Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,418,386	G→A	intergenic (‑157/‑285)	kilR ← / → sieB	killing protein, Rac prophage, FtsZ inhibitor protein/phage superinfection exclusion protein, Rac prophage

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,418,386	0	G	A	100.0%	195.0 / NA	61	intergenic (‑157/‑285)	kilR/sieB	killing protein, Rac prophage, FtsZ inhibitor protein/phage superinfection exclusion protein, Rac prophage
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (33/28);  total (33/28)

GAACTTTGTTGATGCGGTGTCTGGTGCCTCCAGGTGACTGCAACCAGTTAACAATTACAGTCGGCTTTCCCACCCAAACCAATAAGGACTAACATGACTTTTAACTGTGCCACGTGCGCTTAGCCGCATTCACCGCATCACAAAATTCACTTTAAAAAGGGCGGACATCAGCCGAACTTCAAGAAAAAAACTGATGCCGCCAGGACTACACACAGCAATGTCGTTATTTACAACCGGAGGCGCACTCCCACCATTTAAATTTA  >  NC_000913/1418252‑1418514                                                                                                                                       |                                                                                                                                 gAACTTTGTTGATGCGGTGTCTGGTGCCTCCAGGTGACTGCAACCAGTTAACAATTACAGTCGGCTTTCCCACCCAAACCAATAAGGACTAACATGACTTTTAACTGTGCCACGTGCGCTTAGCCGCATTCACCACATc                                                                                                                              <  2:643834/139‑1 (MQ=255)                  tgtCTGGTGCCGCCAGGTGACTGCAACCAGTTAACAATTACAGTCGGCTTTCCCACCCAAACCAATAAGGACTAACATGACTTTTAACTGTGCCACGTGCGCTTAGCCGCATTCACCACATCACAAAATTCACTTTaaa                                                                                                             <  2:1046971/139‑1 (MQ=255)                   gtCTGGTGCCTCCAGGTGACTGCAACCAGTTAACAATTACAGTCGGCTTTCCCACCCAAACCAATAAGGACTAACATGACTTTTAACTGTGCCACGTGCGCTTAGCCGCATTCACCACATCACAAAATTCACTTTaaaa                                                                                                            >  2:1073166/1‑139 (MQ=255)                           ccTCCAGGTGACTGCAACCAGTTAACAATTACAGTCGGCTTTCCCACCCAAACCAATAAGGACTAACATGACTTTTAACTGTGCCACGTGCGCTTAGCCGCATTCACCACATCACAAAATTCACTTTAAAAAGGGCGGa                                                                                                    >  2:1508284/1‑139 (MQ=255)                                  gTGACTGCAACCAGTTAACAATTACAGTCGGCTTTCCCACCCAAACCAATAAGGACTAACATGACTTTTAACTGTGCCACGTGCGCTTAGCCGCATTCACCACATCACAAAATTCACTTTAAAAAGGGCGGACATCAGc                                                                                             >  1:726300/1‑139 (MQ=255)                                                ttAACAATTACAGTCGGCTTTCCCACCCAAACCAATAAGGACTAACATGACTTTTAACTGTGCCACGTGCGCTTAGCCGCATTCACCACATCACAAAATTCACTTTAAAAAGGGCGGACATCAGCCGAACTTCAAGaaa                                                                               >  1:1274336/1‑139 (MQ=255)                                                    cAATTACAGTCGGCTTTCCCACCCAAACCAATAACGACTAACATGACTTTTAACTGGGCCACGTGCGCTTAGCCGTATTCACCACATCACAAAATTCACTTTAAAAAGGGCGGACATCAGCCGAACTTCAAGaaaaaaa                                                                           <  1:1107241/139‑1 (MQ=255)                                                        tACAGTCGGCTTTCCCACCCAAACCAATAAGGACTAACATGACTTTTAACTGTGCCACGTGCGCTTAGCCGCATTCACCACATCACAAAATTCACTTTAAAAAGGGCGGACATCAGCCGAACTTCAAGAAAAAAACTGa                                                                       >  1:667850/1‑139 (MQ=255)                                                         aCAGTCGGTTTTCCCACCCAAACCAATAAGGACTAACATGACTTTTAACTGTGCCACGTGCGCTTAGCCGCATTCACCACAGCACAAAATTCACTTTAAAAAGGACGGACATCAGCCGAACTTCAAGaaaaaaaactga                                                                      >  1:613918/1‑134 (MQ=37)                                                          cAGTCGGCTTTCCCACCCAAACCAATAAGGACTAACATGACTTTTAACTGTGCCACGTGCGCTTAGCCGCATTCACCACATCACAAAATTCACTTTAAAAAGGGCGGACATCAGCCGAACTTCAAGAAAAAAACTGATg                                                                     >  2:476539/1‑139 (MQ=255)                                                          cAGTCGGCTTTCCCACCCAAACCAATAAGGACTAACATGACTTTTAACTGTGCCACGTGCGCTTAGCCGCATTCACCACATCACAAAATTCACTTTAAAAAGGGCGGACATCAGCCGAACTTCAAGAAAAAAACTGATg                                                                     >  1:423863/1‑139 (MQ=255)                                                             tCGGCTTTCCCACCCAAACCAATCAGGACTAACATGACTTTTAACTGTGCCACGTGCGCTTAGCCGCATTCACCACATCACAAAATTCACTTTAAAAAGGGCGGACATCAGCCGTACTTCAAGAAAAAAACTCATgcgg                                                                  >  1:169068/1‑137 (MQ=37)                                                              cGGCTTTCCCACCCAAACCAATAAGGACTAACATGACTTTTAACTGTGCCACGTGCGCTTAGCCGCATTCACCACATCACAAAATTCACTTTAAAAAGGGCGGACATCAGCCGAACTTCAAGAAAAAAACTGATgccgc                                                                 <  2:667850/139‑1 (MQ=255)                                                              cGGCTTTCCCACCCAAACCAATAAGGACTAACATGACTTTTAACTGTGCCACGTGCGCTTAGCCGCATTCACCACATCACAAAATTCACTTTAAAAAGGGCGGACATCAGCCGAACTTCAAGAAAAAAACTGATgccgc                                                                 <  1:1073166/139‑1 (MQ=255)                                                               ggCTTTCCCACCCAAACCAATAAGGACTAACATGACTTTTAACTGTGCCACGTGCGCTTAGCCGCATTCACCACATCGCAAAATTCACTTTAAAAAGGGCGGACATCAGCCGAACTTCAAGAAAAAAACTGATgccgcc                                                                >  2:1333263/1‑139 (MQ=255)                                                               ggCTTTCCCACCCAAACCAATAAGGACTAACATGACTTTTAACTGTGCCACGTGCGCTTAGCCGCATTCACCACATCACAAAATTCACTTTAAAAAGGGCGGACATCAGCCGAACTTCAAGAAAAAAACTGATgccgc                                                                 >  1:1236263/1‑138 (MQ=255)                                                               ggCTTTCCCACCCAAACCAATAAGGACTAACATGACTTTTAACTGTGCCACGTGCGCTTAGCCGCATTCACCACATCACAAAATTCACTTTAAAAAGGGCGGACATCAGCCGAACTTCAAGAAAAAAACTGATgccgc                                                                 <  2:1236263/138‑1 (MQ=255)                                                                 cTTTCCCACCCAAACCAATAAGGACTAACATGACTTTTAACTGTGCCACGTGCGCTTAGCCGCATTCACCACATCACAAAATTCACTTTAAAAAGGGCGGACATCAGCCGAACTTCAAGAAAAAAACTGATGCCGCCAg                                                              >  1:276234/1‑139 (MQ=255)                                                                   ttCCCACCCAAACCAATAAGGACTAACATGACTTTTAACTGTGCCACGTGCGCTTAGCCGCATTCACCACATCACAAAATTCACTTTAAAAAGGGCGGACATCAGCCGAACTTCAAGAAAAAAACTGATGCCGCCAGGa                                                            <  1:386480/139‑1 (MQ=255)                                                                              aCCAATAAGGACTAACATGACTTTTAACTGTGCCACGTGCGCTTAGCCGCATTCACCACATCACAAAATTCACTTTAAAAAGGGCGGACATCAGCCGAACTTCAAGAAAAAAACTGATgccgc                                                                 <  1:1024952/123‑1 (MQ=255)                                                                              aCCAATAAGGACTAACATGACTTTTAACTGTGCCACGTGCGCTTAGCCGCATTCACCACATCACAAAATTCACTTTAAAAAGGGCGGACATCAGCCGAACTTCAAGAAAAAAACTGATgccgc                                                                 >  2:1024952/1‑123 (MQ=255)                                                                                cAATAAGGACTAACATGACTTTTAACTGTGCCACGTGCGCTTAGCCGCATTCACCACATCGCAAAATTCACTTTAAAAAGGGCGGACATCAGCCGAACTTCAAGAAAAAAACTGATGCCGCCAGGACTACACACAGCaa                                               <  1:1333263/139‑1 (MQ=255)                                                                                cAATAAGGACTAACATGACTTTTAACTGTGCCACGTGCGCTTAGCCGCATTCACCACATCACAAAATTCACTTTAAAAAGGGCGGACATCAGCCGAACTTCAAGAAAAAATCTGATGCCGCCAGGACTACACACAGCaa                                               <  1:1308431/139‑1 (MQ=255)                                                                                 aaTAAGGACTAACATGACTTTTAACTGTGCCACGTGCGCTTAGCCGCATTCACCACATCACAAAATTCACTTTAAAAAGGGCGGACATCAGCCGAACTTCAAGAAAAAAACTGATGCCGCCAGGACTACACACAGCAAt                                              <  2:423863/139‑1 (MQ=255)                                                                                   tAAGGACTAACATGACTTTTAACTGTGCCACGTGCGCTTAGCCGCATTCACCACATCACAAAATTCACTTTAAAAAGGGCGGACATCAGCCGAACTTCAAGAAAAAAACTGATGCCGCCAGGACTACACACAGCAATGt                                            >  1:1343963/1‑139 (MQ=255)                                                                                     aGGACTAACATGACTTTTAACTGTGCCACGTGCGCTTAGCCGCATTCACCACATCACAAAATTCACTTTAAAAAGGGCGGACATCAGCCGAACTTCAAGAAAAAAACTGATGCCGCCAGGACTACACACAGCAATGTCg                                          <  1:415583/139‑1 (MQ=255)                                                                                     aGGACTAACATGACTTTTAACTGTGCCACGTGCGCTTAGCCGCATTCACCACATCACAAAATTCACTTTAAAAAGGGCGGACATCAGCCGAACTTCAAGAAAAAAACTGATGCCGCCAGGACTACACACAGCAATGTCg                                          <  2:1274336/139‑1 (MQ=255)                                                                                      ggACTAACATGACTTTTAACTGTGCCACGTGCGCTTAGCCGCATTCACCACATCACAAAATTCACTTTAAAAAGGGCGGACATCAGCCGAACTTCAAGAAAAAAACTGATGCCGCCAGGACTACACACAGCAATGTCGt                                         <  1:704720/139‑1 (MQ=255)                                                                                       gACTAACATGACTTTTAACTGTGCCACGTGCGCTTAGCCGCATTCACCACATCACAAAATTCACTTTAAAAAGGGCGGACATCAGCCGAACTTCAAGAAAAAAACTGATGCCGCCAGGACTACACACAGCAATGTCGtt                                        >  1:278405/1‑139 (MQ=255)                                                                                        aCTAACATGACTTTTAACTGTGCCACGTGCGCTTAGCCGCATTCACCACATCACAAAATTCACTTTAAAAAGGGCGGACATCAGCCGAACTTCaa                                                                                   <  2:1106939/95‑1 (MQ=255)                                                                                        aCTAACATGACTTTTAACTGTGCCACGTGCGCTTAGCCGCATTCACCACATCACAAAATTCACTTTAAAAAGGGCGGACATCAGCCGAACTTCaa                                                                                   >  1:1106939/1‑95 (MQ=255)                                                                                        aCTAACATGACTTTTAACTGTGCCACGTGCGCTTAGCCGCATTCACCACATCACAAAATTCACTTTAAAAAGGGCGGACATCAGCCGAACTTCAAGAAAAAAACTGATGCCGCCAGGACTACACACAGCAATGTCGTTa                                       >  2:3903/1‑139 (MQ=255)                                                                                         cTAACATGACTTTTAACTGTGCCACGTGCGCTTAGCCGCATTCACCACATCACAAAATTc                                                                                                                     <  1:899563/60‑1 (MQ=255)                                                                                         cTAACATGACTTTTAACTGTGCCACGTGCGCTTAGCCGCATTCACCACATCACAAAATTc                                                                                                                     >  2:899563/1‑60 (MQ=255)                                                                                          tAACATGACTTTTAACTGTGCCACGTGCGCTTAGCCGCATTCACCACATCACAAAATTCACTTTAAAAAGGGCGGACATCAGCCGAACTTCAAGAAAAAAACTGATgccgc                                                                 <  1:937947/111‑1 (MQ=255)                                                                                          tAACATGACTTTTAACTGTGCCACGTGCGCTTAGCCGCATTCACCACATCACAAAATTCACTTTAAAAAGGGCGGACATCAGCCGAACTTCAAGAAAAAAACTGATgccgc                                                                 >  2:937947/1‑111 (MQ=255)                                                                                          