Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,473,372	(T)6→7	intergenic (‑126/‑232)	yfdO ← / → yfdP	CPS‑53 (KpLE1) prophage; putative defective phage replication protein O/CPS‑53 (KpLE1) prophage; protein YfdP

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,473,366	1	.	T	100.0%	163.9 / NA	47	intergenic (‑120/‑238)	yfdO/yfdP	CPS‑53 (KpLE1) prophage; putative defective phage replication protein O/CPS‑53 (KpLE1) prophage; protein YfdP
Reads supporting (aligned to +/- strand):  ref base . (0/0);  new base T (26/21);  total (26/21)

GCGCAGGTCAAATCATCCTGCGTTCCCCACTGGCGCTTTTTAGGGCTGAATACAACCGCATCAGGATGGCGAGTTAAAAAATCCTGTTCATCCGTCTGCGTGTCCGGTTGCGAAGCGTCCGGACGAGAAGG‑TTTTTTATCTGACGGATCATGTTTTGATTTTACTGACGGATCCCCGCCAGATTCTGACGGGTGAAAACCCGATTTTTTGCCAGATTTCGACGCATCAAATTTTGACGGGTCAGATTTTGA  >  NC_000913/2473236‑2473486                                                                                                                                    |                                                                                                                         gcgcAGGTCAAATCATCCTGCGTTCCCCACTGGCGCTTTTTAGGGCTGAATACAACCGCATCAGGATGGCGAGTTAAAAAATCCTGTTCATCCGTCTGCGTGTCCGGTTGCGAAGCGTCCGGACGAGAAGG‑tttttttat                                                                                                                 <  2:1078790/140‑4 (MQ=255) gcgcAGGTCAAATCATCCTGCGTTCCCCACTGGCGCTTTTTAGGGCTGAATACAACCGCATCAGGATGGCGAGTTAAAAAATCCTGTTCATCCGTCTGCGTGTCCGGTTGCGAAGCGTCCGGACGAGAAGG‑tttttttat                                                                                                                 <  2:42562/140‑4 (MQ=255)    cAGGTCAAATCATCCTGCGTTCCCCACTGGCGCTTTTTAGGGCTGAATACAACCGCATCAGGATGGCGAGTTAAAAAATCCTGTTCATCCGTCTGCGTGTCCGGTTGCGAAGCGTCCGGACGAGAAGGTTTTTTTATCTg                                                                                                               >  1:490275/1‑140 (MQ=255)     aGGTCAAATCCTCCTGCGTTCCCCACTGGCGCTTTTTAGGGCTGAATACAACCGCATCAGGATGGCGAGTTAAAAAATCCTGTTCATCCGTCTGCGTGTCCGGTTGCGAAGCGTCCGGACGAGAAGGTTTTTTTATCTGa                                                                                                              <  2:678707/140‑1 (MQ=255)       gTCAAATCATCCTGCGTTCCCCACTGGCGCTTTTTAGGGCTGAATACAACCGCATCAGGATGGCGAGTTAAAAAATCCTGTTCATCCGTCTGCGTGTCCGGTTGCGAAGCGTCCGGACGAGAAGGTTTTTTTATCTGACg                                                                                                            >  2:1045274/1‑140 (MQ=255)       gTCAAATCATCCTGCGTTCCCCACTGGCGCTTTTTAGGGCTGAATACAACCGCATCAGGATGGCGAGTTAAAAAATCCTGTTCATCCGTCTGCGTGTCCGGTTGCGAAGCGTCCGGACGAGAAGGTTTTTTTATCTGACg                                                                                                            >  1:64645/1‑140 (MQ=255)          aaaTCATCCTGCGTTCCCCACTGGCGCTTTTTAGGGCTGAATACAACCGCATCAGGATGGCGAGTTAAAAAATCCTGTTCATCCGTCTGCGTGTCCGGTTGCGAAGCGTCCGGACGAGAAGGTTTTTTTATCTg                                                                                                               >  1:189283/1‑134 (MQ=255)          