Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,429,714	A→C	A222A (GCA→GCC)	stfR →	putative prophage side tail fiber protein StfR

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,429,714	0	A	C	100.0%	84.9 / NA	31	A222A (GCA→GCC)	stfR	putative prophage side tail fiber protein StfR
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base C (15/16);  total (15/16)

TGCGGCTGATGCTGCGGACTCAGCACGCGCAGCCAGCACGTCAGCCGGACAGGCCGCGTCGTCGGCTCAGTCAGCGTCTTCCAGCGCAGGAACGGCATCAACAAAGGCCACTGAAGCATCAAAAAGTGCTGCCGCTGCAGAGTCCTCAAAAAGCGCGGCGGCCACCAGTGCCGGTGCGGCGAAAACGTCAGAAACGAATGCTTCAGCGTCACTACAATCAGCAGCCACATCTGCAT‑CCACCGCGACCACGAAGGCATCAGAAGCTGCGACCTCGGCCCGGGATGCGGCGGCCTCAAAAGAAGCGGCAAAATCATCAGAAACGAACGCATCATCAAGCGCCAGTAGTGCAGCTTCCTCGGCAACGGCGGCAGGAAATTCCGCGAAGGCGGCAAAAACGTCCGAGACGAACGCCAGGTCTTCTGAAACGGCAGCGGGACAGAGCGCCTCGGCTGCGGCAGGCT  >  NC_000913/1429480‑1429940                                                                                                                                                                                                                                           |                                                                                                                                                                                                                                    tgtgactgatccaactgACTCAGCACGCGCCGCCAGCACGTCCGCCGGACAGGCTGCATCGTCAGCTCAGGAAGCGTCCTCCGGCGCAGAAGCGGCATCAGCAAAGGCCCCTGAAGCGGAAAAAAGTGCCGCAGCAGCAGAGTCCTCAAAAAACGCGGCGGCCACCAGTGCCGGTGCGGCGAAAACGTCAGAAACGAATGCTGCAGCGTCACAACAATCAGCCGCCACGTCTGCCT‑CCACCGCGGCCACg                                                                                                                                                                                                                     >  1:55669/17‑250 (MQ=255)                tgACTCAGCACGCGCCGCCAGCACGTCCGCCGGACAGGCTGCATCGTCAGCTCAGGAAGCGTCCTCCGGCGCAGAAGCGGCATCAGCAAAGGCCACTGAAGCGGAAAAAAGTGCCGCAGCCGCAGAGTCCTCAAAAAACGCGGCGGCCACCAGTGCCGGTGCGGCGAAAACGTCAGAAACGAATGCTGCAGCGTCACAACAATCAGCCGCCACGTCTGCCT‑CCACCGCGGCCACGAAAGCGTCAGaggccg                                                                                                                                                                                                     >  1:267531/2‑246 (MQ=255)                 gACTCAGCACGCGCCGCCAGCACGTCCGCCGGACAGGCTGCATCGTCAGCTCAGGAAGCGTCCTCCGGCGCAGAAGCGGCATCAGCAAAGGCCACTGAAGCGGAAAAAAGTGCCGCAGCCGCAGAGTCCTCAAAAAACGCGGCGGCCACCAGTGCCGGTGCGGCGAAAACGTCAGAAACGAATGCTGCAGCGTCACAACAATCAGCCGCCACGTCTGCCT‑CCACCGCGGCCACGAAAGCGTCAGaggcc                                                                                                                                                                                                      <  1:277937/249‑5 (MQ=255)                      aGCACGCGCCGCCAGCACGTCCGCCGGACAGGCTGCATCGTCAGCTCAGGAAGCGTCCTCCGGCGCAGAAGCGGCATCAGCAAAGGCCACTGAAGCGGAAAAAAGGGCCGCAGCCGCAGAGTCCTCAAAAAACGCGGCGGCCACCAGTGCCGGTGCGGCGAAAACGTCAGAAACGAATGCTGCATCGTCACAACAATCAGCCGCCACGTCTGCCT‑CCACCGCGGCCACGaaagagtcagaggacgccactt                                                                                                                                                                                               >  1:211129/1‑231 (MQ=255)                         