Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,558,955	(T)5→6	coding (98/1209 nt)	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	2,558,950	1	.	T	100.0%	105.3 / NA	31	L31L (CTG→CTT)	intZ	CPZ‑55 prophage; putative phage integrase IntZ
Reads supporting (aligned to +/- strand):  ref base . (0/0);  new base T (15/16);  total (15/16)

GATCGGGGTTATCCAGTCGTTAAATCAAGGTATCCGGTTTTGAGCAAGACACCACTCACAGCAAAGGCCATAGACGCCGCACAGCCGCAGGACAAGCCCTATAAACTCACCGATTCACTGACGCCGGGGCTG‑TTTTTGCTGGTGCATCCCAACGGTTCGAAATACTGGCGATTCAGGTATTGGCTGAATAAACGAGAGTTTTTGCAGGCCATTGGAGTTTACCCGCTAATCACACTCAAAGAAGCACGCAGGCGCGCCACGGAGAG  >  NC_000913/2558819‑2559084                                                                                                                                     |                                                                                                                                       gATCGGGGTTATCCAGTCGTTAAATCAAGGTATCCGGTTTTGAGCAAGACACCACTCACAGCAAAGGCCATAGACGCCGCACAGCCGCAGGACAAGCCCTATAAACTCACCGATTCACTGACGCCGGGGCTG‑ttttttgc                                                                                                                                <  1:432726/140‑4 (MQ=255) gATCGGGGTTATCCAGTCGTTAAATCAAGGTATCCGGTTTTGAGCAAGACACCACTCACAGCAAAGGCCATAGACGCCGCACAGCCGCAGGACAAGCCCTATAAACTCACCGATTCACTGACGCCGGGGCTG‑ttttttgc                                                                                                                                <  1:532321/140‑4 (MQ=255)     ggggTTATCCAGTCGTTAAATCAAGGTATCCGGTTTTGAGCAAGACACCACTCACAGCAAAGGCCATAGACGCCGCACAGCCGCAGGACAAGCCCTATAAACTCACCGATTCACTGACGCCGGGGCTGTTTTTTGCTGGt                                                                                                                             >  1:413423/1‑140 (MQ=255)           aTCCAGTCGTTAAATCAAGGTATCCGGTTTTGAGCAAGACACCACTCACAGCAAAGGCCATAGACGCCGCACAGCCGCAGGACAAGCCCTATAAACTCACCGATTCACTGACGCCGGGGCTGTTTTTTGCTGGTGCATcc                                                                                                                       >  2:287051/1‑140 (MQ=255)                 tCGTTAAATCAAGGTATCCGGTTTTGAGCAAGACACCACTCACAGCAAAGGCCATAGACGCCGCACAGCCGCAGGACAAGCCCTATAAACTCACCGATTCACTGACGCCGGGGCTGTTTTTTGCTGGTGCATCCCaa                                                                                                                    <  2:494166/137‑1 (MQ=255)                 tCGTTAAATCAAGGTATCCGGTTTTGAGCAAGACACCACTCACAGCAAAGGCCATAGACGCCGCACAGCCGCAGGACAAGCCCTATAAACTCACCGATTCACTGACGCCGGGGCTGTTTTTTGCTGGTGCATCCCaa                                                                                                                    >  1:494166/1‑137 (MQ=255)                 tCGTTAAATCAAGGTATCCGGTTTTGAGCAAGACACCACTCACAGCAAAGGCCATAGACGCCGCACAGCCGCAGGACAAGCCCTATAAACTCACCGATTCACTGACGCCGGGGCTGTTTTTTGCTGGTGCATCCCAACgg                                                                                                                 >  2:500283/1‑140 (MQ=255)                              gTATCCGGTTTTGAGCAAGACACCACTCACAGCAAAGGCCATAGACGCCGCACAGCCGCAGGACAAGCCCTATAAACTCACCGATTCACTGACGCCGGGGCTGTTTTTTGCTGGTGCATCCCAACGGTTCGAAATACTgg                                                                                                    <  2:413423/140‑1 (MQ=255)                              gTATCCGGTTTTGAGCAAGACACCACTCACAGCAAAGGCCATAGACGCCGCACAGCCGCAGGACAAGCCCTATAAACTCACCGATTCACTGACGCCGGGGCTGTTTTTTGCTGGTGCATCCCAACGGTTCGAAATACTgg                                                                                                    <  1:269092/140‑1 (MQ=255)                                   cGGTTTTGAGCAAGACACCACTCACAGCAAAGGCCATAGACGCCGCACAGCCGCAGGACAAGCCCTATAAACTCACCGATTCACTGACGCCGGGGCTGTTTTTTGCTGGTGCATCCCAACGGTTCGAAATACTGGCGAtt                                                                                               <  2:499293/140‑1 (MQ=255)                                             cAAGACACCACTCACAGCAAAGGCCATAGACGCCGCACAGCCGCAGGACAAGCCCTATAAACTCACCGATTCACTGACGCCGGGGCTGTTTTTTGCTGGTGCATCCCAACGGTTCGAAATACTGGCGATTCAGGTATTgg                                                                                     <  1:84603/140‑1 (MQ=255)                                                     cacTCACAGCAAAGGCCATAGACGCCGCACAGCCGCAGGACAAGCCCTATAAACTCACCGATTCACTGACGCCGGGGCTGTTTTTTGCTGGTGCATCCCAACGGTTCGAAATACTGGCGATTCAGGt                                                                                          <  1:508642/127‑1 (MQ=255)                                                     cacTCACAGCAAAGGCCATAGACGCCGCACAGCCGCAGGACAAGCCCTATAAACTCACCGATTCACTGACGCCGGGGCTGTTTTTTGCTGGTGCATCCCAACGGTTCGAAATACTGGCGATTCAGGt                                                                                          >  2:508642/1‑127 (MQ=255)                                                     cacTCACAGCAAAGGCCATAGACGCCGCACAGCCGCAGGACAAGCCCTATAAACTCACCGATTCACTGACGCCGGGGCTGTTTTTTGCTGGTGCATCCCAACGGTTCGAAATACTGGCGATTCAGGTATTGGCTGAATaa                                                                             >  1:54371/1‑140 (MQ=255)                                                          acaGCAAAGGCCATAGACGCCGCACAGCCGCAGGACAAGCCCTATAAACTCACCGATTCACTGACGCCGGGGCTGTTTTTTGCTGGTGCATCCCAACGGTTCGAAATACTGGCGATTCAGGTATTGGCTGAATAAACgag                                                                        >  2:538868/1‑140 (MQ=255)                                                               aaaGGCCATAGACGCCGCACAGCCGCAGGACAAGCCCTATAAACTCACCGATTCACTGACGCCGGGGCTGTTTTTTGCTGGTGCATCCCAACGGTTCGAAATACTGGCGATTCAGGTATTGGCTGAATAAACGAGAGttt                                                                   >  2:93694/1‑140 (MQ=255)                                                                  ggCCATAGACGCCGCACAGCCGCAGGACAAGCCCTATAAACTCACCGATTCACTGACGCCGGGGCTGTTTTTTGCTGGTGCATCCCAACGGTTCGAAATACTGGCGATTCAGGTATTGGCTGAATAAACGAGAGTTTTTg                                                                <  1:500283/140‑1 (MQ=255)                                                                    ccATAGACGCCGCACAGCCGCAGGACAAGCCCTATAAACTCACCGATTCACTGACGCCGGGGCTGTTTTTTGCTGGTGCATCCCAACGGTTCGAAATACTGGCGATTCAGGTATTGGCTGAATAAACGAGAGTTTTTGCa                                                              <  2:461871/140‑1 (MQ=255)                                                                    ccATAGACGCCGCACAGCCGCAGGACAAGCCCTATAAACTCACCGATTCACTGACGCCGGGGCTGTTTTTTGCTGGTGCATCCCAACGGTTCGAAATACTGGCGATTCAGGTATTGGCTGAATAAACGAGAGTTTTTGCa                                                              <  2:54371/140‑1 (MQ=255)                                                                        aGACGCCGCACAGCCGCAGGACAAGCCCTATAAACTCACCGATTCACTGACGCCGGGGCTGTTTTTTGCTGGTGCATCCCAACGGTTCGAAATACTGGCGATTCAGGTATTGGCTGAATAAACGAGAGTTTTTGCAGGcc                                                          >  1:242262/1‑140 (MQ=255)                                                                             ccgcACAGCCGCAGGACAAGCCCTATAAACTCACCGATTCACTGACGCCGGGGCTGTTTTTTGCTGGTGCATCCCAACGGTTCGAAATACTGGCGATTCAGGTATTGGCTGAATAAACGAGAGTTTTTGCAGGCCATTgg                                                     >  2:20326/1‑140 (MQ=255)                                                                             ccgcACAGCCGCAGGACAAGCCCTATAAACTCACCGATTCACTGACGCCGGGGCTGTTTTTTGCTGGTGCATCCCAACGGTTCGAAATACTGGCGATTCAGGTATTGGCTGAATAAACGAGAGTTTTTGCAGGCCATTgg                                                     >  1:261028/1‑140 (MQ=255)                                                                                