Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,777,977	A→T	intergenic (+195/+169)	ypjF → / ← ypjA	CP4‑57 prophage; toxin of the YpjF‑YfjZ toxin‑antitoxin system/adhesin‑like autotransporter

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,777,977	0	A	T	100.0%	144.0 / NA	36	intergenic (+195/+169)	ypjF/ypjA	CP4‑57 prophage; toxin of the YpjF‑YfjZ toxin‑antitoxin system/adhesin‑like autotransporter
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base T (16/20);  total (16/20)

GCTCTACCGGCTTGCTAAAAACTAATGTGAAATAAACGCTTAAATACAGAGCAGACTGAAGGAAAGCAAAATGCTAATCTCATAGACGAAGAGACTCCCGCTGTAACCTCCCCTCCCCCGAAAAAACCTGACATTTTCTTTTAGGACCAACAATGGGACCAAAATGAAAATTGAACTGAAGATTACAATCAATTTAACAACAAGTTACACAACCAATTCAGACTCCGCCAGCCCACCAATCATGATTGGACGGTGTAAGGACAACACCAACAAAAACAGGAAGTTAGAAGTCTCAGCAAAACACCGACCAGACGGTGAGGAGACATAAAAGGATACGCAAAGGAGCCGCGGCTCCTGGTAACATGAAAGCCCACAGATGTGGGCTTTTTCGTTGATGGTCAGAACGACCAGTTCACACCAGCTACCGCGTTCCACGGGGATTC  >  NC_000913/2777748‑2778190                                                                                                                                                                                                                                      |                                                                                                                                                                                                                      gcTCTACCGGCTTGCTAAAAACTAATGTGAAATAAACGCTTAAATACAGAGCAGACTGAAGGAAAGCAAAATGCTAATCTCATAGACGAAGAGACTCCCGCTGTAACCTCCCCTCCCCCGAAAAAACCTGACATTTTCTTTTAGGACCAACAATGGGACCAAAATGAAAATTGAACTGAAGATTACAATCAATTTAACAACAAGTTACACAACCAATTCAGACTCCGCCTGCccacca                                                                                                                                                                                                               <  1:210976/238‑1 (MQ=255)                              aaaTAAACGCTTAAATACAGAGCAGACTGAAGGAAAGCAAAATGCTAATCTCATAGACGAAGAGACTCCCGCTGTAACCTCCCCTCCCCCGAAAAAACCTGACATTTTCTTTTAGGACCAACAATGGGACCAAAATGAAAATTGAACTGAAGATTACAATCAATTTAACAACAAGTTACACAACCAATTCAGACTCCGCCTGCCCACCAATCATGATTGGACGGTGTAAGGACAACAcc                                                                                                                                                                                 >  4:4704/1‑239 (MQ=255)                                          aaaTACAGAGCAGACTGAAGGAAAGCAAAATGCTAATCTCATAGACGAAGAGACTCCCGCTGTAACCTCCCCTCCCCCGAAAAAACCTGACATTTTCTTTTAGGACCAACAATGGGACCAAAATGAAAATTGAACTGAAGATTACAATCAATTTAACAACAAGTTACACAACCAATTCAGACTCCGCCTGCCCACCAATCATGATTGGACGGTGTAAGGACAACACCAACAAAAACAgg                                                                                                                                                                     <  3:4704/239‑1 (MQ=255)                                                  agCAGACTGAAGGAAAGCAAAATGCTAATCTCATAGACGAAGAGACTCCCGCTGTAACCTCCCCTCCCCCGAAAAAACCTGACATTTTCTTTTAGGACCAACAATGGGACCAAAATGAAAATTGAACTGAAGATTACAATCAATTTAACAACAAGTTACACAACCAATTCAGACTCCGCCTGCCCACCAATCATGATTGGACGGTGTAAGGACAACACCAACAAAAACAGGAAGTTAGa                                                                                                                                                             >  4:12455/1‑239 (MQ=255)                                                         tGAAGGAAAGCAAAATGCTAATCTCATAGACGAAGAGACTCCCGCTGTAACCTCCCCTCCCCCGAAAAAACCTGACATTTTCTTTTAGGACCAACAATGGGACCAAAATGAAAATTGAACTGAAGATTACAATCAATTTAACAACAAGTTACACAACCAATTCAGACTCCGCCTGCCCACCAATCATGATTGGAc                                                                                                                                                                                                  <  4:463747/195‑1 (MQ=255)                                                         tGAAGGAAAGCAAAATGCTAATCTCATAGACGAAGAGACTCCCGCTGTAACCTCCCCTCCCCCGAAAAAACCTGACATTTTCTTTTAGGACCAACAATGGGACCAAAATGAAAATTGAACTGAAGATTACAATCAATTTAACAACAAGTTACACAACCAATTCAGACTCCGCCTGCCCACCAATCATGATTGGAc                                                                                                                                                                                                  >  3:463747/1‑195 (MQ=255)                                                                       aTGCTAATCTCATAGACGAAGAGACTCCCGCTGTAACCTCCCCTCCCCCGAAAAAACCTGACATTTTCTTTTAGGACCAACAATGGGACCAAAATGAAAATTGAACTGAAGATTACAATCAATTTAACAACAAGTTACACAACCAATTCAGACTCCGCCTGCCCACCAATCATGATTGGACGGTGTAAGGACAACACCAACAAAAACAGGAAGTTAGAAGTCTCAGCAAAACACCGAcc                                                                                                                                        <  3:308863/239‑1 (MQ=255)                                                                                       