Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	296,077	A→G	T340T (ACT→ACC)	intF ←	CP4‑6 prophage; putative phage integrase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	296,077	0	A	G	100.0%	154.5 / NA	43	T340T (ACT→ACC)	intF	CP4‑6 prophage; putative phage integrase
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (18/25);  total (18/25)

TAATGCTCTGTTGTGCGCTGAACGCGGCTCAATAATTTTGCCACTTTTACTGTTACTTCTGAAAACCCAACCCTCCTTATTTACGTCAGAATTTGGGGATTGCGCTAGTACATTTAACAATTCAGAAACATAAGGAGTGAGAGGGATGATACGTTCACCTTCGATCTTGTCTTTAATTCGCATGCTTGACCATTTGAAATCTACGTCTGACCAGCGAAGCGACGCAATTTCTTCACGCCGAGCACCAGTGAGCAAAAGTACTTGGAGATAG  >  NC_000913/295942‑296212                                                                                                                                        |                                                                                                                                        tAATGCTCTGTTGTGCGCTGAACGCGGCTCAATAATTTTGCCACTTTTACTGTTACTTCTGAAAACCCAACCCTCCTTATTTACGTCAGAATTTGGGGATTGCGCTAGTACATTTAACAATTCAGAAACATAAGGGGTga                                                                                                                                     <  2:314402/140‑1 (MQ=255)   aTGCTCTGTTGTGCGCTGAACGCGGCTCAATAATTTTGCCACTTTTACTGTTACTTCTGAAAACCCAACCCTCCTTATTTACGTCAGAATTTGGGGATTGCGCTAGTACATTTAACAATTCAGAAACATAAGGGGTgaga                                                                                                                                   <  2:129951/140‑1 (MQ=255)      ctctGTTGTGCGCTGAACGCGGCTCAATAATTTTGCCACTTTTACTGTTACTTCTGAAAACCCAACCCTCCTTATTTACGTCAGAATTTGGGGATTGCGCTAGTACATTTAACAATTCAGAAACATAAGGGGTGAGAggg                                                                                                                                <  2:102562/140‑1 (MQ=255)        ctGTTGTGCGCTGAACGCGGCTCAATAATTTTGCCACTTTTACTGTTACTTCTGAAAACCCAACCCTCCTTATTTACGTCAGAATTTGGGGATTGCGCTAGTACATTTAACAATTCAGAAACATAAGGGGTGAGAGGgat                                                                                                                              <  2:752500/140‑1 (MQ=255)         tgttgtGCGCTGAACGCGGCTCAATAATTTTGCCACTTTTACTGTTACTTCTGAAAACCCAACCCTCCTTATTTACGTCAGAATTTGGGGATTGCGCTAGTACATTTAACAATTCAGAAACATAAGGGGTgag                                                                                                                                    <  2:623667/133‑1 (MQ=255)         tgttgtGCGCTGAACGCGGCTCAATAATTTTGCCACTTTTACTGTTACTTCTGAAAACCCAACCCTCCTTATTTACGTCAGAATTTGGGGATTGCGCTAGTACATTTAACAATTCAGAAACATAAGGGGTgag                                                                                                                                    >  1:623667/1‑133 (MQ=255)         tgttgtGCGCTGAACGCGGCTCAATAATTTTGCCACTTTTACTGTTACTTCTGAAAACCCAACCCTCCTTATTTACGTCAGAATTTGGGGATTGCGCTAGTACATTTAACAATTCAGAAACATAAGGGGTGAGAGGgatg                                                                                                                             <  2:517452/140‑1 (MQ=255)           ttgtGCGCTGAACGCGGCTCAATAATTTTGCCACTTTTACTGTTACTTCTGAAAACCCAACCCTCCTTATTTACGTCAGAATTTGGGGATTGCGCTAGTACATTTAACAATTCAGAAACATAAGGGGTGAGAGGgatgat                                                                                                                           <  2:603619/140‑1 (MQ=255)           ttgtGCGCTGAACGCGGCTCAATAATTTTGCCACTTTTACTGTTACTTCTGAAAACCCAACCCTCCTTATTTACGTCAGAATTTGGGGATTGCGCTAGTACATTTAACAATTCAGAAACATAAGGGGTGAGAGGgatgat                                                                                                                           <  