aCGCGCCGCCAGCACGTCCGCCGGACAGGCTGCATCGTCAGCTCAGGAAGCGTCCTCCGGCGCAGAAGCGGCATCAGCAAAGGCCACTGAAGCGGAAAAAAGTGCCGCAGCCGCAGAGTCCTCAAAAAACGCGGCGGCCACCAGTGCCGGTGCGGCGAAAACGTCAGAAACGAATGCTGCAGCGTCACAACAATCAGCCGCCACGTCTGCCT‑CCACCGCGGCCACGAAAGCGTCAGaggccgccacttc                                                                                                                                                                                              >  1:109587/1‑237 (MQ=255)                          cgcgCCGCCAGCCCGTCCGCCGGACAGGCTGCATCTTCAGCTCAGGAAGCGGCCTCCGGCGCAGAAGCGGCATCAGCAAAGGCCACGGAAGCGGAAAAAAGTGCCGCAGCCGCAAAGTCCTCAAAAAACGCGGCGGCCACCAGTGCCGGTGCGGCGAAAACGTCAGAAAGGAATGCTGCAGCGGCACAACAATCAGCCGCCACGTCTGCCC‑CCACCGCGGCCACGAAAGCGTCAGaggccgccacttcagc                                                                                                                                                                                           <  2:315197/251‑16 (MQ=255)                          cgcgCCGCCAGCACGGCCGCCGGACAGGCTGCATCGTCAGCTCAGGAAGCGTCCTCCGGCGAAGAAGCGGCAACAGCAAAGGCCACTGAAGCGGAAAAAAGTGCCGCAGCCGCAGAGTCCTCAAAAAACGCGGCGGCCACCAGTGCCGGTGCGGCGAAAACGTCAGAAACGATTGCTGCAGCGTCACAACAATCAGCCGCCACGTCTGCCT‑CCACCGCGGCCACGAAAGCGTCAGaggccgccacttcagc                                                                                                                                                                                           <  1:224851/251‑16 (MQ=255)                                                gACAGGCTGCATCGTCAGCTCAGGAAGCGTCCTCCGGCGCAGAAGCGGCATCAGCAAAGGCCACTGAAGCGGAAAAAAGGGCCGCAGCCGCAGAGTCCTCAAAAAACGCGGCGGCCACCAGTGCCGGTGCGGCGAAAACGTCAGAAACGAATGCTGCAGCGTCACAACAATCAGCCGCCACGTCTGCCT‑CCACCGCGGCCACGAAAGCGTCAGAGGCCGCCACTTCAGCACGAGATGCGGTGGCCGCaaaa                                                                                                                                                                     <  1:290812/251‑1 (MQ=255)                                                               cagctaaggaagCGTCCTCCGGCGCAGAAGCGGCATCAGCAAAGGCCACTGAAGCGGAAAAAAGTGCCGCAGCCGCAGAGTCCTCAAAAAACGCGGCGGCCACCAGTGCCGGTGCGGCGAAAACGTCAGAAACGAATGCTGCAGCGTCACAACAATCAGCCGCCACGTCTGCCT‑CCACCGCGGCCACGAAAGCGTCAGAGGCCGCCACTTCAGCACGAGATGCGGTGGCCTCAAAAGAGGCCGCAAAatc                                                                                                                                                       >  2:292519/11‑250 (MQ=255)                                                                                      gcagaagcGGCATCAGCAAAGGCCACTGAAGCGGAAAAAAGTGCCGCAGCCGCAGAGTCCTCAAAAAACGCGGCGGCCACCAGTGCCGGTGCGGCGAAAACGTCAGAAACGAATGCTGCAGCGTCACAACAATCAGCCGCCACGTCTGCCT‑CCACCGCGGCCACGAAAGCGTCAGAGGCCGCCACTTCAGCACGAGATGCGGTGGCCTCAAAAGAGGCAGCAAAATCATCAGAAACGAACGc                                                                                                                                        <  1:140396/235‑1 (MQ=255)                                                                                      gcagaagcGGCATCAGCAAAGGCCACTGAAGCGGAAAAAAGTGCCGCAGCCGCAGAGTCCTCAAAAAACGCGGCGGCCACCAGTGCCGGTGCGGCGAAAACGTCAGAAACGAATGCTGCAGCGTCACAACAATCAGCCGCCACGTCTGCCT‑CCACCGCGGCCACGAAAGCGTCAGAGGCCGCCACTTCAGCACGAGATGCGGTGGCCTCAAAAGAGGCAGCAAAATCATCAGAAACGAACGc                                                                                                                                        >  2:140396/8‑242 (MQ=255)                                                                                      gcAGGAGCGGCATCAGCAAAGGCCACTGAGACGAAAAAAAGTGCCCCAGCCTCAGAGCCCTCAAAAAACGCGGCGGCCACCAGTGCCGGTGCGGCGAAAACGTCAGAAACGAATGCGGCAGCGTCACAACAATCACCCGCACCGTCTGCCC‑CCACCGCTGCCACGAAAGCGGCAGAGGCCGCCACGTCAGCACGAGATGCGGTGGCCTCAAAAGAGGCAGCAAAATCATCAGAATCGAACGCATCATCAAg                                                                                                                               <  2:228919/251‑1 (MQ=255)                                                                                        agaagcGGCATCAGCAAAGGCCACTGAAGCGGAAAAAAGTGCCGCAGCCGCAGAGTCCTCAAAAAACGCGGCGGCCACCAGTGCCGGTGCGGCGAAAACGTCAGAAACGAATGCTGCAGCGTCACAACAATCAGCCGCCACGTCTGCCT‑CCACCGCGGCCACGAAAGCGTCAGAGGCCGCCACTTCAGCACGAGATGCGGTGGCCTCAAAAGAGGCAGCAAACTCATCAGAAACGAACGCATCATCAAgtg                                                                                                                             >  2:282569/6‑249 (MQ=255)                                                                                                   cagcaaAGGCCACTGAAGCGGACAAAAGCGCCGCAGCCGCCGAGTCCTCAAAAAACGCGGCGGCCACCAGTGCCGGCGCGGCGAAAACGTCAGAAACGAATGCTGCAGCGCCACAACAATCAGCCGCCACGTCTGCCTACCAC‑GCGGCCACGCAAGCGTCAGAGGCCGCCACTTCAGCACGAGATGCGGGGGCCTCAAAAGAGGCAGCAAAATCATCAGAAACGAACGCATCATCAAGTGccggtcgggc                                                                                                                   >  2:187912/4‑242 (MQ=255)                                                                                                        aaGGCCACTGAAGCGGAAAAAAGTGCCGCAGCCGCAGAGTCCTCAAAAAACGCGGCGGCCACCAGTGCCGGTGCGGCGAAAACGTCAGAAACGAATGCTGCAGCGTCACAACAATCAGCCGCCACGTCTGCCT‑CCACCGCGGCCACGAAAGCGTCAGAGGCCGCCACTTCAGCACGAGATGCGGTGGCCTCAAAAGAGGCAGCAAAATCATCAGAAACGAACGCATCATCAAGTGCCGGTCGTGCAGCTTc                                                                                                             >  2:124821/1‑251 (MQ=255)                                                                                                           gCCACTGAAGCGGAAAAAAGTGCCGCAGCCGCAGAGTCCTCAAAAAACGCGGCGGCCACCAGTGCCGGTGCGGCGAAAACGTCAGAAACGAATGCTGCAGCGTCACAACAATCAGCCGCCACGTCTGCCT‑CCACCGCGGCCACGAAAGCGTCAGAGGCCGCCACTTCAGCACGAGATGCGGTGGCCTCAAAAGAGGCAGCAAAATCATCAGAAACGAACGCATCATCAAGTGCCGGTCGTGCAGCTTCCTc                                                                                                          <  1:282569/251‑1 (MQ=255)                                                                                                                     cggaaaaaaGTGCCGCAGCCGCAGAGTCCTCAAAAAACGCGGCGGCCACCAGTGCCGGTGCGGCGAAAACGTCAGAAACGAATGCTGCAGCGTCACAACAATCAGCCGCCACGTCTGCCT‑CCACCGCGGCCACGAAAGCGTCAGAGGCCGCCACTTCAGCACGAGATGCGGTGGCCTCAAAAGAGGCAGCAAAATCATCAGAAACGAACGCATCATCAAGTGCCGGTCGTGCAGCTTCCTCGGCAAcggcg                                                                                                >  2:25873/5‑251 (MQ=255)                                                                                                                      ggaaaaaagtcccgcagccgCAGAGTCCTCAAAAAACGCGGCGGCCACCAGTGCCGGTGCGGCGAAAACGTCAGAAACGAATGCTGCAGCGTCACAACAATCAGCCGCCACGTCTGCCT‑CCACCGCGGCCACGAAAGCGTCAGAGGCCGCCACTTCAGCACGAGATGCGGTGGCCTCAAAAGAGGCAGCAAAATCATCAGAAACGAACGCATCATCAAGTGCCGGTCGTGCAGCTTCCTCGGCAAcggcgg                                                                                               <  1:90255/232‑1 (MQ=255)                                                                                                                            aaGTGCCGCAGCCGCAGAGTCCTCAAAAAACGCGGCGGCCACCAGGGCCGGTGCGGCGAAAACGTCAGAAACGAATGCTGCAGCGTCACAACAATCAGCCGCCACGTCTGCCT‑CCACCGCGGCCACGAAAGCGTCAGAGGCCGCCACTTCAGCACGAGATGCGGTGGCCTCAAAAGAGGCAGCAAAATCATCAGAAACGAACGCATCATCAAGTGCCGGTCGTGCAGCTTCCTCGGCAACGGCGGCAgaaa                                                                                         <  1:387432/251‑4 (MQ=255)                                                                                                                             agtgccgcagccgCAGAGTCCTCAAAAAACGCCGCGGCCACCAGTGCCGGTGCGGCGAAAACGTCAGAAACGAACGCTGCAGCGTCACAACAATCAGCCGCCACGTCTGCCT‑CCACCGCGGCCACGAAAGCGTCAGAGGCCGCCACTTCAGCACGAGATGCGGCGGCCTCAAAAGAGGCAGCAAAATCCTCCGAAACGAACGCATCATCAAGCGCCGGTCGTGCAGCTTCCTCGGCAACGGCGGCAgaaa                                                                                         >  1:148141/13‑247 (MQ=255)                                                                                                                                    cagccgCAGAGTCCTCAAAAAACGCGGCGGCCACCAGTGCCGGTGCGGCGAAAACGTCAGAAACGAATGCTGCAGCGTCACAACAATCAGCCGCCACGTCTGCCT‑CCACCGCGGCCACGAAAGCGTCAGAGGCCGCCACTTCAGCACGAGATGCGGTGGCCTCAAAAGAGGCAGCAAAATCATCAGAAACGAACGCATCATCAAGTGCCGGTCGTGCAGCTTCCTCGGCAACGGCGGCAGAAAATTctgcc                                                                                 <  2:49892/246‑5 (MQ=255)                                                                                                                                      gccgCAGAGTCCTCAAAAAACGCGGCGGCCACCAGTGCCGGTGCGGCGAAAACGTCAGAAACGAATGCTGCAGCGTCACAACAATCAGCCGCCACGTCTGCCT‑CCACCGCGGCCACGAAAGCGTCAGAGGCCGCCACTTCAGCACGAGATGCGGTGGCCTCAAAAGAGGCAGCAAAATCATCAGAAACGAACGCATCATCAAGTGCCGGTCGTGCAGCTTCCTCGGCAACGGCGGCAGAAAATTctgccag                                                                               <  1:25873/248‑7 (MQ=255)                                                                                                                                                ccTCAAAAAACGCGGCGGCCACCAGTGCCGGTGCGGCGAAAACGACAGAAACGAATGCTGCAGCGTCACAACAATCAGCCGCCACGTCTGCCT‑CCACCGCGGCCACGAAAGCGTCAGAGGCCGCCACTTCAGCACGAGAAGCGGTGGCCTCAAAAGAGGCAGCACAATCATCAGAAACGACCGCATCATCAAGTGCCGGTCGTGCAGCTTCCTCGGCAACGGCGGCAGAAAATTATGCCAGGGCGGCaaa                                                                      >  1:193819/1‑250 (MQ=255)                                                                                                                                                        aacgcgGCGGCCCCCAGGGCCGGGGGGGCGAAAACGTCGGAAACGAATGCTGCAGCGTCACAACAAGCAGCCGCCACGTCTGCCT‑CCACCGCGGCCACGAAAGCGTCAGAGGCCGCCACTTCAGCACGAGATGCGGTGGCCTCAAAAGAGGCAGCAAAATCATCAGAAACGAACGCATCATCAAGTGCCGGTCGTGCAGCTTCCTCGGCAACGGCGGCAGAAAATTCTGCCAGGGCGGCAAAAACGTCCga                                                             <  2:109587/249‑1 (MQ=255)                                                                                                                                                            cggcggCCACCAGTGCCGGTGCGGCGAAAACGTCAGAAACGAATGCTGCAGCGTCACAACAATCAGCCGCCACGTCTGCCT‑CCACCGCGGCCACGAAAGCGTCAGAGGCCGCCACTTCAGCACGAGATGCGGTGGCCTCAAAAGAGGCAGCAAAATCATCAGAAACGAACGCATCATCAAGTGCCGGTCGTGCAGCTTCCTCGGCAACGGCGGCAGAAAATTATGCCAGGGCGGCAAAAACGTCCGAGACg                                                         >  1:378681/1‑251 (MQ=255)                                                                                                                                                                      caGTGCCGGTGCGGCGAAAACGTCAGAAACGAATGCTGCAGCGTCACAACAATCAGCCGCCACGTCTGCCT‑CCACCGCGGCCACGAAAGCGTCAGAGGCCGCCACTTCAGCACGAGATGCGGTGGCCTCAAAAGAGGCAGCAAAATCATCAGAAACGAACGCATCATCAAGTGCCGGTCGTGCCGCTTCCTCGGCAACGGCGGCAGACAATTCTGCAAGGGCGGCAAAAACGACCGAGACGAATGCCAggg                                               >  2:332566/1‑250 (MQ=255)                                                                                                                                                                               ggtggagAAAACGTAAGAAACGAATGCTGCAGCGTCACAACAATCAGCCGCCACGTCTGCCT‑CCACCGCGGCCACGAAAGCGTCAGAGGCCGCCACTTCAGCACGAGATGCGGTGGCCTCAAAAGAGGCAGCAAAATCATCAGAAACGAACGCATCATCAAGTGCCGGTCGTGCAGCTTCCTCGGCAACGGCGGCAGAAAATTCTGCCAGGGCGGCAAAAACGTCCGAGACGAATGCCAGGTCATCTGaaa                                      <  1:346502/245‑1 (MQ=255)                                                                                                                                                                                gcgccgAAAAGGCCAGAGACGAAGGCTGCAGCGTACCAACAACCAGCCGCCACGTCTGCCT‑CCACCGCGGCCACGAAAGCGTCAGAGGCCGCCACTTCAGCACGAGATGCGGTGGCCTCAAAAGAGGCAGCAAAATCATCAGAAACGAACGCATCATCAAGTGCCGGTCGTGCAGCTTCCGCGGCAACGGCGGCAGAAAATTCTGCCAGGGCGGCAGAAACGTCCGATACGAATGCCAGTGCATCTGAAAc                                     <  2:267531/247‑1 (MQ=255)                                                                                                                                                                                  ggcgAAAACGTCAGAAACGAATGCTGCAGCGTCACAACAATCAGCCGCCACGTCTGCCT‑CCCCCGCGGCCACGAAAGCGTCAGAGGCCGCCACTTCAGCACGAGATGCGGTGGCCTCAAAAGAGGCAGCAAAATCATCAGAAACGAACGCATCATCAAGTGCCGGTCGTGCAGCTTCCTCGGCAACGGCGGCAGAAAATTCTGCCAGGGCGGCAAAAACGTCCGAGACGAATGCCAGGTCATCTGAAAcag                                   <  1:218591/251‑3 (MQ=255)                                                                                                                                                                                                           gcAGCGCCACAACAATCAGCCGCCACGTCTGCCC‑CCCCCGCGGCCACGAAAGCTTCAGAGGACGCCACTTCAGCACGAGATGTGGTGGCCTCAAAAGAGGCAGCAAAATCATCAGAAACGAACGCATCATCAAGTGCCGTTCGTGCAGCTTCCTCGGCAACGGCGGCAGAAAATTCTGCCAGGGCGGCAAAAACGTCCGAGACGAATGCCAGGTCATCTGAAACAGCAGCGGAACGGAGCGCCTctgccg           <  1:359887/249‑6 (MQ=255)                                                                                                                                                                                                                   acaaCAATCAGCCGCCACGTCTGCCT‑CCACCGCGGCCACGAAAGCGTCAGAGGCCGCCACTTCAGCACGAGATGCGGTGGCCTCAAAAGAGGCAGCAAAATCATCAGAAACGAACGCATCATCAAGTGCCGGTCGTGCAGCTTCCTCGGCAACGGCGGCAGAAAATTCTGCCAGGGCGGCAAAAACGTCCGAGACGAATGCCAGGTCATCTGAAACCGCAGCGGCACGGAGCGACTCTGCCGCGGCAgacg  >  2:362131/4‑248 (MQ=255)                                                                                                                                                                                                                                           |                                                                                                                                                                                                                                    TGCGGCTGATGCTGCGGACTCAGCACGCGCAGCCAGCACGTCAGCCGGACAGGCCGCGTCGTCGGCTCAGTCAGCGTCTTCCAGCGCAGGAACGGCATCAACAAAGGCCACTGAAGCATCAAAAAGTGCTGCCGCTGCAGAGTCCTCAAAAAGCGCGGCGGCCACCAGTGCCGGTGCGGCGAAAACGTCAGAAACGAATGCTTCAGCGTCACTACAATCAGCAGCCACATCTGCAT‑CCACCGCGACCACGAAGGCATCAGAAGCTGCGACCTCGGCCCGGGATGCGGCGGCCTCAAAAGAAGCGGCAAAATCATCAGAAACGAACGCATCATCAAGCGCCAGTAGTGCAGCTTCCTCGGCAACGGCGGCAGGAAATTCCGCGAAGGCGGCAAAAACGTCCGAGACGAACGCCAGGTCTTCTGAAACGGCAGCGGGACAGAGCGCCTCGGCTGCGGCAGGCT  >  NC_000913/1429480‑1429940

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