aaaTCATCCTGCGTTCCCCACTGGCGCTTTTTAGGGCTGAATACAACCGCATCAGGATGGCGAGTTAAAAAATCCTGTTCATCCGTCTGCGTGTCCGGTTGCGAAGCGTCCGGACGAGAAGGTTTTTTTATCTg                                                                                                               <  2:189283/134‑1 (MQ=255)          aaaTCATCCTGCGTTCCCCACTGGCGCTTTTTAGGGCTGAATACAACCGCATCAGGATGGCGAGTTAAAAAATCCTGTTCATCCGTCTGCGTGTCCGGTTGCGAAGCGTCCGGACGAGAAGGTTTTTTTATCTGACGGAt                                                                                                         >  1:991049/1‑140 (MQ=255)            atcatcCTGCGTTCCCCACTGGCGCTTTTTAGGGCTGAATACAACCGCATCAGGATGGCGAGTTAAAAAATCCTGTTCATCCGTCTGCGTGTCCGGTTGCGAAGCGTCCGGACGAGAAGGTTTTTTTATCTGACGGATCa                                                                                                       >  1:235938/1‑140 (MQ=255)            atcatcCTGCGTTCCCCACTGGCGCTTTTTAGGGCTGAATACAACCGCATCAGGATGGCGAGTTAAAAAATCCTGTTCATCCGTCTGCGTGTCCGGTTGCGAAGCGTCCGGACGAGAAGGTTTTTTTATCTGACGGATCa                                                                                                       >  2:631110/1‑140 (MQ=255)                 ccTGCGTTCCCCACTGGCGCTTTTTAGGGCTGAATACAACCGCATCAGGATGGCGAGTTAAAAAATCCTGTTCATCCGTCTGCGTGTCCGGTTGCGAAGCGTCCGGACGAGAAGGTTTTTTTATCTGACGGATCATGttt                                                                                                  >  2:1085071/1‑140 (MQ=255)                 ccTGCGTTCCCCACTGGCGCTTTTTAGGGCTGAATACAACCGCATCAGGATGGCGAGTTAAAAAATCCTGTTCATCCGTCTGCGTGTCCGGTTGCGAAGCGTCCGGACGAGAAGGTTTTTTTATCTGACGGATCATGttt                                                                                                  >  1:158956/1‑140 (MQ=255)                      gTTCCCCACTGGCGCTTTTTAGGGCTGAATACAACCGCATCAGGATGGCGAGTTAAAAAATCCTGTTCATCCGTCTGCGTGTCCGGTTGCGAAGCGTCCGGACGAGAAGGTTTTTTTATCTGACGGATCATGTTTTGAtt                                                                                             >  2:429159/1‑140 (MQ=255)                         ccccACTGGCGCTTTTTAGGGCTGAATACAACCGCATCAGGATGGCGAGTTAAAAAATCCTGTTCATCCGTCTGCGTGTCCGGTTGCGAAGCGTCCGGACGAGAAGGTTTTTTTATCTGACGGATCATGTTTTGATTTTa                                                                                          <  2:490275/140‑1 (MQ=255)                           ccACTGGCGCTTTTTAGGGCTGAATGCAACCGCATCAGGATGGCGAGTTAAAAAATCCTGTTCATCCGTCTGCGTGTCCGGTTGCGAAGCGTCCGGACGAGAAGGTTTTTTTATCTGACGGATCATGTTTTGATTTTACt                                                                                        <  2:236322/140‑1 (MQ=255)                              cTGGCGCTTTTTAGGGCTGAATACAACCGCATCAGGATGGCGAGTTAAAAAATCCTGTTCATCCGTCTGCGTGTCCGGTTGCGAAGCGTCCGGACGAGAAGGTTTTTTTATCTGACGGATCATGTTTTGATTTTACTGAc                                                                                     <  2:235938/140‑1 (MQ=255)                                    cTTTTTAGGGCTGAATACAACCGCATCAGGATGGCGAGTTAAAAAATCCTGTTCATCCGTCTGCGTGTCCGGTTGCGAAGCGTCCGGACGAGAAGGTTTTTTTATCTGACGGATCATGTTTTGATTTTACTGACGGATcc                                                                               <  1:582634/140‑1 (MQ=255)                                    