Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,559,952	G→A	R365R (AGG→AGA)	intZ →	CPZ‑55 prophage; putative phage integrase IntZ

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,559,952	0	G	A	100.0%	82.5 / NA	25	R365R (AGG→AGA)	intZ	CPZ‑55 prophage; putative phage integrase IntZ
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (11/14);  total (11/14)

GTATCGGGTACAAGTCGATAGCCACAGGCCACGGCTGGCGCACAACGTTCAGCACCGCACTTAACGAATCAGGCAGATACTCGCCGGATTGGATTGAGATCCAACTAGCCCACGTCCCGAAGGGAATAAGGGGCGTTTATAACCAGGCTGCCTACCTGAAGCAACGGCGAGCAATGATGCAGGATTACGCCGACGCTATTGATTCAATATTGGCAGGTAACGGCAATCCTCTAGAACCGGAATGAATAATTAAGCGGC  >  NC_000913/2559822‑2560079                                                                                                                                   |                                                                                                                                gcaTCGGGTACAAGTCGATAGCCGTATGACACGGCTGGCGCTCAACGTTCAGCACCGCACTTAACGAATCAGGCAGATACTCGCCGGATTGGATTGAGATCCAACTAGCCCACGTCCCGAAGGGAATAAgagg                                                                                                                               <  2:296055/131‑1 (MQ=255)         tACAAGTCGATAGCCACAGGCCACGGCTGGCGCACAACGTTCAGCACCGCACTTAACGAATCAGGCAGATACTCGCCGGATTGGATTGAGATCCAACTAGCCCACGTCCCGAAGGGAATAAGAGGCGTTtata                                                                                                                       >  1:365807/1‑133 (MQ=255)         tACAAGTCGATAGCCACAGGCCACGGCTGGCGCACAACGTTCAGCACCGCACTTAACGAATCAGGCAGATACTCGCCGGATTGGATTGAGATCCAACTAGCCCACGTCCCGAAGGGAATAAGAGGCGTTtata                                                                                                                       <  2:94110/133‑1 (MQ=255)                            gCCACGGCTGGCGCACAACGTTCAGCACCGCACTTAACGAATCAGGCAGATACTCGCCGGATTGGATTGAGATCCAACTAGCCCACGTCCCGAAGGGAATAAGAGGCGTTTATAACCAGGCTGCCTACCTGaa                                                                                                    >  1:89174/1‑133 (MQ=255)                              cACGGCTGGCGCACAACGTTCAGCACCGCACTTAACGAATCAGGCAGATACTCGCCGGATTGGATTGAGATCCAACTAGCCCACGTCCCGAAGGGAATAAGAGGCGTTTATAACCAGGCTGCCTACCTGAAGc                                                                                                  <  2:457140/133‑1 (MQ=255)                                  gCTGGCGCACAACGTTCAGCACCGCACTTAACGAATCAGGCAGATACTCGCCGGATTGGATTGAGATCCAACTAGCCCACGTCCCGAAGGGAATAAGAGGCGTTTATAACCAGGCTGCCTACCTGAAGCAACg                                                                                              <  2:315991/133‑1 (MQ=255)                                      gcgcACAACGTTCAGCACCGCACTTAACGAATCAGGCAGATACTCGCCGGATTGGATTGAGATCCAACTAGCCCACGTCCCGAAGGGAATAAGAGGCGTTTATAACCAGGCTGCCTACCTGAAGCAACGGCGa                                                                                          >  2:77653/1‑133 (MQ=255)                                      gcgcACAACGTTCAGCACCGCACTTAACGAATCAGGCAGATACTCGCCGGATTGGATTGAGATCCAACTAGCCCACGTCCCGAAGGGAATAAGAGGCGTTTATAACCAGGCTGCCTACCTGAAGCAACGGCGa                                                                                          >  2:409637/1‑133 (MQ=255)                                          acaACGTTCAGCACCGCACTTAACGAATCAGGCAGATACTCGCCGGATTGGATTGAGATCCAACTAGCCCACGTCCCGAAGGGAATAAGAGGCGTTTATAACCAGGCTGCCTACCTGAAGCAACGGCGAGCaa                                                                                      <  2:99269/133‑1 (MQ=255)                                          acaACGTTCAGCACCGCACTTAACGAATCAGGCAGATACTCGCCGGATTGGATTGAGATCCAACTAGCCCACGTCCCGAAGGGAATAAGAGGCGTTTATAACCAGGCTGCCTACCTGAAGCAACGGCGAGCaa                                                                                      <  1:152625/133‑1 (MQ=255)                                           caACGTTCAGCACCGCACTTAACGAATCAGGCAGATACTCGCCGGATTGGATTGAGATCCAACTAGCCCACGTCCCGAAGGGAATAAGAGGCGTTTATAACCAGGCTGCCTACCTGAAGCAACGGCGAGCAat                                                                                     <  2:587647/133‑1 (MQ=255)                                                               aaCGAATCAGGCAGATACTCGCCGGATTGGATTGAGATCCAACTAGCCCACGTCCCGAAGGGAATAAGAGGCGTTTATAACCAGGCTGCCTACCTGAAGCAACGGCGAGCAATGATGCAGGATTACGCCGACg                                                                 >  1:425801/1‑133 (MQ=255)                                                                      