Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,199,794	C→T	R338H (CGT→CAT)	intE ←	e14 prophage; putative integrase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,199,794	0	C	T	100.0%	129.6 / NA	37	R338H (CGT→CAT)	intE	e14 prophage; putative integrase
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (18/19);  total (18/19)

TGGCGTTGAGATGCTTAAAGGTTCACAACGCTACTTTGCTCCATCCTTTACCTCGATCATCATGATAACGATCGGTTTGTTGTTGTGTTTTATGACCAAGTAGTTTTTGTGTGTCTAACCCCTGTTCTTTATACAGACGTTCAGATAAAGACCTTTGCTCATGGAATGTCGCAGGTGAACCCTCTCCCCAGTCAATTCTTGCTAAATCTCTCGCTTTACTAAAATTCATCGTCAATGTATTGGCTTTAACCTGCGCTCCGCGCTCTGCT  >  NC_000913/1199657‑1199925                                                                                                                                          |                                                                                                                                    tgGCGTTGAGATGCTTAAAGGTTCACAACGCTACTTTGCTCCATCCTTTACCTCGATCATCATGATAACGATCGGTTTGTTGTTGTGTTTTATGACCAAGTAGTTTTTGTGTGTCTAACCCCTGTTCTTTATACAGATGt                                                                                                                                   >  2:462251/1‑140 (MQ=255) tgGCGTTGAGATGCTTAAAGGTTCACAACGCTACTTTGCTCCATCCTTTACCTCGATCATCATGATAACGATCGGTTTGTTGTTGTGTTTTATGACCAAGTAGTTTTTGTGTGTCTAACCCCTGTTCTTTATACAGATGt                                                                                                                                   >  1:393444/1‑140 (MQ=255)  ggCGTTGAGATGCTTAAAGGTTCACAACGCTACTTTGCTCCATCCTTTACCTCGATCATCATGATAACGATCGGTTTGTTGTTGTGTTTTATGACCAAGTAGTTTTTGTGTGTCTAACCCCTGTTCTTTATACAGATGtt                                                                                                                                  <  2:116674/140‑1 (MQ=255)           aTGCTTAAAGGTTCACAACGCTACTTTGCTCCATCCTTTACCTCGATCATCATGATAACGATCGGTTTGTTGTTGTGTTTTATGACCAAGTAGTTTTTGTGTGTCTAACCCCTGTTCTTTATACAGATGtt                                                                                                                                  <  2:592046/131‑1 (MQ=255)           aTGCTTAAAGGTTCACAACGCTACTTTGCTCCATCCTTTACCTCGATCATCATGATAACGATCGGTTTGTTGTTGTGTTTTATGACCAAGTAGTTTTTGTGTGTCTAACCCCTGTTCTTTATACAGATGtt                                                                                                                                  >  1:592046/1‑131 (MQ=255)              cTTAAAGGTTCACAACGCTACTTTGCTCCATCCTTTACCTCGATCATCATGATAACGATCGGTTTGTTGTTGTGTTTTATGACCAAGTAGTTTTTGTGTGTCTAACCCCTGTTCTTTATACAGATGTTTAGATAAAGAcc                                                                                                                      >  1:58062/1‑140 (MQ=255)              cTTAAAGGTTCACAACGCTACTTTGCTCCATCCTTTACCTCGATCATCATGATAACGATCGGTTTGTTGTTGTGTTTTATGACCAAGTAGTTTTTGTGTGTCTAACCCCTGTTCTTTATACAGATGTTCAGATAAAGAcc                                                                                                                      >  1:137028/1‑140 (MQ=255)              