cTTTTTAGGGCTGAATACAACCGCATCAGGATGGCGAGTTAAAAAATCCTGTTCATCCGTCTGCGTGTCCGGTTGCGAAGCGTCCGGACGAGAAGGTTTTTTTATCTGACGGATCATGTTTTGATTTTACTGACGGATcc                                                                               <  2:480466/140‑1 (MQ=255)                                      ttttAGGGCTGAATACAACCGCATCAGGATGGCGAGTTAAAAAATCCTGTTCATCCGTCTGCGTGTCCGGTTGCGAAGCGTCCGGACGAGAAGGTTTTTTTATCTGACGGATCATGTTTTGATTTTACTGACGGATcccc                                                                             >  2:858829/1‑140 (MQ=255)                                      ttttAGGGCTGAATACAACCGCATCAGGATGGCGAGTTAAAAAATCCTGTTCATCCGTCTGCGTGTCCGGTTGCGAAGCGTCCGGACGAGAAGGTTTTTTTATCTGACGGATCATGTTTTGATTTTACTGACGGATcccc                                                                             >  2:453291/1‑140 (MQ=255)                                       tttAGGGCTGAATACAACCGCATCAGGATGGCGAGTTAAAAAATCCTGTTCATCCGTCTGCGTGTCCGGTTGCGAAGCGTCCGGACGAGAAGGTTTTTTTATCTGACGGATCATGTTTTGATTTTACTGACGGATCCCCg                                                                            <  2:1048416/140‑1 (MQ=255)                                       tttAGGGCTGAATACAACCGCATCAGGATGGCGAGTTAAAAAATCCTGTTCATCCGTCTGCGTGTCCGGTTGCGAAGCGTCCGGACGAGAAGGTTTTTTTATCTGACGGATCATGTTTTGATTTTACTGACGGATCCCCg                                                                            >  1:1048416/1‑140 (MQ=255)                                         tAGGGCTGAATACAACCGCATCAGGATGGCGAGTTAAAAAATCCTGTTCATCCGTCTGCGTGTCCGGTTGCGAAGCGTCCGGACGAGAAGGTTTTTTTATCTGACGGATCATGTTTTGATTTTACTGACGGATCCCCGcc                                                                          <  1:429159/140‑1 (MQ=255)                                              cTGAATACAACCGCATCAGGATGGCGAGTTAAAAAATCCTGTTCATCCGTCTGCGTGTCCGGTTGCGAAGCGTCCGGACGAGAAGGTTTTTTTATCTGACGGATCATGTTTTGATTTTACTGACGGATCCCCGCCAGAtt                                                                     <  1:858829/140‑1 (MQ=255)                                              cTGAATACAACCGCATCAGGATGGCGAGTTAAAAAATCCTGTTCATCCGTCTGCGTGTCCGGTTGCGAAGCGTCCGGACGAGAAGGTTTTTTTATCTGACGGATCATGTTTTGATTTTACTGACGGATCCCCGCCAGAtt                                                                     <  1:453291/140‑1 (MQ=255)                                                 aaTACAACCGCATCAGGATGGCGAGTTAAAAAATCCTGTTCATCCGTCTGCGTGTCCGGTTGCGAAGCGTCCGGACGAGAAGGTTTTTTTATCTGACGGATCATGTTTTGATTTTACTGACGGATCCCCGCCAGATTCTg                                                                  >  1:998033/1‑140 (MQ=255)                                                 aaTACAACCGCATCAGGATGGCGAGTTAAAAAATCCTGTTCATCCGTCTGCGTGTCCGGTTGCGAAGCGTCCGGACGAGAAGGTTTTTTTATCTGACGGATCATGTTTTGATTTTACTGACGGATCCCCGCCAGATTCTg                                                                  >  2:653845/1‑140 (MQ=255)                                                 aaTACAACCGCATCAGGATGGCGAGTTAAAAAATCCTGTTCATCCGTCTGCGTGTCCGGTTGCGAAGCGTCCGGACGAGAAGGTTTTTTTATCTGACGGATCATGTTTTGATTTTACTGACGGATCCCCGCCAGATTCTg                                                                  >  1:579082/1‑140 (MQ=255)                                                        