ctaaGAGGCTCCCGCTGTAACCTCACCTCCCCCGAAAAAACCTGACATTTTCGTTTAGGACCAACAATGGGACCAAAATGAAAATTGAACTGAAGATTACAATCAATTTAACAACAAGTTACACAACCAATTCAGACTCCGCCTGCCCACCAATCATGATTGGACGGTGTAAGGACAACACCAACAAAAACAGGAAGTTAGAAGTCTCAGCAAAACACCGACCAGACGGTgagga                                                                                                                            <  2:84473/233‑1 (MQ=255)                                                                                          agagACTCCCGCTGTAACCTCCCCTCCCCCGAAAAAACCTGACATTTTCTTTTAGGACCAACAATGGGACCAAAATGAAAATTGAACTGAAGATTACAATCAATTTAACAACAAGTTACACAACCAATTCAGACTCCGCCTGCCCACCAATCATGATTGGACGGTGTAAGGACAACACCAACAAAAACAGGAAGTTAGAAGTCTCAGCAAAACACCGAcc                                                                                                                                        <  1:66285/220‑1 (MQ=255)                                                                                          agagACTCCCGCTGTAACCTCCCCTCCCCCGAAAAAACCTGACATTTTCTTTTAGGACCAACAATGGGACCAAAATGAAAATTGAACTGAAGATTACAATCAATTTAACAACAAGTTACACAACCAATTCAGACTCCGCCTGCCCACCAATCATGATTGGACGGTGTAAGGACAACACCAACAAAAACAGGAAGTTAGAAGTCTCAGCAAAACACCGAcc                                                                                                                                        >  2:66285/1‑220 (MQ=255)                                                                                          agagACTCCCGCTGTAACCTCCCCTCCCCCGAAAAAACCTGACATTTTCTTTTAGGACCAACAATGGGACCAAAATGAAAATTGAACTGAAGATTACAATCAATTTAACAACAAGTTACACAACCAATTCAGACTCCGCCTGCCCACCAATCATGATTGGACGGTGTAAGGACAACACCAACAAAAACAGGAAGTTAGAAGTCTCAGCAAAACACCGACCAGACGGTGAGGAGACATa                                                                                                                      <  3:12455/238‑1 (MQ=255)                                                                                                                  tccccCGAAAAAACCTGACATTTTCTTTTAGGACCAACAATGGGACCAAAATGAAAATTGAACTGAAGATTACAATCAATTTAACAACAAGTTACACAACCAATTCAGACTCCGCCTGCCCACCAATCATGATTGGACGGTGTAAGGACAACACCAACAAAAACAGGAAGTTAGAAGTCTCAGCAAAACACCGACCAGACGGTGAGGAGACATAAAAGGATACGCAAAGGAGCCGCGGc                                                                                             <  3:294070/239‑1 (MQ=255)                                                                                                                    ccccGAAAAAACCTGACATTTTCTTTTAGGACCAACAATGGGACCAAAATGAAAATTGAACTGAAGATTACAATCAATTTAACAACAAGTTACACAACCAATTCAGACTCCGCCTGCCCACCAATCATGATTGGACGGTGTAAGGACAACACCAACAAAAACAGGAAGTTACAAGTCTCAGCAAAACACCGACCAGACGGTGAGGCGACATAAAAGGTAACGCAAAGGAGCAGCGGCt                                                                                            >  4:294070/1‑238 (MQ=255)                                                                                                                      ccGAAAAAACCTGACATTTTCTTTTAGGACCAACAATGGGACCAAAATGAAAATTGAACTGAAGATTACAATCAATTTAACAACAAGTTACACAACCAATTCAGACTCCGCCTGCCCACCAATCATGATTGGACGGTGTAAGGACAACACCAACAAAAACAGGAAGTTAGAAGTCTCAGCAAAACACCGACCAGACGGTGAGGAGACATAAAAGGATACGCAAAGGAGCCGCGGCTCCt                                                                                         <  3:138607/239‑1 (MQ=255)                                                                                                                         aaaaaaCCTGACATTTTCTTTTAGGACCAACAATGGGACCAAAATGAAAATTGAACTGAAGATTACAATCAATTTAACAACAAGTTACACAACCAATTCAGACTCCGCCTGCCCACCAATCATGATTGGAc                                                                                                                                                                                                  <  1:85057/131‑1 (MQ=255)                                                                                                                         aaaaaaCCTGACATTTTCTTTTAGGACCAACAATGGGACCAAAATGAAAATTGAACTGAAGATTACAATCAATTTAACAACAAGTTACACAACCAATTCAGACTCCGCCTGCCCACCAATCATGATTGGAc                                                                                                                                                                                                  >  2:85057/1‑131 (MQ=255)                                                                                                                                                                  aaaTGAAAATTGAACTGAAGATTACAATCAATTTAACAACAAGTTACACAACCAATTCAGACTCCGCCTGCCCACCAATCATGATTGGACGGTGTAAGGACAACACCAACAAAAACAGGAAGTTAGAAGTCTCAGCAAAACACCGACCAGACGGTGAGGAGACATAAAAGGATACGCAAAGGAGCCGCGGCTCCTGGTAACATGAAAGCCCACAGAtgtg                                                                >  1:86777/1‑220 (MQ=255)                                                                                                                                                                  