cAGGCAGATACTCGCCGGATTGGATTGAGATCCAACTAGCCCACGTCCCGAAGGGAATAAGAGGCGTTTATAACCAGGCTGCCTACCTGAAGCAACGGCGAGCAATGATGCAGGATTACGCCGACGCTATTGa                                                          <  2:370009/133‑1 (MQ=255)                                                                                   gCCGGATTGGATTGAGATCCAACTAGCCCACGTCCCGAAGGGAATAAGAGGCGTTTATAACCAGGCTGCCTACCTGAAGCAACGGCGAGCAATGATGCAGGAATACGCCGGCGCGATCGATTCAGTATTGGCa                                             >  1:292799/1‑133 (MQ=255)                                                                                       gattggattgAGATCCAACTAGCCCACGTCCCGAAGGGAATAAGAGGCGTTTATAACCAGGCTGCCTACCTGAAGCAACGGCGAGCAATGATGCAGGATTACGCCGACGCTATTGATTCAATATTGGCAGGTa                                         >  1:476620/1‑133 (MQ=255)                                                                                           ggattgAGATCCAACTAGCCCACGTCCCGAAGGGAATAAGAGGCGTTTATAACCAGGCTGCCTACCTGAAGCAACGGCGAGCAATGATGCAGGATTACGCCGACGCTATTGATTCAATATTGGCAGGTAACgg                                     <  1:535339/133‑1 (MQ=255)                                                                                              ttgAGATCCGCCTAGTCCACGTCCAGCAAGGAATAAGAGGCGTTTATAACCAGGCTGCCTACCTGAAGCAACGGCGAGCAATGATGCAGGATTACGCCGACGCTATTGATTCAATATTGGCAGGTAACGGCaa                                  <  2:292799/133‑1 (MQ=255)                                                                                              ttgAGATCCAACTAGCCCACGTCCCGAAGGGAATAAGAGGCGTTTATAACCAGGCTGCCTACCTGAAGCAACGGCGAGCAATGATGCATGATTACGCCGACGCTATTGATTCAATATTGGCAGGTAACGGCaa                                  <  2:63546/133‑1 (MQ=255)                                                                                               tgAGATCCAACTAGCCCACGTCCCGAAGGGAATAAGAGGCGTTTATAACCAGGCTGCCTACCTGAAGCAACGGCGAGCAATGATGCAGGATTACGCCGACGCTATTGATTCAATATTGGCAGGTAACGGCAAt                                 <  2:125490/133‑1 (MQ=255)                                                                                                     ccAACTAGCCCACGTCCCGAAGGGAATAAGAGGCGTTTATAACCAGGCTGCCTACCTGAAGCAACGGCGAGCAATGATGCAGGATTACGCCGACGCTATTGATTCAATATTGGCAGGTAACGGCAATCCTCTa                           <  2:455786/133‑1 (MQ=255)                                                                                                             cccACGTCCCGAAGGGAATAAGAGGCGTTTATAACCAGGCTGCCTACCTGAAGCAACGGCGAGCAATGATGCAGGATTACGCCGACGCTATTGATTCAATATTGGCAGGTAACGGCAATCCTCTAGAACCGga                   >  2:496076/1‑133 (MQ=255)                                                                                                             cccACGTCCCGAAGGGAATAAGAGGCGTTTATAACCAGGCTGCCTACCTGAAGCAACGGCGAGCAATGATGCAGGATTACGCCGACGCTATTGATTCAATATTGGCAGGTAACGGCAATCCTCTAGAACCGga                   <  2:89174/133‑1 (MQ=255)                                                                                                               cACGTCCCGAAGGGAATAAGAGGCGTTTATAACCAGGCTGCCTACCTGAAGCAACGGCGAGCAATGATGCAGGATTACGCCGGCGCTATTGATTCAATATTGGCAGGTAACGGCAATCCTCTAGAACCGgaat                 <  1:77653/133‑1 (MQ=255)                                                                                                                 cGTCCCGAAGGGAATAAGAGGCGTTTATAACCAGGCTGCCTACCTGAAGCAACGGCGAGCAATGATGCAGGATTACGCCGACGCTATTGATTCAATATTGGCAGGTAACGGCAATCCTCTAGAACCGgaatga               >  1:449494/1‑133 (MQ=255)                                                                                                                 cGTCCCGAAGGGAATAAGAGGCGTTTATAACCAGGCTGCCTACCTGAAGCAACGGCGAGCAATGATGCAGGATTACGCCGACGCTATTGATTCAATATTGGCAGGTAACGGCAATCCTCTAGAACCGgaatga               >  1:387818/1‑133 (MQ=255)                                                                                                                              aTAAGAGGCGTTTATAACCAGGCTGCCTACCTGAAGCAACGGCGAGCAATGATGCAGGATTACGCCGACGCTATTGATTCAATATTGGCAGGTAACGGCAATCCTCTAGAACCGGAATGAATAATTAAGCGGc  >  2:527324/1‑133 (MQ=255)                                                                                                                                   |                                                                                                                                GTATCGGGTACAAGTCGATAGCCACAGGCCACGGCTGGCGCACAACGTTCAGCACCGCACTTAACGAATCAGGCAGATACTCGCCGGATTGGATTGAGATCCAACTAGCCCACGTCCCGAAGGGAATAAGGGGCGTTTATAACCAGGCTGCCTACCTGAAGCAACGGCGAGCAATGATGCAGGATTACGCCGACGCTATTGATTCAATATTGGCAGGTAACGGCAATCCTCTAGAACCGGAATGAATAATTAAGCGGC  >  NC_000913/2559822‑2560079

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