Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,777,841	A→G	intergenic (+59/+305)	ypjF → / ← ypjA	CP4‑57 prophage; toxin of the YpjF‑YfjZ toxin‑antitoxin system/adhesin‑like autotransporter YpjA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,777,841	0	A	G	100.0%	120.4 / NA	34	intergenic (+59/+305)	ypjF/ypjA	CP4‑57 prophage; toxin of the YpjF‑YfjZ toxin‑antitoxin system/adhesin‑like autotransporter YpjA
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (22/12);  total (22/12)

CAGTCTCCATATATTTCCGTAGTAGATATTCTGCGAGCAAGGCGCTCTACCGGCTTGCTAAAAACTAATGTGAAATAAACGCTTAAATACAGAGCAGACTGAAGGAAAGCAAAATGCTAATCTCATAGACGAAGAGACTCCCGCTGTAACCTCCCCTCCCCCGAAAAAACCTGACATTTTCTTTTAGGACCAACAATGGGACCAAAATGAAAATTGAACTGAAGATTACAATCAATTTAACAACAAGTTACACAACCAATTCAGACTCCGCC  >  NC_000913/2777705‑2777976                                                                                                                                         |                                                                                                                                        caGTCTCCATATATTTCCGTAGTAGATATTCTGCGAGCAAGGCGCTCTACCGGCTTGCTAAAAACTAATGTGAAATAAACGCTTAAATACAGAGCAGACTGAAGGAAAGCAAAATGCTAATCTCATAGACGAAGAGGCTc                                                                                                                                      <  2:18114/140‑1 (MQ=255)    tctcCATATATTTCCGTAGTAGATATTCTGCGAGCAAGGCGCTCTACCGGCTTGCTAAAAACTAATGTGAAATAAACGCTTAAATACAGAGCAGACTGAAGGAAAGCAAAATGCTAATCTCATAGACGAAGAGGCTCCCg                                                                                                                                   >  2:77936/1‑140 (MQ=255)    tctcCATATATTTCCGTAGTAGATATTCTGCGAGCAAGGCGCTCTACCGGCTTGCTAAAAACTAATGTGAAATAAACGCTTAAATACAGAGCAGACTGAAGGAAAGCAAAATGCTAATCTCATAGACGAAGAGGCTCCCg                                                                                                                                   >  2:164485/1‑140 (MQ=255)    tctcCATATATTTCCGTAGTAGATATTCTGCGAGCAAGGCGCTCTACCGGCTTGCTAAAAACTAATGTGAAATAAACGCTTAAATACAGAGCAGACTGAAGGAAAGCAAAATGCTAATCTCATAGACGAAGAGGCTCCCg                                                                                                                                   >  1:354014/1‑140 (MQ=255)     ctcCATATATTTCCGTAGTAGATATTCTGCGAGCAAGGCGCTCTACCGGCTTGCTAAAAACTAATGTGAAATAAACGCTTAAATACAGAGCAGACTGAAGGAAAGCAAAATGCTAATCTCATAGACGAAGAGGCTCCCGc                                                                                                                                  >  1:190115/1‑140 (MQ=255)                tCCGTAGTAGATATTCTGCGAGCAAGGCGCTCTACCGGCTTGCTAAAAACTAATGTGAAATAAACGCTTAAATACAGAGCAGACTGAAGGAAAGCAAAATGCTAATCTCATAGACGAAGAGGCTCCCGCTGTAAcctccc                                                                                                                       >  1:117106/1‑140 (MQ=255)                tCCGTAGTAGATATTCTGCGAGCAAGGCGCTCTACCGGCTTGCTAAAAACTAATGTGAAATAAACGCTTAAATACAGAGCAGACTGAAGGAAAGCAAAATGCTAATCTCATAGACGAAGAGGCTCCCGCTGTAAcctccc                                                                                                                       <  1:304456/140‑1 (MQ=255)                         gATATTCTGCGAGCAAGGCGCTCTACCGGCTTGCTAAAAACTAATGTGAAATAAACGCTTAAATACAGAGCAGACTGAAGGAAAGCAAAATGCTAATCTCATAGACGAAGAGGCTCCCGCTGTAACCTCCCCTCCCCCGa                                                                                                              >  1:39549/1‑140 (MQ=255)                                tGCGAGCAAGGCGCTCTACCGGCTTGCTAAAAACTAATGTGAAATAAACGCTTAAATACAGAGCAGACTGAAGGAAAGCAAAATGCTAATCTCATAGACGAAGAGGCTCCCGCTGTAACCTCCCCTCCCCCGAAAAAAcc                                                                                                       <  2:39549/140‑1 (MQ=255)                                 gCGAGCAAGGCGCTCTACCGGCTTGCTAAAAACTAATGTGAAATAAACGCTTAAATACAGAGCAGACTGAAGGAAAGCAAAATGCTAATCTCATAGACGAAGAGGCTCCCGCTGTAACCTCCCCTCCCCCGaaa                                                                                                            <  2:386626/134‑1 (MQ=255)                                 gCGAGCAAGGCGCTCTACCGGCTTGCTAAAAACTAATGTGAAATAAACGCTTAAATACAGAGCAGACTGAAGGAAAGCAAAATGCTAATCTCATAGACGAAGAGGCTCCCGCTGTAACCTCCCCTCCCCCGaaa                                                                                                            >  1:386626/1‑134 (MQ=255)                                 gCGAGCAAGGCGCTCTACCGGCTTGCTAAAAACTAATGTGAAATAAACGCTTAAATACAGAGCAGACTGAAGGAAAGCAAAATGCTAATCTCATAGACGAAGAGGCTCCCGCTGTAACCTCCCCTCCCCCGAAAAAACCt                                                                                                      >  1:97822/1‑140 (MQ=255)                                                 aCCGGCTTGCTAAAAACTAATGTGAAATAAACGCTTAAATACAGAGCAGACTGAAGGAAAGCAAAATGCTAATCTCATAGACGAAGAGGCTCCCGCTGTAACCTCCCCTCCCCCGAAAAAACCTGACATTTTCTTTTAgg                                                                                      <  1:146971/140‑1 (MQ=255)                                                  ccGGCTTGCTAAAAACTAATGTGAAATAAACGCTTAAATACAGAGCAGACTGAAGGAAAGCAAAATGCTAATCTCATAGACGAAGAGGCTCCCGCTGTAACCTCCCCTCCCCCGAAAAAACCTGACATTTTCTTTTAGGa                                                                                     <  2:97822/140‑1 (MQ=255)                                                    ggCTTGCTAAAAACTAATGTGAAATAAACGCTTAAATACAGAGCAGACTGCAGGAAAGCAAAATGCTAATCTCATAGACGAAGAGGCTCCCGCTGTAACCTCCCCTCCCCCGAAAAAACCTGACATTTTCTTTTAGGAcc                                                                                   <  2:354014/140‑1 (MQ=255)                                                          cTAAAAACTAATGTGAAATAAACGCTTAAATACAGAGCAGACTGAAGGAAAGCAAAATGCTAATCTCATAGACGAAGAGGCTCCCGCTTTAACTTCCCCTCCCCCGAAAAAACCTGACATTTTCTTTTGGGCCcaaaata                                                                             >  2:109563/1‑136 (MQ=255)                                                          cTAAAAACTAATGTGAAATAAACGCTTAAATACAGAGCAGACTGAAGGAAAGCAAAATGCTAATCTCATAGACGAAGAGGCTCCCGCTGTAACCTCCCCTCCCCCGAAAAAACCTGACATTTTCTTTTAGGACCAACAAt                                                                             >  2:233485/1‑140 (MQ=255)                                                          cTAAAAACTAATGTGAAATAAACGCTTAAATACAGAGCAGACTGAAGGAAAGCAAAATGCTAATCTCATAGACGAAGAGGCTCCCGCTGTAACCTCCCCTCCCCCGAAAAAACCTGACATTTTCTTTTAGGACCAACAAt                                                                             >  2:222356/1‑140 (MQ=255)                                                                          aaTAAACGCTTAAATACAGAGCAGACTGAAGGAAAGCAAAATGCTAATCTCATAGACGAAGAGGCTCCCGCTGTAACCTCCCCTCCCCCGAAAAAACCTGACATTTTCTTTTAGGACCAACAATGGGACCAAAATGaaaa                                                             <  2:258480/140‑1 (MQ=255)                                                                               aCGCTTAAATACAGAGCAGACTGAAGGAAAGCAAAATGCTAATCTCATAGACGAAGAGGCTCCCGCTGTAACCTCCCCTCCCCCGAAAAAACCTGACATTTTCTTTTAGGACCAACAATGGGACCAAAATGAAAATTGaa                                                        >  1:266653/1‑140 (MQ=255)                                                                                   ttAAATACAGAGCAGACTGAAGGAAAGCAAAATGCTAATCTCATAGACGAAGAGGCTCCCGCTGTAACCTCCCCTCCCCCGAAAAAACCTGACATTTTCTTTTAGGACCAACAATGGGACCAAAATGAAAATTGAACTGa                                                    <  1:19111/140‑1 (MQ=255)                                                                                           agagCAGACTGAAGGAAAGCAAAATGCTAATCTCATAGACGAAGAGGCTCCCGCTGTAACCTCCCCTCCCCCGAAAAAACCTGACATTTTCTTTTAGGACCAACAATGGGACCAAAATGAAAATTGAACTGAAGATTAca                                            <  1:144971/140‑1 (MQ=255)                                                                                             agCAGACTGAAGGAAAGCAAAATGCTAATCTCATAGACGAAGAGGCTCCCGCTGTAACCTCCCCTCCCCCGAAAAAACCTGACATTTTCTTTTAGGACCAACAATGGGACCAAAATGAAAATTGAACTGAAGATTAcaat                                          >  1:204247/1‑140 (MQ=255)                                                                                             