tAACATGACTTTTAACTGTGCCACGTGCGCTTAGCCGCATTCACCACATCACAAAATTCACTTTAAAAAGGGCGGACATCAGCCGAACTTCAAG‑AAAAAACTGATGCCGCCAGGACTACACACAGCAATGTCGTTAttt                                    >  2:27476/1‑139 (MQ=255)                                                                                                 aCTTTTAACTGTGCCACGTGCGCTTAGCCGCATTCACCACATCACAAAATTCACTTTAAAAAGGGCGGACATCAGGCGAACTTCAAGAAAAAAACTGATGCCGCCAGGACTac                                                        >  2:970169/1‑113 (MQ=255)                                                                                                 aCTTTTAACTGTGCCACGTGCGCTTAGCCGCATTCACCACATCACAAAATTCACTTTAAAAAGGGCGGACATCAGCCGAACTTCAAGAAAAAAACTGATgccgc                                                                 <  1:836906/104‑1 (MQ=255)                                                                                                 aCTTTTAACTGTGCCACGTGCGCTTAGCCGCATTCACCACATCACAAAATTCACTTTAAAAAGGGCGGACATCAGCCGAACTTCAAGAAAAAAACTGATgccgc                                                                 >  2:836906/1‑104 (MQ=255)                                                                                                 aCTTTTAACTGTGCCACGTGCGCTTAGCCGCATTCACCACATCACAAAATTCACTTTAAAAAGGGCGGACATCAGCCGAACTTCAAGAAAAAAACTGATGCCGCCAGGACTac                                                        <  1:970169/113‑1 (MQ=255)                                                                                                  cTTTTAACTGTGCCACGTGCGCTTAGCCGCATTCACCACATCACAAAATTCACTTTAAAAAGGGCGGACATCAGCCGAACTTCAAGAAAAAAACTGATGCCGCCAGGACTACACACAGCAATGTCGTTATTTACAACCg                             >  2:790877/1‑139 (MQ=255)                                                                                                      tAACTGTGCCACGTGCGCTTAGCCGCATTCACCACATCACAAAATTCACTTTAAAAAGGGCGGACATCAGCCGAACTTCAAGAAAAAAACTGATGCCGCCAGGACTACACACAGCa                                                >  2:55146/1‑116 (MQ=255)                                                                                                      tAACTGTGCCACGTGCGCTTAGCCGCATTCACCACATCACAAAATTCACTTTAAAAAGGGCGGACATCAGCCGAACTTCAAGAAAAAAACTGATGCCGCCAGGACTACACACAGCa                                                <  1:55146/116‑1 (MQ=255)                                                                                                      tAACTGTGCCACGTGCGCTTAGCCGCATTCACCACATCACAAAATTCACTTTAAAAAGGGCGGACATCAGCCGAACTTCAAGAAAAAAACTGATGCCGCCAGGACTACACACAGCAATGTCGTTAttt                                    >  2:183124/1‑128 (MQ=255)                                                                                                      tAACTGTGCCACGTGCGCTTAGCCGCATTCACCACATCACAAAATTCACTTTAAAAAGGGCGGACATCAGCCGAACTTCAAGAAAAAAACTGATGCCGCCAGGACTACACACAGCAATGTCGTTAttt                                    <  1:183124/128‑1 (MQ=255)                                                                                                            tgCCACGTGCGCTTAGCCGCATTCACCACATCACAAAATTc                                                                                                                     >  2:1218800/1‑41 (MQ=255)                                                                                                            tgCCACGTGCGCTTAGCCGCATTCACCACATCACAAAATTc                                                                                                                     <  1:1218800/41‑1 (MQ=255)                                                                                                            tgCCACGTGCGCTTAGCCGCATTCACCACATCACAAAATTCACTTTAAAAAGGGCGGACATCAGCCGAACTTCAAGAAAAAAACTGATGCCGCCAGGACTACACACAGCAATGTCGTTATTTACAACCGGAGGCGCACt                   >  1:681936/1‑139 (MQ=255)                                                                                                            tgCCACGTGCGCTTAGCCGCATTCACCACATCACAAAATTCACTTTAAAAAGGGCGGACATCAGCCGAACTTCAAGAAAAAAACTGATGCCGCCAAGACTACACACAGCAATGTCGTTATTTACAACCGGAGGCGCACt                   >  1:1040862/1‑139 (MQ=255)                                                                                                             gCCACGTGCGCTTAGCCGCATTCACCACATCACAAAATTCACt                                                                                                                  <  1:577019/43‑1 (MQ=255)                                                                                                             gCCACGTGCGCTTAGCCGCATTCACCACATCACAAAATTCACt                                                                                                                  >  2:577019/1‑43 (MQ=255)                                                                                                                 cGTGCGCTTAGCCGCATTCACCACATCACAAAATTCACTTTAAAAAGGGCGGACATCAGCCGAACTTCAAGAAAAAAACTGATGCCGCCAGGACTACACACAGCAATGTCGTTATTTACAACCGGAGgc                        <  2:531412/129‑1 (MQ=255)                                                                                                                 cGTGCGCTTAGCCGCATTCACCACATCACAAAATTCACTTTAAAAAGGGCGGACATCAGCCGAACTTCAAGAAAAAAACTGATGCCGCCAGGACTACACACAGCAATGTCGTTATTTACAACCGGAGgc                        >  1:531412/1‑129 (MQ=255)                                                                                                                 cGTGCGCTTAGCCGCATTCACCACATCACAAAATTCACTTTAAAAAGGGCGGACATCAGCCGAACTTCAAGAAAAAAACTGATGCCGCCAGGACTACACACAGCAATGTCGTTATTTACAACCGGAGGCGCACTCccac              >  1:73736/1‑139 (MQ=255)                                                                                                                    gcgcTTAGCCGCATTCACCACATCACAAAATTCACTTTAAAAAGGGCGGACATCAGCCGAACTTCAAGAAAAAAACTGATGCCGCCAGGACTACACACAGCAATGTCGTTATTTACAACCGGAGGCGCACTCCCACCat           <  2:276234/139‑1 (MQ=255)                                                                                                                      gcTTAGCCGCATTCACCACATCACAAAATTCACTTTAAAAAGGGCGGACATCAGCCGAACTTCAAGAAAAAAACTGATgccgc                                                                 >  2:162480/1‑83 (MQ=255)                                                                                                                      gcTTAGCCGCATTCACCACATCACAAAATTCACTTTAAAAAGGGCGGACATCAGCCGAACTTCAAGAAAAAAACTGATgccgc                                                                 <  1:162480/83‑1 (MQ=255)                                                                                                                       cTTAGCCGCATTCACCACATCACAAAATTCACTTTAAAAAGGGCGGACATCAGCCGAACTTCAAGAAAAAAACTGATGCCGCCAGGACTACACACAGCAATGTCGTTATTTACAACCGGAgg                         <  2:597604/122‑1 (MQ=255)                                                                                                                       cTTAGCCGCATTCACCACATCACAAAATTCACTTTAAAAAGGGCGGACATCAGCCGAACTTCAAGAAAAAAACTGATGCCGCCAGGACTACACACAGCAATGTCGTTATTTACAACCGGAgg                         >  1:597604/1‑122 (MQ=255)                                                                                                                             cGCATTCACCACATCACAAAATTCACTTTAAAAAGGGCGGACATCAGCCGAACTTCAAGAAAAAAACTGATGCCGCCAAGACTACACACAGCAATGTCGTTATTTACAACCGGAGGCGCACTCCCACCatttaaattta  <  2:1040862/139‑1 (MQ=255)                                                                                                                                       |                                                                                                                                 GAACTTTGTTGATGCGGTGTCTGGTGCCTCCAGGTGACTGCAACCAGTTAACAATTACAGTCGGCTTTCCCACCCAAACCAATAAGGACTAACATGACTTTTAACTGTGCCACGTGCGCTTAGCCGCATTCACCGCATCACAAAATTCACTTTAAAAAGGGCGGACATCAGCCGAACTTCAAGAAAAAAACTGATGCCGCCAGGACTACACACAGCAATGTCGTTATTTACAACCGGAGGCGCACTCCCACCATTTAAATTTA  >  NC_000913/1418252‑1418514

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