Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	578,489	T→C	F128S (TTC→TCC)  S55P (TCA→CCA)	rzpD → rzoD →	DLP12 prophage; putative prophage endopeptidase RzpD DLP12 prophage; putative prophage lysis lipoprotein RzoD

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	578,489	0	T	C	100.0%	83.4 / NA	26	F128S (TTC→TCC)  S55P (TCA→CCA)	rzpD rzoD	DLP12 prophage; putative prophage endopeptidase RzpD DLP12 prophage; putative prophage lysis lipoprotein RzoD
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (8/18);  total (8/18)

TGAAGCCACCACGGCCTCCGGCGTGGATAATGCAGCCTCCCCCCGACTGGCAGACACCGCTGAACGGGATTATTTCACCCTCAGAGAGAGGCTGATCACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTG  >  NC_000913/578415‑578561                                                                           |                                                                         tGAAGCCACCACGGCCTCCGGCGTGGATAATGCAGCCTCCCCCCGACTGGCAGACACCGCTGAACGGGATTATTCCACCCt                                                                    <  1:124956/81‑1 (MQ=18)  gAAGCCACCACGGCCTCCGGCGTGGATAATGCAGCCTCCCCCCGACTGGCAGACACCGCTGAACGGGATTATTCCACCCt                                                                    >  2:124999/1‑80 (MQ=21)  gAAGCCACCACGGCCTCCGGCGTGGATAATGCAGCCTCCCCCCGACTGGCAGACACCGCTGAACGGGATTATTCCACCCt                                                                    >  1:124988/1‑80 (MQ=21)    aGCCACCACGGCCTCCGGCGTGGATAATGCAGCCTCCCCCCGACTGGCAGACACCGCTGAACGGGATTATTCCACCCt                                                                    >  2:811733/1‑78 (MQ=21)    aGCCACCACGGCCTCCGGCGTGGATAATGCAGCCTCCCCCCGACTGGCAGACACCGCTGAACGGGATTATTCCACCCt                                                                    >  2:124996/1‑78 (MQ=21)                   cGGCGTGGATAATGCAGCCTCCCCCCGACTGGCAGACACCGCTGAACGGGATTATTCCACCCTCAGAGAGAGGCTGATCa                                                   <  1:124959/80‑1 (MQ=255)                   cGGCGTGGATAATGCAGCCTCCCCCCGACTGGCAGACACCGCTGAACGGGATTATTCCACCCTCAGAGAGAGGCTGATCAc                                                  <  2:124957/81‑1 (MQ=255)                   cGGCGTGGATAATGCAGCCTCCCCCCGACTAGCAGACACCGCTGAACGGGATTATTCCACCCTCAGAGAGAGGCTGATCa                                                   <  2:124958/80‑1 (MQ=17)                         ggATAATGCAGCCTCCCCCCGACTGGCAGACACCGCTGAACGGGATTATTCCACCCTCAGAGAGAGGCTGATCACTATGc                                             >  2:125000/1‑80 (MQ=255)                          gATAATGCAGCCTCCCCCCGACTGGCAGACACCGCTGAACGGGATTATTCCACCCTCAGAGAGAGGCTGATCACTATGCaa                                           <  2:124960/81‑1 (MQ=255)                               tGCAGCCTCCCCCCGACTGGCAGACACCGCTGAACGGGATTATTCCACCCTCAGAGAGAGGCTGATCACTATGCAAAaaca                                      <  1:124961/81‑1 (MQ=255)                               tGCAGCCTCCCCCCGACTGGCAGACACCGCTGAACGGGATTATTCCACCCTCAGAGAGAGGCTGATCACTATGCAAAaaca                                      <  1:124962/81‑1 (MQ=255)                                 cAGCCTCCCCCCGACTGGCAGACACCGCTGAACGGGATTATTCCACCCTCAGAGAGAGGCTGATCACTATGCAAAaacaac                                    <  1:684716/81‑1 (MQ=255)                                   gCCTCCCCCCGACTGGCAGACACCGCTGAACGGGATTATTCCACCCTCAGAGAGAGGCTGATCACTATGCAAAAACAACTg                                  <  2:124963/81‑1 (MQ=255)                                        cccccGACTGGCAGACACCGCTGAACGGGATTATTCCACCCTCAGAGAGAGGCTGATCACTATGCAAAAACAACTggaagg                             <  2:124965/81‑1 (MQ=255)                                        cccccGACTGGCAGACACCGCTGAACGGGATTATTCCACCCTCAGAGAGAGGCTGATCACTATGCAAAAACAACTggaagg                             <  1:124964/81‑1 (MQ=255)                                         ccccGACTGGCAGACACCGCTGAACGGGATTATTCCACCCTCAGAGAGAGGCTGATCACTATGCAAAAACAACTggaagg                             >  1:125001/1‑80 (MQ=255)                                          cccGACTGGCAGACACCGCTGAACGGGATTATTCCACCCTCAGAGAGAGGCTGATCACTATGCAAAAACAACTggaaggaa                           <  2:124966/81‑1 (MQ=255)                                            cGACTGGCAGACACCGCTGAACGGGATTATTCCACCCTCAGAGAGAGGCTGATCACTATGCAAAAACAACTGGAAGGAAcc                         <  1:124967/81‑1 (MQ=255)                                                    aGACACCGCTGAACGGGATTATTCCACCCTCAGAGAGAGGCTGATCACTATGCAAAAACAACTGGAAGGAACCCAGAAGta                 <  1:124968/81‑1 (MQ=255)                                                    aGACACCGCTGAACGGGATTATTCCACCCTCAGAGAGAGGCTGATCACTATGCAAAAACAACTGGAAGGAACCCAGAAGta                 >  2:124998/1‑81 (MQ=255)                                                           gCTGAACGGGATTATTCCACCCTCAGAGAGAGGCTGATCACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAAt          <  1:124969/81‑1 (MQ=255)                                                              gAACGGGATTATTCCACCCTCAGAGAGAGGCTGATCACTATGGAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAg       >  2:125014/1‑81 (MQ=255)                                                               aaCGGGATTATTCCACCCTCAGAGAGAGGCTGATCACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGc      <  1:124970/81‑1 (MQ=255)                                                                  gggATTATTCCACCCTCAGAGAGAGGCTGATCACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGt   <  1:236768/81‑1 (MQ=255)                                                                   ggATTATTCCACCCTCAGAGAGAGGCTGATCACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTg  <  2:124971/81‑1 (MQ=255)                                                                           |                                                                         TGAAGCCACCACGGCCTCCGGCGTGGATAATGCAGCCTCCCCCCGACTGGCAGACACCGCTGAACGGGATTATTTCACCCTCAGAGAGAGGCTGATCACTATGCAAAAACAACTGGAAGGAACCCAGAAGTATATTAATGAGCAGTG  >  NC_000913/578415‑578561

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: ‑