2:389294/140‑1 (MQ=255)           ttgtGCGCTGAACGCGGCTCAATAATTTTGCCACTTTTACTGTTACTTCTGAAAACCCAACCCTCCTTATTTACGTCAGAATTTGGGGATTGCGCTAGTACATTTAACAATTCAGAAACATAAGGGGTGAGAGGgatgat                                                                                                                           <  1:931487/140‑1 (MQ=255)                cgcTGAACGCGGCTCAATAATTTTGCCACTTTTACTGTTACTTCTGAAAACCCAACCCTCCTTATTTACGTCAGAATTTGGGGATTGCGCTAGTACATTTAACAATTCAGAAACATAAGGGGTGAGAGGGATGATACGtt                                                                                                                      <  1:136485/140‑1 (MQ=255)                     aaCGCGGCTCAATAATTTTGCCACTTTTACTGTTACTTCTGAAAACCCAACCCTCCTTATTTACGTCAGAATTTGGGGATTGCGCTAGTACATTTAACAATTCAGAAACATAAGGGGTGAGAGGGATGATACGTTCACCt                                                                                                                 >  2:720739/1‑140 (MQ=255)                             tCAATAATTTTGCCACTTTTACTGTTACTTCTGAAAACCCAACCCTCCTTATTTACGTCAGAATTTGGGGATTGCGCTAGTACATTTAACAATTCAGAAACATAAGGGGTGAGAGGGATGATACGTTCACCTTCGATCtt                                                                                                         <  2:258650/140‑1 (MQ=255)                                ataatTTTGCCACTTTTACTGTTACTTCTGAAAACCCAACCCTCCTTATTTACGTCAGAATTTGGGGATTGCGCTAGTACATTTAACAATTCAGAAACATAAGGGGTGAGAGGGATGATACGTTCACCTTCGATCTTGTc                                                                                                      <  1:270542/140‑1 (MQ=255)                                ataatTTTGCCACTTTTACTGTTACTTCTGAAAACCCAACCCTCCTTATTTACGTCAGAATTTGGGGATTGCGCTAGTACATTTAACAATTCAGAAACATAAGGGGTGAGAGGGATGATACGTTCACCTTCGATCTTGTc                                                                                                      <  1:291227/140‑1 (MQ=255)                                      ttGCCACTTTTACTGTTACTTCTGAAAACCCAACCCTCCTTATTTACGTCAGAATTTGGGGATTGCGCTAGTACATTTTACAATTCAGAAACATAAGGGGTGAGAGGGATGATACGTTCACCTTCGATCTTGTCTTTAAt                                                                                                >  2:809307/1‑140 (MQ=255)                                         ccACTTTTACTGTTACTTCTGAAAACCCAACCCTCCTTATTTACGTCAGAATTTGGGGATTGCGCTAGTACATTTTACAATTCAGAAACATAAGGGGTGAGAGGGATGATACGTTCACCTTCGATCTTGTCTTTAATTCg                                                                                             <  1:809307/140‑1 (MQ=255)                                         ccACTTTTACTGTTACTTCTGAAAACCCAACCCTCCTTATTTACGTCAGAATTTGGGGATTGCGCTAGTACATTTAACAATTCAGAAACATAAGGGGTGAGAGGGATGATACGTTCACCTTCGATCTTGTCTTTAATTCg                                                                                             <  2:130028/140‑1 (MQ=255)                                                                            ctTATTTACGTCAGAATTTGGGGATTGCGCTAGTACATTTAACAATTCAGAAACATAAGGGGTGAGAGGGATGATACGTTCACCTTCGATCTTGTCTTTAATTCGCATGCTTGACCATTTGAAATCTACGTCTg                                                                <  1:808962/134‑1 (MQ=255)                                                                            ctTATTTACGTCAGAATTTGGGGATTGCGCTAGTACATTTAACAATTCAGAAACATAAGGGGTGAGAGGGATGATACGTTCACCTTCGATCTTGTCTTTAATTCGCATGCTTGACCATTTGAAATCTACGTCTg                                                                >  2:808962/1‑134 (MQ=255)                                                                            ctTATTTACGTCAGAATTTGGGGATTGCGCTAGTACATTTAACAATTCAGAAACATAAGGGGTGAGAGGGATGATACGTTCACCTTCGATCTTGTCTTTAATTCGCATGCTTGACCATTTGAAATCTACGTCTGACCagc                                                          >  1:73111/1‑140 (MQ=255)                                                                            ctTATTTACGTCAGAATTTGGGGATTGCGCTAGTACATTTAACAATTCAGAAACATAAGGGGTGAGAGGGATGATACGTTCACCTTCGATCTTGTCTTTAATTCGCATGCTTGACCATTTGAAATCTACGTCTGACCagc                                                          >  2:106451/1‑140 (MQ=255)                                                                                tttACGTCAGAATTTGGGGATTGCGCTAGTACATTTAACAATTCAGAAACATAAGGGGTGAGAGGGATGATACGTTCACCTTCGATCTTGTCTTTAATTCGCATGCTTGACCATTTGAAATCTACGTCTGACCagcgaag                                                      >  1:854901/1‑140 (MQ=255)                                                                                     gTCAGAATTTGGGGATTGCGCTAGTACATTTAACAATTCAGAAACATAAGGGGTGAGAGGGATGATACGTTCACCTTCGATCTTGTCTTTAATTCGCATGCTTGACCATTTGAAATCTACGTCTGACCAGCGAAGCGACg                                                 >  1:416955/1‑140 (MQ=255)                                                                                      tCAGAATTTGGGGATTGCGCTAGTACATTTAACAATTCAGAAACATAAGGGGTGAGAGGGATGATACGTTCACCTTCGATCTTGTCTTTAATTCGCATGCTTGACCATTTGAAATCTACGTCTGACCAGCGAAGCGACGc                                                >  1:393220/1‑140 (MQ=255)                                                                                                    ttGCGCTAGTACATTTAACAATTCAGAAACATAAGGGGTGAGAGGGATGATACGTTCACCTTCGATCTTGTCTTTAATTCGCATGCTTGACCATTTGAAATCTACGTCTGACCAGCGAAGCGACGCAATTTCTTCACGcc                                  <  2:73111/140‑1 (MQ=255)                                                                                                      gcgcTAGTACATTTAACAATTCAGAAACATAAGGGGTGAGAGGGATGATACGTTCACCTTCGATCTTGTCTTTAATTCGCATGCTTGACCATTTGAAATCTACGTCTGACCAGCGAAGCGACGCAAt                                             <  1:713591/127‑1 (MQ=255)                                                                                                      gcgcTAGTACATTTAACAATTCAGAAACATAAGGGGTGAGAGGGATGATACGTTCACCTTCGATCTTGTCTTTAATTCGCATGCTTGACCATTTGAAATCTACGTCTGACCAGCGAAGCGACGCAAt                                             >  2:713591/1‑127 (MQ=255)                                                                                                       cgcTAGTACATTTAACAATTCAGAAACATAAGGGGTGAGAGGGATGATACGTTCACCTTCGATCTTGTCTTTAATTCGCATGCTTGACCATTTGAAATCTACGTCTGACCAGCGAAGCGACGCAATTTCTTCACGCCGAg                               >  1:57436/1‑140 (MQ=255)                                                                                                       cgcTAGTACATTTAACAATTCAGAAACATAAGGGGTGAGAGGGATGATACGTTCACCTTCGATCTTGTCTTTAATTCGCATGCTTGACCATTTGAAATCTACGTCTGACCAGCGAAGCGACGCAATTTCTTCACGCCGAg                               >  2:618817/1‑140 (MQ=255)                                                                                                               cATTTAACAATTCAGAAACATAAGGGGTGAGAGGGATGATACGTTCACCTTCGATCTTGTCTTTAATTCGCATGCTTGACCATTTGAAATCTACGTCTGACCAGCGAAGCGACGCAATTTCTTCACGCCGAACACCa                          >  2:880112/1‑137 (MQ=255)                                                                                                               cATTTAACAATTCAGAAACATAAGGGGTGAGAGGGATGATACGTTCACCTTCGATCTTGTCTTTAATTCGCATGCTTGACCATTTGAAATCTACGTCTGACCAGCGAAGCGACGCAATTTCTTCACGCCGAACACCa                          <  1:880112/137‑1 (MQ=255)                                                                                                                  ttAACAATTCAGAAACATAAGGGGTGAGAGGGATGATACGTTCACCTTCGATCTTGTCTTTAATTCGCATGCTTGACCATTTGAAATCTACGTCTGACCAGCGAAGCGACGCAATTTCTTCACGCCGAGCACCAGTGAGc                    >  2:22161/1‑140 (MQ=255)                                                                                                                      cAATTCAGAAACATAAGGGGTGAGAGGGATGATACGTTCACCTTCGATCTTGTCTTTAATTCGCATGCTTGACCATTTGAAATCTACGTCTGACCAGCGAAGCGACGCAATTTCTTCACGCCGAGCACCAGTGAGCaaaa                >  1:751512/1‑140 (MQ=255)                                                                                                                       aaTTCAGAAACATAAGGGGTGAGAGGGATGATACGTTCACCTTCGATCTTGTCTTTAATTCGCATGCTTGACCATTTGAAATCTACGTCTGACCAGCGAAGCGACGCAATTTCTTCACGCCGAGCACCAGTGAGCAAAAg               <  2:416955/140‑1 (MQ=255)                                                                                                                       aaTTCAGAAACATAAGGGGTGAGAGGGATGATACGTTCACCTTCGATCTTGTCTTTAATTCGCATGCTTGACCATTTGAAATCTACGTCTGACCAGCGAAGCGACGCAATTTCTTCACGCCGAGCACCAGTGAGCAAAAg               <  2:751512/140‑1 (MQ=255)                                                                                                                         ttCAGAAACATAAGGGGTGAGAGGGATGATACGTTCACCTTCGATCTTGTCTTTAATTCGCATGCTTGACCATTTGAAATCTACGTCTGACCAGCGAAGCGACGCAATTTCTTCACGCCGAGCACCAGt                        >  1:702986/1‑129 (MQ=255)                                                                                                                         ttCAGAAACATAAGGGGTGAGAGGGATGATACGTTCACCTTCGATCTTGTCTTTAATTCGCATGCTTGACCATTTGAAATCTACGTCTGACCAGCGAAGCGACGCAATTTCTTCACGCCGAGCACCAGt                        <  2:702986/129‑1 (MQ=255)                                                                                                                           cAGAAACATAAGGGGTGAGAGGGATGATACGTTCACCTTCGATCTTGTCTTTAATTCGCATGCTTGACCATTTGAAATCTACGTCTGACCAGCGAAGCGACGCAATTTCTTCACGCCGAGCACCAGTGAGCAAAAGTACt           <  1:618817/140‑1 (MQ=255)                                                                                                                           cAGAAACATAAGGGGTGAGAGGGATGATACGTTCACCTTCGATCTTGTCTTTAATTCGCATGCTTGACCATTTGAAATCTACGTCTGACCAGCGAAGCGACGCAATTTCTTCACGCCGAGCACCAGTGAGCAAAAGTACt           <  2:57436/140‑1 (MQ=255)                                                                                                                                 cATAAGGGGTGAGAGGGATGATACGTTCACCTTCGATCTTGTCTTTAATTCGCATGCTTGACCATTTGAAATCTACGTCTGACCAGCGAAGCGACGCAATTTCTTCACGCCGAGCACCAGTGAGCAAAAGTACTTGgaga     <  1:106451/140‑1 (MQ=255)                                                                                                                                   tAAGGGGTGAGAGGGATGATACGTTCACCTTCGATCTTGTCTTTAATTCGCATGCTTGACCATTTGAAATCTACGTCTGACCAGCGAAGCGACGCAATTTCTTCACGCCGAGCACCAGTGAGCAAAAGTACTTGGAGATa   >  1:706753/1‑140 (MQ=255)                                                                                                                                    aaGGGGTGAGAGGGATGATACGTTCACCTTCGATCTTGTCTTTAATTCGCATGCTTGACCATTTGAAATCTACGTCTGACCAGCGAAGCGACGCAATTTCTTCACGCCGAGCACCAGTGAGCAAAAGTACTTGGAGATAg  >  2:278684/1‑140 (MQ=255)                                                                                                                                        |                                                                                                                                        TAATGCTCTGTTGTGCGCTGAACGCGGCTCAATAATTTTGCCACTTTTACTGTTACTTCTGAAAACCCAACCCTCCTTATTTACGTCAGAATTTGGGGATTGCGCTAGTACATTTAACAATTCAGAAACATAAGGAGTGAGAGGGATGATACGTTCACCTTCGATCTTGTCTTTAATTCGCATGCTTGACCATTTGAAATCTACGTCTGACCAGCGAAGCGACGCAATTTCTTCACGCCGAGCACCAGTGAGCAAAAGTACTTGGAGATAG  >  NC_000913/295942‑296212

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: ‑