Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,767,507	(C)7→9	intergenic (+152/‑203)	rnlB → / → yfjP	CP4‑57 prophage; antitoxin RnlB/CP4‑57 prophage; putative GTP‑binding protein YfjP

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,767,500	1	.	C	100.0%	162.4 / NA	45	intergenic (+145/‑210)	rnlB/yfjP	CP4‑57 prophage; antitoxin RnlB/CP4‑57 prophage; putative GTP‑binding protein YfjP
Reads supporting (aligned to +/- strand):  ref base . (0/0);  new base C (21/24);  total (21/24)
*	NC_000913	2,767,500	2	.	C	100.0%	165.5 / NA	45	intergenic (+145/‑210)	rnlB/yfjP	CP4‑57 prophage; antitoxin RnlB/CP4‑57 prophage; putative GTP‑binding protein YfjP
Reads supporting (aligned to +/- strand):  ref base . (0/0);  new base C (21/24);  total (21/24)

TCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATTAACCCCCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTT‑‑CCC‑CCCC‑TTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGTAAATGGTGCTGTGAGTTCAGAAAGATTCTGCAATCTATGTGCATTGAAAAAATCTTCAGATAGA  >  NC_000913/2767366‑2767629                                                                                                                                        ||                                                                                                                                    tctAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATTAACCCCCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTT‑‑ccc‑cc                                                                                                                               <  1:200832/140‑1 (MQ=255)  ctAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATTAACCCCCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTT‑‑ccc‑ccc                                                                                                                              <  1:1010725/140‑1 (MQ=255)              gTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATTAACCCCCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCC‑CCCC‑TTTAAACtt                                                                                                                   <  1:442349/140‑1 (MQ=255)                                 ggCATGATATTAACTTGTCCAATATGATCAAATAGCATTAACCCCCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCC‑CCCC‑TTTAAACTTCTCAATAATGTCACCAAtt                                                                                                <  2:1027499/140‑1 (MQ=255)                                       atatTAACTTGTCCAATATGATCAAATAGCATTAACCCCCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCC‑CCCC‑TTTAAACTTCTCAATAATGTCACCAATTTTCTgg                                                                                          <  1:112577/140‑1 (MQ=255)                                       atatTAACTTGTCCAATATGATCAAATAGCATTAACCCCCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCC‑CCCC‑TTTAAACTTCTCAATAATGTCACCAATTTTCTgg                                                                                          <  2:1051574/140‑1 (MQ=255)                                          ttAACTTGTCCAATATGATCAAATAGCATTAACCCCCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCC‑CCCC‑TTTAAACTTCTCAATAATGTCACCAATTTTCTGGaaa                                                                                       <  2:598726/140‑1 (MQ=255)                                                  tCCAATATGATCAAATAGCATTAACCCCCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCC‑CCCC‑TTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTatga                                                                               >  2:515353/1‑140 (MQ=255)                                                   ccAATATGATCAAATAGCATTAACCCCCCCTCACAACGTACTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTCATTTT‑‑CCCACCCCATTTAAAATTCTCAATAATGTCAACACTTTTCCGGAAATCCTattac                                                                              >  2:138129/1‑137 (MQ=255)                                                    cAATATGATCAAATAGCATTAACCCCCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCC‑CCCC‑TTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTatgatg                                                                             >  2:249194/1‑140 (MQ=255)                                                       tatGATCAAATAGCATTAACCCCCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCC‑CCCC‑TTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGcc                                                                           <  1:632066/139‑1 (MQ=255)                                                       tatGATCAAATAGCATTAACCCCCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCC‑CCCC‑TTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGcc                                                                           >  2:632066/1‑139 (MQ=255)                                                         ttaTCAAATAGCATTCACCCCCCCCCACAACGTTCTTGATAGGGAACACGTTTTCCCCTATGCACCCCCGACTGAATTTCCCCC‑CCCC‑CTTAAACTTCTCAAGAATGTCACCAATTTTCTGGAAATCCTATGATGCCttt                                                                        <  2:419801/138‑1 (MQ=255)                                                            tCAAATAGCATTAACCCCCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCC‑CCCC‑TTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTccc                                                                     <  2:868996/140‑1 (MQ=255)                                                             cAAATAGCATTAACCCCCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCC‑CCCC‑TTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCg                                                                    >  1:557042/1‑140 (MQ=255)                                                                 tAGCATTAACCCCCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCC‑CCCC‑TTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGTaa                                                                >  2:758083/1‑140 (MQ=255)                                                                  aGCATTAACCCCCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCC‑CCCC‑TTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGTaaa                                                               <  1:950975/140‑1 (MQ=255)                                                                     aTTAACCCCCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTCCACCCACGACTAAATTTCCCCC‑CCCC‑TTTAACCTTCTCAATAATGTCACCAATTTTCTATTACTCCTATTATGCGTTTCCCGGTAAAttt                                                            >  2:669483/1‑138 (MQ=255)                                                                     aTTAA‑CCCCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCC‑CCCC‑TTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGTAAATGGt                                                           >  1:780096/1‑140 (MQ=255)                                                                      ttAACCCCCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCC‑CCCC‑TTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGTAAATGGt                                                           >  2:776752/1‑140 (MQ=255)                                                                      ttAACCCCCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCC‑CCCC‑TTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGTAAATGGt                                                           >  1:644451/1‑140 (MQ=255)                                                                         aCCCCCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCC‑CCCC‑TTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGTAAATGGTGCt                                                        <  1:387342/140‑1 (MQ=255)                                                                              cccTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCTCGACTAAATTTCCCCC‑CCCC‑TTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGTaa                                                                <  2:948741/127‑1 (MQ=255)                                                                              cccTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCC‑CCCC‑TTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCg                                                                    >  2:979241/1‑123 (MQ=255)                                                                              cccTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCC‑CCCC‑TTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCg                                                                    <  1:979241/123‑1 (MQ=255)                                                                              cccTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCC‑CCCC‑TTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGTaa                                                                >  1:948741/1‑127 (MQ=255)                                                                              cccTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCC‑CCCC‑TTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGTAAATGGTGCTGTGAg                                                   <  1:669483/140‑1 (MQ=255)                                                                                          ccTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCC‑CCCC‑TTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGTAAATGGTGCTGTGAGTTCAGAAAGAtt                                       >  2:457895/1‑140 (MQ=255)                                                                                          ccTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCC‑CCCC‑TTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGTAAATGGTGCTGTGAGTTCAGAAAGAtt                                       >  2:441379/1‑140 (MQ=255)                                                                                           cTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCC‑CCCC‑TTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGTAAATGGTGCTGTGAGTTCAGAAAGATTc                                      >  2:930310/1‑140 (MQ=255)                                                                                            tGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCC‑CCCC‑TTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGTAAATGGTGCTGTGAGTTCAGAAAGATTCt                                     <  1:441379/140‑1 (MQ=255)                                                                                             gCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCC‑CCCC‑TTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGTAAATGGTGCTGTGAGTTCAGAAAGATTCTg                                    <  1:254588/140‑1 (MQ=255)                                                                                             gCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCC‑CCCC‑TTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGTAAATGGTGCTGTGAGTTCAGAAAGATTCTg                                    <  1:138129/140‑1 (MQ=255)                                                                                             gCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCC‑CCCC‑TTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGTAAATGGTGCTGTGAGTTCAGAAAGATTCTg                                    <  1:831590/140‑1 (MQ=255)                                                                                              cATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCC‑CCCC‑TTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGTAAATGGTGCTGTGAGTTCAGAAAGATTCTGc                                   <  1:999700/140‑1 (MQ=255)                                                                                                tAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCC‑CCCC‑TTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGTAAATGGTGCTGTGAGTTCAGAAAGATTCTGCaa                                 <  2:844648/140‑1 (MQ=255)                                                                                                tAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCC‑CCCC‑TTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGTAAATGGTGCTGTGAGTTCAGAAAGATTCTGCaa                                 <  2:780096/140‑1 (MQ=255)                                                                                                   ggAACACGTTTTCTCCTGTGCACCCACGACTAAATTTCCCCC‑CCCC‑TTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGTAAATGGTGCTGTGAGTTCAGAAAGATTCTGCAATCt                              >  2:706762/1‑140 (MQ=255)                                                                                                   ggAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCC‑CCCC‑TTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGTAAATGGTGCTGTGAGTTCAGAAAGATTCTGCAATc                               >  2:242356/1‑139 (MQ=255)                                                                                                   ggAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCC‑CCCC‑TTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGTAAATGGTGCTGTGAGTTCAGAAAGATTCTGCAATc                               <  1:242356/139‑1 (MQ=255)                                                                                                   ggAACACGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCC‑CCCC‑TTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGTAAATGGTGCTGTGAGTTCAGAAAGATTCTGCAATCt                              >  2:801949/1‑140 (MQ=255)                                                                                                        acGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCC‑CCCC‑TTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGTAAATGGTGCTGTGAGTTCAGAAAGATTCTGCAATCTAtgtg                         >  2:270643/1‑140 (MQ=255)                                                                                                        acGTTTTCCCCTGTGCACCCACGACTAAATTTCCCCC‑CCCC‑TTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGTAAATGGTGCTGTGAGTTCAGAAAGATTCTGCAATCTAtgtg                         >  1:946186/1‑140 (MQ=255)                                                                                                                cccGGTGCACCCACGAGTAAATTTCCCCC‑CCCC‑TGTAAACTTCTCAATAATGTCGCCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGTAAATGGTGCTGTGAGTGCAGAAAGATTCTGCAATCTAAGTGCATTGaaa                 <  2:399395/140‑1 (MQ=255)                                                                                                                 ccTGTGCACCCACGACTAAATTTCCCCC‑CCCC‑TTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGTAAATGGTGCTGTGAGTTCAGAAAGATTCTGCAATCTATGTGCATTGaaaa                <  2:644451/140‑1 (MQ=255)                                                                                                                    gtgCACCCACGACTAAATTTCCCCC‑CCCC‑TTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGTAAATGGTGCTGTGAGTTCAGAAAGATTCTGCAATCTATGTGCATTGAAAAAAt             >  1:182133/1‑140 (MQ=255)                                                                                                                       cACCCACGACTAAATTTCCCCC‑CCCC‑TTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGTAAATGGTGCTGTGAGTTCAGAAAGATTCTGCAATCTATGTGCATTGAAAAAATCtt          <  1:706762/140‑1 (MQ=255)                                                                                                                          ccACGACTAAATTTCCCCC‑CCCC‑TTTAAACTTCTCAATAATGTCACCCATTTTCTGGAAATCCTATGATGCCTTTCCCGGTAAATGGTGCTGTGAGTTCAGAAAGATTCTGCAATCTATGTGCATTGAAAAAATCTTCag       >  1:970873/1‑140 (MQ=255)                                                                                                                           cACGACTAAATTTCCCCC‑CCCC‑TTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGTAAATGGTGCTGTGAGTTCAGAAAGATTCTGCAATCTATGTGCATTGAAAAAATCTTCaga      <  1:475340/140‑1 (MQ=255)                                                                                                                            aCGACTAAATTTCCCCC‑CCCC‑TTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGTAAATGGTGCTGTGAGTTCAGAAAGATTCTGCAATCTATGTGCATTGAAAAAATCTTCagat     <  1:515353/140‑1 (MQ=255)                                                                                                                            aCGACTAAATTTCCCCC‑CCCC‑TTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGTAAATGGTGCTGTGAGTTCAGAAAGATTCTGCAATCTATGTGCATTGAAAAAATCTTCagat     <  2:616311/140‑1 (MQ=255)                                                                                                                             cGACTAAATTTCCCCC‑CCCC‑TTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGTAAATGGTGCTGTGAGTTCAGAAAGATTCTGCAATCTATGTGCATTGAAAAAATCTTCag       >  2:642058/1‑137 (MQ=255)                                                                                                                             cGACTAAATTTCCCCC‑CCCC‑TTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGTAAATGGTGCTGTGAGTTCAGAAAGATTCTGCAATCTATGTGCATTGAAAAAATCTTCag       <  1:642058/137‑1 (MQ=255)                                                                                                                               aCTAAATTTCCCCC‑CCCC‑TTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGTAAATGGTGCTGTGAGTTCAGAAAGATTCTGCAATCTATGTGCATTGAAAAAATCTTCagataga  >  1:474947/1‑140 (MQ=255)                                                                                                                                        ||                                                                                                                                    TCTAAACGAACCAGTATAGAATTCGCCCTTTTGGCATGATATTAACTTGTCCAATATGATCAAATAGCATTAACCCCCCCTCACAACGTCCTGCATAGGGAACACGTTTTCCCCTGTGCACCCACGACTAAATTT‑‑CCC‑CCCC‑TTTAAACTTCTCAATAATGTCACCAATTTTCTGGAAATCCTATGATGCCTTTCCCGGTAAATGGTGCTGTGAGTTCAGAAAGATTCTGCAATCTATGTGCATTGAAAAAATCTTCAGATAGA  >  NC_000913/2767366‑2767629

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