aaaTGAAAATTGAACTGAAGATTACAATCAATTTAACAACAAGTTACACAACCAATTCAGACTCCGCCTGCCCACCAATCATGATTGGACGGTGTAAGGACAACACCAACAAAAACAGGAAGTTAGAAGTCTCAGCAAAACACCGACCAGACGGTGAGGAGACATAAAAGGATACGCAAAGGAGCCGCGGCTCCTGGTAACATGAAAGCCCACAGAtgtg                                                                <  2:86777/220‑1 (MQ=255)                                                                                                                                                                  aaaTGAAAATTGAACTGAAGATTACAATCAATTTAACAACAAGTTACACAACCAATTCAGACTCCGCCTGCCCACCAATCATGAATGGa                                                                                                                                                                                                   >  4:308718/1‑89 (MQ=255)                                                                                                                                                                  aaaTGAAAATTGAACTGAAGATTACAATCAATTTAACAACAAGTTACACAACCAATTCAGACTCCGCCTGCCCACCAATCATGAATGGa                                                                                                                                                                                                   <  3:308718/89‑1 (MQ=255)                                                                                                                                                                                             tcaatTTAACAACAAGTTACACAACCAATTCAGACTCCGCCTGCCCACCAATCa                                                                                                                                                                                                           <  2:2276/54‑1 (MQ=255)                                                                                                                                                                                             tcaatTTAACAACAAGTTACACAACCAATTCAGACTCCGCCTGCCCACCAATCa                                                                                                                                                                                                           >  1:2276/1‑54 (MQ=255)                                                                                                                                                                                             tcaatTTAACAACAAGTTACACAACCAATTCAGACTCCGCCTGCCCACCAATCATGATTgg                                                                                                                                                                                                    >  1:168429/1‑61 (MQ=255)                                                                                                                                                                                             tcaatTTAACAACAAGTTACACAACCAATTCAGACTCCGCCTGCCCACCAATCATGATTgg                                                                                                                                                                                                    <  2:168429/61‑1 (MQ=255)                                                                                                                                                                                                                   aaCCAATTCAGACTCCGCCTGCCCACCAATCATGATTGGa                                                                                                                                                                                                   <  1:89703/40‑1 (MQ=255)                                                                                                                                                                                                                    aCCAATTCAGACTCCGCCTGCCCACCAATCATGATTGGa                                                                                                                                                                                                   <  3:381171/39‑1 (MQ=255)                                                                                                                                                                                                                    aCCAATTCAGACTCCGCCTGCCCACCAATCATGATTGGa                                                                                                                                                                                                   >  4:381171/1‑39 (MQ=255)                                                                                                                                                                                                                     ccAATTCAGACTCCGCCTGCCCACCAATCATGATTGGACGGTGTAAGGACAACACCAACAAAAACAGGAAGTTAGAAGTCTCAGCAAAACACCGACCAGACGGTGAGGAGACATAAAAGGATACGCAAAGGAGCCGCGGCTCCTGGTAACATGAAAGCCCACAGATGTGGGCTTTTTCGTTGATGGTCAGAACGACCAGTTCACACCAGCTACCGCGTTCCACGGGGATTc  >  2:193276/1‑231 (MQ=255)                                                                                                                                                                                                                     ccAATTCAGACTCCGCCTGCCCACCAATCATGATTGGACGGTGTAAGGACAACACCAACAAAAACAGGAAGTTAGAAGTCTCAGCAAAACACCGACCAGACGGTGAGGAGACATAAAAGGATACGCAAAGGAGCCGCGGCTCCTGGTAACATGAAAGCCCACAGATGTGGGCTTTTTCGTTGATGGTCAGAACGACCAGTTCACACCAGCTACCGCGTTCCACGGGGATTc  <  1:193276/231‑1 (MQ=255)                                                                                                                                                                                                                        aTTCAGACTCCGCCTGCCCACCAATCATGATTGGACGGTGTAAGGACAACACCAACAAAAACAGGAAGTTAGAAGTCTCAGCAAAACACCGACCa                                                                                                                                       <  2:138987/95‑1 (MQ=255)                                                                                                                                                                                                                        aTTCAGACTCCGCCTGCCCACCAATCATGATTGGACGGTGTAAGGACAACACCAACAAAAACAGGAAGTTAGAAGTCTCAGCAAAACACCGACCa                                                                                                                                       >  1:138987/1‑95 (MQ=255)                                                                                                                                                                                                                             gACTCCGCCTGCCCACCAATCATGATTGGACGGTGTAAgg                                                                                                                                                                                         >  2:89703/1‑40 (MQ=255)                                                                                                                                                                                                                               cTCCGCCTGCCCACCAATCATGATTGGACGGTGTAAGGACAACACCAACAAAAACAGGAAGTTAGAAGtct                                                                                                                                                        >  2:92526/1‑71 (MQ=255)                                                                                                                                                                                                                               cTCCGCCTGCCCACCAATCATGATTGGACGGTGTAAGGACAACACCAACAAAAACAGGAAGTTAGAAGtct                                                                                                                                                        <  1:92526/71‑1 (MQ=255)                                                                                                                                                                                                                                  cGCCTGCCCACCAATCATGATTGGACGGTGTAAGGACAACACCAACAAAAACAGGAAGTTAGAAGTCTCAGCAAAACACCGACCAGACGGTGAGGAGACATAAAAGGATACGCAAAGGAGCCGCGGCTCCTGGTAACATGAAAGCCCACAGATGTGGGCttt                                                          <  3:428817/162‑1 (MQ=255)                                                                                                                                                                                                                                  cGCCTGCCCACCAATCATGATTGGACGGTGTAAGGACAACACCAACAAAAACAGGAAGTTAGAAGTCTCAGCAAAACACCGACCAGACGGTGAGGAGACATAAAAGGATACGCAAAGGAGCCGCGGCTCCTGGTAACATGAAAGCCCACAGATGTGGGCttt                                                          >  4:428817/1‑162 (MQ=255)                                                                                                                                                                                                                                      |                                                                                                                                                                                                                      GCTCTACCGGCTTGCTAAAAACTAATGTGAAATAAACGCTTAAATACAGAGCAGACTGAAGGAAAGCAAAATGCTAATCTCATAGACGAAGAGACTCCCGCTGTAACCTCCCCTCCCCCGAAAAAACCTGACATTTTCTTTTAGGACCAACAATGGGACCAAAATGAAAATTGAACTGAAGATTACAATCAATTTAACAACAAGTTACACAACCAATTCAGACTCCGCCAGCCCACCAATCATGATTGGACGGTGTAAGGACAACACCAACAAAAACAGGAAGTTAGAAGTCTCAGCAAAACACCGACCAGACGGTGAGGAGACATAAAAGGATACGCAAAGGAGCCGCGGCTCCTGGTAACATGAAAGCCCACAGATGTGGGCTTTTTCGTTGATGGTCAGAACGACCAGTTCACACCAGCTACCGCGTTCCACGGGGATTC  >  NC_000913/2777748‑2778190

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