agCAGACTGAAGGAAAGCAAAATGCTAATCTCATAGACGAAGAGGCTCCCGCTGTAACCTCCCCTCCCCCGAAAAAACCTGACATTTTCTTTTAGGACCAACAATGGGACCAAAATGAAAATTGAACTGAAGATTAca                                            >  2:18467/1‑138 (MQ=255)                                                                                             agCAGACTGAAGGAAAGCAAAATGCTAATCTCATAGACGAAGAGGCTCCCGCTGTAACCTCCCCTCCCCCGAAAAAACCTGACATTTTCTTTTAGGACCAACAATGGGACCAAAATGAAAATTGAACTGAAGATTAca                                            <  1:18467/138‑1 (MQ=255)                                                                                               cAGACTGAAGGAAAGCAAAATGCTAATCTCATAGACGAAGAGGCTCCCGCTGTAACCTCCCCTCCCCCGAAAAAACCTGACATTTTCTTTTAGGACCAACAATGGGACCAAAATGAAAATTGAACTGAAGATTAcaatca                                        >  1:241076/1‑140 (MQ=255)                                                                                               cAGACTGAAGGAAAGCAAAATGCTAATCTCATAGACGAAGAGGCTCCCGCTGTAACCTCCCCTCCCCCGAAAAAACCTGACATTTTCTTTTAGGACCAACAATGGGACCAAAATGAAAATTGAACTGAAGATTAcaatca                                        >  2:338781/1‑140 (MQ=255)                                                                                                  aCTGAAGGAAAGCAAAATGCTAATCTCATAGACGAAGAGGCTCCCGCTGTAACCTCCCCTCCCCCGAAAAAACCTGACATTTTCTTTTAGGACCAACAATGGGACCAAAATGAAAATTGAACTGAAGATTACAATCAAtt                                     >  1:257762/1‑140 (MQ=255)                                                                                                  aCTGAAGGAAAGCAAAATGCTAATCTCATAGACGAAGAGGCTCCCGCTGTAACCTCCCCTCCCCCGAAAAAACCTGACATTTTCTTTTAGGACCAACAATGGGACCAAAATGAAAATTGAACTGAAGATTACAATCAAtt                                     >  2:279158/1‑140 (MQ=255)                                                                                                    tGAAGGAAAGCAAAATGCTAATCTCATAGACGAAGAGGCTCCCGCTGTAACCTCCCCTCCCCCGAAAAAACCTGACATTTTCTTTTAGGACCAACAATGGGACCAAAATGAAAATTGAACTGAAGATTACAATCAATTTa                                   >  2:13984/1‑140 (MQ=255)                                                                                                            aGCAAAATGCTAATCTCATAGACGAAGAGGCTCCCGCTGTAACCTCCCCTCCCCCGAAAAAACCTGACATTTTCTTTTAGGACCAACAATGGGACCAAAATGAAAATTGAACTGAAGATTACAATCAATTTAACAACAAg                           >  2:279863/1‑140 (MQ=255)                                                                                                            aGCAAAATGCTAATCTCATAGACGAAGAGGCTCCCGCTGTAACCTCCCCTCCCCCGAAAAAACCTGACATTTTCTTTTAGGACCAACAATGGGACCAAAATGAAAATTGAACTGAAGATTACAATCAATTTAACAACAAg                           >  2:313194/1‑140 (MQ=255)                                                                                                                      tAATCTCATAGACGAAGAGGCTCCCGCTGTAACCTCCCCTCCCCCGAAAAAACCTGACATTTTCTTTTAGGACCAACAATGGGACCAAAATGAAAATTGAACTGAAGATTACAATCAATTTAACAACAAGTTACACAAcc                 <  1:77936/140‑1 (MQ=255)                                                                                                                        aTCTCATAGACGAAGAGGCTCCCGCTGTAACCTCCCCTCCCCCGAAAAAACCTGACATTTTCTTTTAGGACCAACAATGGGACCAAAATGAAAATTGAACTGAAGATTACAATCAATTTAACAACAAGTTACACAACCaa               >  2:97813/1‑140 (MQ=255)                                                                                                                                     agagGCTCCCGCTGTAACCTCCCCTCCCCCGAAAAAACCTGACATTTTCTTTTAGGACCAACAATGGGACCAAAATGAAAATTGAACTGAAGATTACAATCAATTTAACAACAAGTTACACAACCAATTCAGACTCCGcc  >  1:223424/1‑140 (MQ=255)                                                                                                                                         |                                                                                                                                        CAGTCTCCATATATTTCCGTAGTAGATATTCTGCGAGCAAGGCGCTCTACCGGCTTGCTAAAAACTAATGTGAAATAAACGCTTAAATACAGAGCAGACTGAAGGAAAGCAAAATGCTAATCTCATAGACGAAGAGACTCCCGCTGTAACCTCCCCTCCCCCGAAAAAACCTGACATTTTCTTTTAGGACCAACAATGGGACCAAAATGAAAATTGAACTGAAGATTACAATCAATTTAACAACAAGTTACACAACCAATTCAGACTCCGCC  >  NC_000913/2777705‑2777976

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