Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,776,963	T→C	Y29Y (TAT→TAC)	ypjJ →	CP4‑57 prophage; DUF987 domain‑containing protein YpjJ

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,776,963	0	T	C	100.0%	46.0 / NA	14	Y29Y (TAT→TAC)	ypjJ	CP4‑57 prophage; DUF987 domain‑containing protein YpjJ
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (5/9);  total (5/9)

CAATGACGATATACCGCCAGCATCCTGAGTCCCGAATCTTTCGCTACTGCACCGGAAAATATCAGTGGCACGGTAGCGTCTGTCATTACACCGGCAGGGATGTTCCGGATATCACAGGAGTCCTGGCTGTGTACGCCGAACGCCGCAGGACCGCAGCGGACCGTATGCTTGACTGATGAGTATCACCCTGAAC  >  NC_000913/2776902‑2777094                                                              |                                                                                                                                    cAATGACGATATACCGCCAGCATCCTGAGTCCCGAATCTTTCGCTACTGCACCGGCAAATACCAGTGGCACGGTAGCGTCTGTCATTACACCGGCAGGGACGTTCCGGATATCACAGGAGTCCTGGCTGTGTACGCCGaa                                                       <  2:246051/140‑1 (MQ=255)  aaTGACGATATACCGCCAGCATCCTGAGTCCCGAATCTTTCGCTACTGCACCGGCAAATACCAGTGGCACGGTAGCGTCTGTCATTACACCGGCAGGGACGTTCCGGATATCACAGGAGTCCTGGCTGTGTACGCCGAAc                                                      <  2:64560/140‑1 (MQ=255)               cGCCAGCATCCTGAGTCCCGAATCTTTCGCTACTGCACCGGCAAATACCAGTGGCACGGTAGCGTCTGTCATTACACCGGCAGGGACGTTCCGGATATCACAGGAGTCCTGGCTGTGTACGCCGAACGCCGCAGGACCGc                                         >  2:245797/1‑140 (MQ=255)                gCCAGCATCCTGAGTCCCGAATCTTTCGCTACTGCACCGGCAAATACCAGTGGCACGGTAGCGTCTGTCATTACACCGGCAGGGACGTTCCGGATATCACAGGAGTCCTGGCTGTGTACGCCGAACGCCGCAGGACCGCa                                        >  1:172010/1‑140 (MQ=255)                 ccAGCATCCTGAGTCCCGAATCTTTCGCTACTGCACCGGCAAATACCAGTGGCACGGTAGCGTCTGTCATTACACCGGCAGGGACGTTCCGGATATCACAGGAGTCCTGGCTGTGTACGCCGAACGCCGCAGGACCGCAg                                       >  1:159736/1‑140 (MQ=255)                 ccAGCATCCTGAGTCCCGAATCTTTCGCTACTGCACCGGCAAATACCAGTGGCACGGTAGCGTCTGTCATTACACCGGCAGGGACGTTCCGGATATCACAGGAGTCCTGGCTGTGTACGCCGAACGCCGCAGGACCGCAg                                       >  2:145520/1‑140 (MQ=255)                    gCATCCTGAGTCCCGAATCTTTCGCTACTGCACCGGCAAATACCAGTGGCACGGTAGCGTCTGTCATTACACCGGCAGGGACGTTCCGGATATCACAGGAGTCCTGGCTGTGTACGCCGAACGCCGCAGGACCGCAGCgg                                    >  2:252455/1‑140 (MQ=255)                        ccTGAGTCCCGAATCTTTCGCTACTGCACCGGCAAATACCAGTGGCACGGTAGCGTCTGTCATTACACCGGCAGGGACGTTCCGGATATCACAGGAGTCCTGGCTGTGTACGCCGAACGCCGCAGGACCGCAGCGGACCg                                <  1:106871/140‑1 (MQ=255)                                 cGAATCTTTCGCTACTGCACCGGCAAATACCAGTGGCACGGTAGCGTCTGTCATTACACCGGCAGGGACGTTCCGGATATCACAGGAGTCCTGGCTGTGTACGCCGAACGCCGCAGGACCGCAGCGGACCGTATGCTTGa                       <  1:145520/140‑1 (MQ=255)                                 cGAATCTTTCGCTACTGCACCGGCAAATACCAGTGGCACGGTAGCGTCTGTCATTACACCGGCAGGGACGTTCCGGATATCACAGGAGTCCTGGCTGTGTACGCCGAACGCCGCAGGACCGCAGCGGACCGTATGCTTGa                       <  1:252455/140‑1 (MQ=255)                                      cTTTCGCTACTGCACCGGCAAATACCAGTGGCACGGTAGCGTCTGTCATTACACCGGCAGGGACGTTCCGGATATCACAGGAGTCCTGGCTGTGTACGCCGAACGCCGCAGGACCGCAGCGGACCGTATGCTTGACtgat                  <  1:134844/140‑1 (MQ=255)                                           gCTACTGCACCGGCAAATACCAGTGGCACGGTAGCGTCTGTCATTACACCGGCAGGGACGTTCCGGATATCACAGGAGTCCTGGCTGTGTACGCCGAACGCCGCAGGACCGCAGCGGACCGTATGCTTGACTGATGAGTa             <  1:323060/140‑1 (MQ=255)                                               cTGCACCGGCAAATACCAGTGGCACGGTAGCGTCTGTCATTACACCGGCAGGGACGTTCCGGATATCACAGGAGTCCTGGCTGTGTACGCCGAACGCCGCAGGACCGCAGCGGACCGTATGCTTGACTGATGAGTATCAc         <  1:76215/140‑1 (MQ=255)                                                      ggcaaaTACCAGTGGCACGGTAGCGTCTGTCATTACACCGGCAGGGACGTTCCGGATATCACAGGAGTCCTGGCTGTGTACGCCGAACGCCGCAGGACCGCAGCGGACCGTATGCTTGACTGATGAGTATCACCCTGAAc  <  1:258054/137‑1 (MQ=255)                                                              |                                                                                                                                    CAATGACGATATACCGCCAGCATCCTGAGTCCCGAATCTTTCGCTACTGCACCGGAAAATATCAGTGGCACGGTAGCGTCTGTCATTACACCGGCAGGGATGTTCCGGATATCACAGGAGTCCTGGCTGTGTACGCCGAACGCCGCAGGACCGCAGCGGACCGTATGCTTGACTGATGAGTATCACCCTGAAC  >  NC_000913/2776902‑2777094

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