cacaGCCGCAGGACAAGCCCTATAAACTCACCGATTCACTGACGCCGGGGCTGTTTTTTGCTGGTGCATCCCAACGGTTCGAAATACTGGCGATTCAGGTATTGGCTGAATAAACGAGAGTTTTTGCAGGCCATTGGAGt                                                  >  1:88592/1‑140 (MQ=255)                                                                                        cAGGACAAGCCCTATAAACTCACCGATTCACTGACGCCGGGGCTGTTTTTTGCTGGTGCATCCCAACGGTTCGAAATACTGGCGATTCAGGTATTGGCTGAATAAACGAGAGTTTTTGCAGGCCATTGGAGTTTACCCGc                                          >  2:465289/1‑140 (MQ=255)                                                                                            aCAAGCCCTATAAACTCACCGATTCACTGACGCCGGGGCTGTTTTTTGCTGGTGCATCCCAACGGTTCGAAATACTGGCGATTCAGGTATTGGCTGAATAAACGAGAGTTTTTGCAGGCCATTGGAGTTTACCCGCTAAt                                      <  1:360508/140‑1 (MQ=255)                                                                                             cAAGCCCTATAAACTCACCGATTCACTGACGCCGGGGCTGTTTTTTGCTGGTGCATCCCAACGGTTCGAAATACTGGCGATTCAGGTATTGGCTGAATAAACGAGAGTTTTTGCAGGCCATTGGAGTTTACCCGCTAATc                                     <  1:347375/140‑1 (MQ=255)                                                                                              aaGCCCTATAAACTCACCGATTCACTGACGCCGGGGCTGTTTTTTGCTGGTGCATCCCAACGGTTCGAAATACTGGCGATTCAGGTATTGGCTGAATAAACGAGAGTTTTTGCAGGCCATTGGAGTTTACCCGCTAATca                                    <  2:88592/140‑1 (MQ=255)                                                                                                gCCCTATAAACTCACCGATTCACTGACGCCGGGGCTGTTTTTTGCTGGTGCATCCCAACGGTTCGAAATACTGGCGATTCAGGTATTGGCTGAATAAACGAGAGTTTTTGCAGGCCATTGGAGtt                                                 <  2:161473/125‑1 (MQ=255)                                                                                                gCCCTATAAACTCACCGATTCACTGACGCCGGGGCTGTTTTTTGCTGGTGCATCCCAACGGTTCGAAATACTGGCGATTCAGGTATTGGCTGAATAAACGAGAGTTTTTGCAGGCCATTGGAGtt                                                 >  1:161473/1‑125 (MQ=255)                                                                                                              ccGATTCACTGACGCCGGGGCTGTTTTTTGCTGGTGCATCCCAACGGTTCGAAATACTGGCGATTCAGGTATTGGCTGAATAAACGAGAGTTTTTGCAGGCCATTGGAGTTTACCCGCTAATCACACTCAAAGAAGCACg                    <  1:93694/140‑1 (MQ=255)                                                                                                                  ttCACTGACGCCGGGGCTGTTTTTTGCTGGTGCATCCCAACGGTTCGAAATACTGGCGATTCAGGTATTGGCTGAATAAACGAGAGTTTTTGCAGGCCATTGGAGTTTACCCGCTAATCACACTCAAAGAAGCACGCAgg                <  2:465760/140‑1 (MQ=255)                                                                                                                              ggggCTGTTTTTTGCTGGTGCATCCCAACGGTTCGAAATACTGGCGATTCAGGTATTGGCTGAATAAACGAGAGTTTTTGCAGGCCATTGGAGTTTACCCGCTAATCACACTCAAAGAAGCACGCAGGCGCGCCACGgag    <  2:261028/140‑1 (MQ=255)                                                                                                                                ggCTGTTTTTTGCTGGTGCATCCCAACGGTTCGAAATACTGGCGATTCAGGTATTGGCTGAATAAACGAGAGTTTTTGCAGGCCATTGGAGTTTACCCGCTAATCACACTCAAAGAAGCACGCAGGCGCGCCACGGagag  >  2:509845/1‑140 (MQ=255)                                                                                                                                     |                                                                                                                                       GATCGGGGTTATCCAGTCGTTAAATCAAGGTATCCGGTTTTGAGCAAGACACCACTCACAGCAAAGGCCATAGACGCCGCACAGCCGCAGGACAAGCCCTATAAACTCACCGATTCACTGACGCCGGGGCTG‑TTTTTGCTGGTGCATCCCAACGGTTCGAAATACTGGCGATTCAGGTATTGGCTGAATAAACGAGAGTTTTTGCAGGCCATTGGAGTTTACCCGCTAATCACACTCAAAGAAGCACGCAGGCGCGCCACGGAGAG  >  NC_000913/2558819‑2559084

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: ‑