cTTAAAGGTTCACAACGCTACTTTGCTCCATCCTTTACCTCGATCATCATGATAACGATCGGTTTGTTGTTGTGTTTTATGACCAAGTAGTTTTTGTGTGTCTAACCCCTGTTCTTTATACAGATGTTCAGATAAAGAcc                                                                                                                      <  2:306748/140‑1 (MQ=255)                   aGGTTCACAACGCTACTTTGCTCCATCCTTTACCTCGATCATCATGATAACGATCGGTTTGTTGTTGTGTTTTATGACCAAGTAGTTTTTGTGTGTCTAACCCCTGTTCTTTATACAGATGTTCAGATAAAGACCTTTGc                                                                                                                 <  1:549430/140‑1 (MQ=255)                      ttCACAACGCTACTTTGCTCCATCCTTTACCTCGATCATCATGATAACGATCGGTTTGTTGTTGTGTTTTATGACCAAGTAGTTTTTGTGTGTCTAACCCCTGTTCTTTATACAGATGTTCAGATAAAGACCTTTGCTCa                                                                                                              <  2:393444/140‑1 (MQ=255)                        cacaACGCTACTTTGCTCCATCCTTTACCTCGATCATCATGATAACGATCGGTTTGTTGTTGTGTTTTATGACCAAGTAGTTTTTGTGTGTCTAACCCCTGTTCTTTATACAGATGTTCAGATAAAGAcc                                                                                                                      >  1:400442/1‑130 (MQ=255)                        cacaACGCTACTTTGCTCCATCCTTTACCTCGATCATCATGATAACGATCGGTTTGTTGTTGTGTTTTATGACCAAGTAGTTTTTGTGTGTCTAACCCCTGTTCTTTATACAGATGTTCAGATAAAGAcc                                                                                                                      <  2:400442/130‑1 (MQ=255)                           aaCGCTACTTTGCTCCATCCTTTACCTCGATCATCATGATAACGATCGGTTTGTTGTTGTGTTTTATGACCAAGTAGTTTTTGTGTGTCTAACCCCTGTTCTTTATACAGATGTTCAGATAAAGACCTTTGCTCATGGaa                                                                                                         <  1:462251/140‑1 (MQ=255)                                                       gATCATCATGATAACGATCGGTTTGTTGTTGTGTTTTATGACCAAGTAGTTTTTGTGTGTCTAACCCCTGTTCTTTATACAGATGTTCAGATAAAGACCTTTGCTCATGGAATGTCGCAGGTGAACCCTCTCCCCAGTCa                                                                             >  1:19306/1‑140 (MQ=255)                                                                gATAACGATCGGTTTGTTGTTGTGTTTTATGACCAAGTAGTTTTTGTGTGTCTAACCCCTGTTCTTTATACAGATGTTCAGATAAAGACCTTTGCTCATGGAATGTCGCAGGTGAACCCTCTCCCCAGTCAATTCTTGCt                                                                    <  2:137028/140‑1 (MQ=255)                                                                   aaCGATCGGTTTGTTGTTGTGTTTTATGACCAAGTAGTTTTTGTGTGTCTAACCCCTGTTCTTTATACAGATGTTCAGATAAAGACCTTTGCTCATGGAATGTCGCAGGTGAACCCTCTCCCCAGTCAATTCTTGCTaaa                                                                 >  1:69278/1‑140 (MQ=255)                                                                     cGATCGGTTTGTTGTTGTGTTTTATGACCAAGTAGTTTTTGTGTGTCTAACCCCTGTTCTTTATACAGATGTTCAGATAAAGACCTTTGCTCATGGAATGTCGCAGGTGAACCCTCTCCCCAGTCAATTCTTGCTAAAtc                                                               >  2:105030/1‑140 (MQ=255)                                                                       aTCGGTTTGTTGTTGTGTTTTATGACCAAGTAGTTTTTGTGTGTCTAACCCCTGTTCTTTATACAGATGTTCAGATAAAGACCTTTGCTCATGGAATGTCGCAGGTGAACCCTCTCCCCAGTCAATTCTTGCTAAAtctc                                                             >  2:55603/1‑140 (MQ=255)                                                                       aTCGGTTTGTTGTTGTGTTTTATGACCAAGTAGTTTTTGTGTGTCTAACCCCTGTTCTTTATACAGATGTTCAGATAAAGACCTTTGCTCATGGAATGTCGCAGGTGAACCCTCTCCCCAGTCAATTCTTGCTAAAtctc                                                             >  1:326381/1‑140 (MQ=255)                                                                          ggTTTGTTGTTGTGTTTTATGACCAAGTAGTTTTTGTGTGTCTAACCCCTGTTCTTTATACAGATGTTCAGATAAAGACCTTTGCTCATGGAATGTCGCAGGTGAACCCTCTCCCCAGTCAATTCTTGCTAAATCTCTCg                                                          >  2:536651/1‑140 (MQ=255)                                                                           gTTTGTTGTTGTGTTTTATGACCAAGTAGTTTTTGTGTGTCTAACCCCTGTTCTTTATACAGATGTTCAGATAAAGACCTTTGCTCATGGAATGTCGCAGGTGAACCCTCTCCCCAGTCAATTCTTGCTAAATCTCTCGc                                                         <  1:536651/140‑1 (MQ=255)                                                                                         tttATGACCAAGTAGTTTTTGTGTGTCTAACCCCTGTTCTTTATACAGATGTTCAGATAAAGACCTTTGCTCATGGAATGTCGCAGGTGAACCCTCTCCCCAGTCAATTCTTGCTAAATCTCTCGCTTTACTAAAATTCa                                           <  1:55603/140‑1 (MQ=255)                                                                                          ttATGACCAAGTAGTTTTTGTGTGTCTAACCCCTGTTCTTTATACAGATGTTCAGATAAAGACCTTTGCTCATGGAATGTCGCAGGTGAACCCTCTCCCCAGTCAATTCTTGCTAAATCTCTCGCTTTACTAAAATTCAt                                          <  2:87718/140‑1 (MQ=255)                                                                                             tGACCAAGTAGTTTTTGTGTGTCTAACCCCTGTTCTTTATACAGATGTTCAGATAAAGACCTTTGCTCATGGAATGTCGCAGGTGAACCCTCTCCCCAGTCAATTCTTGCTAAATCTCTCGCTTTACTAAAATTCATCGt                                       <  2:228244/140‑1 (MQ=255)                                                                                                ccAAGTAGTTTTTGTGTGTCTAACCCCTGTTCTTTATACAGATGTTCAGATAAAGACCTTTGCTCATGGAATGTCGCAGGTGAACCCTCTCCCCAGTCAATTCTTGCTAAATCTCTCGCTTTACTAAAATTCATCGTCaa                                    >  2:322721/1‑140 (MQ=255)                                                                                                  aaGTAGTTTTTGTGTGTCTAACCCCTGTTCTTTATACAGATGTTCAGATAAAGACCTTTGCTCATGGAATGTCGCAGGTGAACCCTCTCCCCAGTCAATTCTTGCTAAATCTCTCGCTTTACTAAAATTCATCGTCAATg                                  >  1:75677/1‑140 (MQ=255)                                                                                                    gtagtTTTTGTGTGTCTAACCCCTGTTCTTTATACAGATGTTCAGATAAAGACCTTTGCTCATGGAATGTCGCAGGTGAACCCTCTCCCCAGTCAATTCTTGCTAAATCTCTCGCTTTACTAAAATTCATCGTCAATGTa                                <  2:75677/140‑1 (MQ=255)                                                                                                     tagtTTTTGTGTGTCTAACCCCTGTTCTTTATACAGATGTTCAGATAAAGACCTTTGCTCATGGAATGTCGCAGGTGAACCCTCTCCCCAGTCAATTCTTGCTAAATCTCTCGCTTTACTAAAATTCATCGTCAATGTAt                               <  1:402872/140‑1 (MQ=255)                                                                                                     