1 (MQ=255)                                                          tcaGCACAGCCTATACTTTTTTTTAATGTGGAACGTCATTCTCTGTTCCACATGGAAACTGTGGTCGATGCCAGCCGTAt     >  1:445646/1‑80 (MQ=255)                                                            aGCACAGCCTATACTTTTTTTTAATGTGGAACGTCATTCTCTGTTCCACATGGAAACTGTGGTCGATGCCAGCCGTATGAt  >  2:445656/1‑81 (MQ=255)                                                                          |                                                                   ATTACATTCTGAAACCGCAATTTGCAGCTACTCTTAGACCGGAACAGATTAACATCATCAGCACAGCCTATAC‑TTTTTTTAATGTGGAACGTCATTCTCTGTTCCACATGGAAACTGTGGTCGATGCCAGCCGTATGAT  >  NC_000913/2766780‑2766918

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