ccGCATCAGGATGGCGAGTTAAAAAATCCTGTTCATCCGTCTGCGTGTCCGGTTGCGAAGCGTCCGGACGAGAAGGTTTTTTTATCTGACGGATCATGTTTTGATTTTACTGACGGATCCCCGCCAGATTCTGACGGGTg                                                           >  2:824077/1‑140 (MQ=255)                                                          gCATCAGGATGGCGAGTTAAAAAATCCTGTTCATCCGTCTGCGTGTCCGGTTGCGAAGCGTCCGGACGAGAAGGTTTTTTTATCTGACGGATCATGTTTTGATTTTACTGACGGATCCCCGCCAGATTCTGACGGGTGaa                                                         <  1:631110/140‑1 (MQ=255)                                                           cATTAGGATGGCGAGTTAAAAAATCCTGTTCATCCGTCTGCGTGTCCGGTTGCGAAGCGTCCGGACGAGAAGGTTTTTTTATCTGACGGATCATGTTTTGATTTTACTGACGGATCCCCGCCAGATTCTGAc                                                                >  2:211491/1‑132 (MQ=255)                                                           cATTAGGATGGCGAGTTAAAAAATCCTGTTCATCCGTCTGCGTGTCCGGTTGCGAAGCGTCCGGACGAGAAGGTTTTTTTATCTGACGGATCATGTTTTGATTTTACTGACGGATCCCCGCCAGATTCTGAc                                                                <  1:211491/132‑1 (MQ=255)                                                           cATCAGGATGGCGAGTTAAAAAATCCTGTTCATCCGTCTGCGTGTCCGGTTGCGAAGCGTCCGGACGAGAAGGTTTTTTTATCTGACGGATCATGTTTTGATTTTACTGACGGATCCCCGCCAGATTCTGACGGGTGaaa                                                        >  1:438730/1‑140 (MQ=255)                                                             tCAGGATGGCGAGTTAAAAAATCCTGTTCATCCGTCTGCGTGTCCGGTTGCGAAGCGTCCGGACGAGAAGGTTTTTTTATCTGACGGATCATGTTTTGATTTTACTGACGGATCCCCGCCAGATTCTGACGGGTGAAAAc                                                      >  1:346384/1‑140 (MQ=255)                                                                ggATGGCGAGTTAAAAAATCCTGTTCATCCGTCTGCGTGTCCGGTTGCGAAGCGTCCGGACGAGAAGGTTTTTTTATCTGACGGATCATGTTTTGATTTTACTGACGGATCCCCGCCAGATTCTGACGGGTGAAAACCCg                                                   >  1:831713/1‑140 (MQ=255)                                                                  aTGGCGAGTTAAAAAATCCTGTTCATCCGTCTGCGTGTCCGGTTGCGAAGCGTCCGGACGAGAAGGTTTTTTTATCTGACGGATCATGTTTTGATTTTACTGACGGATCCCCGCCAGATTCTGACGGGTGAAAACCCGAt                                                 >  1:285134/1‑140 (MQ=255)                                                                   tGGCGAGTTAAAAAATCCTGTTCATCCGTCTGCGTGTCCGGTTGCGAAGCGTCCGGACGAGAAGGTTTTTTTATCTGACGGATCATGTTTTGATTTTACTGACGGATCCCCGCCAGATTCTGACGGGTGAAAACCCGAtt                                                >  2:404807/1‑140 (MQ=255)                                                                    ggCGAGTTAAAAAATCCTGTTCATCCGTCTGCGTGTCCGGTTGCGAAGCGTCCGGACGAGAAGGTTTTTTTATCTGACGGATCATGTTTTGATTTTACTGACGGATCCCCGCCAGATTCTGACGGGTGAAAACCCGAttt                                               >  2:1041110/1‑140 (MQ=255)                                                                         gTTAAAAAATCCTGTTCATCCGTCTGCGTGTCCGGTTGCGAAGCGTCCGGACGAGAAGGTTTTTTTATCTGACGGATCATGTTTTGATTTTACTGACGGATCCCCGCCAGATTCTGACGGGTGAAAACCCGATTTTTTGc                                          <  2:831713/140‑1 (MQ=255)                                                                                  tCCTGTTCATCCGTCTGCGTGTCCGGTTGCGAAGCGTCCGGACGAGAAGGTTTTTTTATCTGACGGATCATGTTTTGATTTTACTGACGGATCCCCGCCAGATTCTGACGGGTGAAAACCCGATTTTTTGCCAGATTTCg                                 >  1:31246/1‑140 (MQ=255)                                                                                        tCATCCGTCTACGTGTCCGTTTGCGAAGCGTCCGGACGAGAAGGTTTTTTTATCTGACGGATCATGTTTTGATTTTACTGACGGATCCCCGCCAGATTCTGACGGGTGAAAACCCGATTTTTTGCCAGATTTCGACGCAt                           <  2:53362/140‑1 (MQ=255)                                                                                         cATCCGTCTGCGTGTCCGGTTGCGAAGCGTCCGGACGAGAAGGTTTTTTTATCTGACGGATCATGTTTTGATTTTACTGACGGATCCCCGCCAGATTCTGACGGGTGAAAACCCGATTTTTTGCCAGATTTCGACGCATc                          <  1:824077/140‑1 (MQ=255)                                                                                            ccGTCTGCGTGTCCGGTTGCGAAGCGTCCGGACGAGAAGGTTTTTTTATCTGACGGATCATGTTTTGATTTTACTGACGGATCCCCGCCAGATTCTGACGGGTGAAAACCCGATTTTTTGCCAGATTTCGACGCATCaaa                       >  1:46069/1‑140 (MQ=255)                                                                                                  gCGTGTCCGGTTGCGAAGCGTCCGGACGAGAAGGTTTTTTTATCTGACGGATCATGTTTTGATTTTACTGACGGATCCCCGCCAGATTCTGACGGGTGAAAACCCGATTTTTTGCCAGATTTCGACGCATCAAATTTTGa                 <  2:46069/140‑1 (MQ=255)                                                                                                  gCGTGTCCGGTTGCGAAGCGTCCGGACGAGAAGGTTTTTTTATCTGACGGATCATGTTTTGATTTTACTGACGGATCCCCGCCAGATTCTGACGGGTGAAAACCCGATTTTTTGCCAGATTTCGACGCATCAAATTTTGa                 <  2:455142/140‑1 (MQ=255)                                                                                                        ccGGTTGCGAAGCGTCCGGACGAGAAGGTTTTTTTATCTGACGGATCATGTTTTGATTTTACTGACGGATCCCCGCCAGATTCTGACGGGTGAAAACCCGATTTTTTGCCAGATTTCGACGCATCAAATTTTGACGGGTc           <  1:1045274/140‑1 (MQ=255)                                                                                                                gAAGCGTCCGGACGAGAAGGTTTTTTTATCTGACGGATCATGTTTTGATTTTACTGACGGATCCCCGCCAGATTCTGACGGGTGAAAACCCGATTTTTTGCCAGATTTCGACGCATCAAATTTTGACGGGTCAGATTTTg   <  2:31246/140‑1 (MQ=255)                                                                                                                 aaGCGTCCGGACGAGAAGGTTTTTTTATCTGACGGATCATGTTTTGATTTTACTGACGGATCCCCGCCAGATTCTGACGGGTGAAAACCCGATTTTTTGCCAGATTTCGACGCATCAAATTTTGACGGGTCAGATTTTGa  <  1:1041110/140‑1 (MQ=255)                                                                                                                                    |                                                                                                                         GCGCAGGTCAAATCATCCTGCGTTCCCCACTGGCGCTTTTTAGGGCTGAATACAACCGCATCAGGATGGCGAGTTAAAAAATCCTGTTCATCCGTCTGCGTGTCCGGTTGCGAAGCGTCCGGACGAGAAGG‑TTTTTTATCTGACGGATCATGTTTTGATTTTACTGACGGATCCCCGCCAGATTCTGACGGGTGAAAACCCGATTTTTTGCCAGATTTCGACGCATCAAATTTTGACGGGTCAGATTTTGA  >  NC_000913/2473236‑2473486

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