tagtTTTTGTGTGTCTAACCCCTGTTCTTTATACAGATGTTCAGATAAAGACCTTTGCTCATGGAATGTCGCAGGTGAACCCTCTCCCCAGTCAATTCTTGCTAAATCTCTCGCTTTACTAAAATTCATCGTCAATGTAt                               <  2:19306/140‑1 (MQ=255)                                                                                                            tgtgtgTCTAACCCCTGTTCTTTATACAGATGTTCAGATAAAGACCTTTGCTCATGGAATGTCGCAGGTGAACCCTCTCCCCAGTCAATTCTTGCTAAATCTCTCGCTTTACTAAAATTCATCGTCAATGTATTGGCttt                        <  2:236441/140‑1 (MQ=255)                                                                                                              tgtgtCTAACCCCTGTTCTTTATACAGATGTTCAGATAAAGACCTTTGCTCATGGAATGTCGCAGGTGAACCCTCTCCCCAGTCAATTCTTGCTAAATCTCTCGCTTTACTAAAATTCATCGTCAATGTATTGGCTTTaa                      >  2:478567/1‑140 (MQ=255)                                                                                                               gtgtCTAACCCCTGTTCTTTATACAGATGTTCAGATAAAGACCTTTGCTCATGGAATGTCGCAGGTGAACCCTCTCCCCAGTCAATTCTTGCTAAATCTCTCGCTTTACTAAAATTCATCGTCAATGTATTGGCTTTAAc                     <  2:69278/140‑1 (MQ=255)                                                                                                                 gtCTAACCCCTGTTCTTTATACAGATGTTCAGATAAAGACCTTTGCTCATGGAATGTCGCAGGTGAACCCTCTCCCCAGTCAATTCTTGCTAAATCTCTCGCTTTACTAAAATTCATCGTCAATGTAt                               <  2:323044/128‑1 (MQ=255)                                                                                                                 gtCTAACCCCTGTTCTTTATACAGATGTTCAGATAAAGACCTTTGCTCATGGAATGTCGCAGGTGAACCCTCTCCCCAGTCAATTCTTGCTAAATCTCTCGCTTTACTAAAATTCATCGTCAATGTAt                               >  1:323044/1‑128 (MQ=255)                                                                                                                  tCTAACCCCTGTTCTTTATACAGATGTTCAGATAAAGACCTTTGCTCATGGAATGTCGCAGGTGAACCCTCTCCCCAGTCAATTCTTGCTAAATCTCTCGCTTTACTAAAATTCATCGTCAATGTATTGGCTTTAACCTg                  >  2:77981/1‑140 (MQ=255)                                                                                                                             ttCTTTATACAGATGTTCAGATAAAGACCTTTGCTCATGGAATGTCGCAGGTGAACCCTCTCCCCAGTCAATTCTTGCTAAATCTCTCGCTTTACTAAAATTCATCGTCAATGTATTGGCTTTAACCTGCGCTCCGCGct       <  1:77981/140‑1 (MQ=255)                                                                                                                                  tataCAGATGTTCAGATAAAGACCTTTGCTCATGGAATGTCGCAGGTGAACCCTCTCCCCAGTCAATTCTTGCTAAATCTCTCGCTTTACTAAAATTCATCGTCAATGTATTGGCTTTAACCTGCGCTCCGCGCTCTGCt  >  1:83044/1‑140 (MQ=255)                                                                                                                                          |                                                                                                                                    TGGCGTTGAGATGCTTAAAGGTTCACAACGCTACTTTGCTCCATCCTTTACCTCGATCATCATGATAACGATCGGTTTGTTGTTGTGTTTTATGACCAAGTAGTTTTTGTGTGTCTAACCCCTGTTCTTTATACAGACGTTCAGATAAAGACCTTTGCTCATGGAATGTCGCAGGTGAACCCTCTCCCCAGTCAATTCTTGCTAAATCTCTCGCTTTACTAAAATTCATCGTCAATGTATTGGCTTTAACCTGCGCTCCGCGCTCTGCT  >  NC_000913/1199657‑1199925

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: ‑