Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,433,681	A→G	intergenic (‑7/+310)	pinR ← / ← ynaE	Rac prophage; putative site‑specific recombinase/Rac prophage; uncharacterized protein YnaE

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,433,681	0	A	G	100.0%	44.3 / NA	21	intergenic (‑7/+310)	pinR/ynaE	Rac prophage; putative site‑specific recombinase/Rac prophage; uncharacterized protein YnaE
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (9/12);  total (9/12)

CTTCGATTATTTGCTGAGGTTTGATTTTAAAACCTGCACTTTCGATTTCCCGGCGTTGATTTTCGGTGGTCTGATCCAGCGTTGATATCCGACAGTAAGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCTCAGAAAATAATTATGATTATTTTTGTGCATATTTGTATGTACACGTTCGAAAATAAACGAATGCGTATG  >  NC_000913/1433560‑1433787                                                                                                                          |                                                                                                           cttcGATTATTTGCTGAGGTTTGATTTTAAAACCTGCACTTTCGATTTCCCGGCGTTGATTTTCGGTGGTCTGATCCAGCGTTGATATCCGACAGTAAGCAAAAATTCGAGACATAGTGAGGCTCTATACGaa                                                                                                 >  2:469958/1‑133 (MQ=17)       ttattTGCTGAGGTTTGATTTTAAAACCTGCACTTTCGATTTCCCGGCGTTGATTTTCGGTGGTCTGATCCAGCGTTGATATCCGACAGTAAGCAAAAATTCGAGACATAGTGAGGCTCTATACGAAATTGgt                                                                                           >  2:351862/1‑133 (MQ=17)         attTGCTGATGTTTGATTTTAAAACCAGTACTTTCGATTTCCCGGCGTTGATTTTCGGTGGTCTGATCCAGCGTTGATATCCGACAGTAAGCAAAAATTCGAGACATAGTGAGGCTCTATACGAAATTGgtgt                                                                                         <  2:225859/133‑1 (MQ=255)          tttGCTGAGGATTGATTTTAAATCCTGACCTTCTGATTTGCCGACGTTGATTTTGGGTGGTCTGATCCAGCGTTGATATCCGACAGTAAGCAAAAATTCGAGACATAGTGAGGCTCTATATGAAATTGGTGtt                                                                                        <  2:136352/133‑1 (MQ=11)            tGCTGAGGTTTGATTTTAAAACCTGCACTTTCGATTTCCCGGCGTTGATTTTCGGTGGTCTGATCCAGCGTTGATATCCGACAGTAAGCAAAAATTCGAGACATAGTGAGGCTCTATACGAAATTGGTGTtca                                                                                      <  1:396601/133‑1 (MQ=18)               tGAGGTTTCATTTTACAAACTGCACTTTCGCTTTCCCGGCGTTGATTTTCGGTGGTCTGATCCAGCGTTGATATCCGACAGTAAGCAAAAATTCGAGACATAGTGAGGCTCTATACGAAATTGGTGTtcatat                                                                                   <  1:154339/133‑1 (MQ=11)                        aTTTTAAAACCTGCACTTTCGATTTCCCGGCGTTGATTTTCGGTGGTCTGATCCAGCGTTGATATCCGACAGTAAGCAAAAATTCGAGACATAGTGAGGCTCTATACGAAATTGGTGTTCATATCATAATGCa                                                                          >  2:453050/1‑133 (MQ=17)                             aaaaCCTGCACTTTCGATTTCCCGGCGTTGATTTTCGGTGGTCTGATCCAGCGTTGATATCCGACAGTAAGCAAAAATTCGAGACATAGTGAGGCTCTATACGAAATTGGTGTTCATATCATAATGCATCTCa                                                                     <  1:351862/133‑1 (MQ=17)                              aaaCCTGCACTTTCGATTTCCCGGCGTTGATTTTCGGTGGTCTGATCCAGCGTTGATATCCGACAGTAAGCAAAAATTCGAGACATAGTGAGGCTCTATACGAAATTGGTGTTCATATCATAATGCATCTCAg                                                                    >  2:487562/1‑133 (MQ=17)                                         ttCGATTTCCCGGCGTTGATTTTCGGTGGTCTGATCCAGCGTTGATATCCGACAGTAAGCAAAAATTCGAGACATAGTGAGGCTCTATACGAAATTGGTGTTCATATCATAATGCATCTCAGAAAATAATTAt                                                         <  2:31474/133‑1 (MQ=17)                                            gATTTCCCGGCGTTGATTTTCGGTGGTCTGATCCAGCGTTGATATCCGACAGTAAGCAAAAATTCGAGACATAGTGAGGCTCTATACGAAATTGGTGTTCATATCATAATGCATCTCAGAAAATAATTATGat                                                      <  1:487562/133‑1 (MQ=17)                                                   cGGCGTTGATTTTCGGTGGTCTGAGCCAGCGTAGATATCCGTCAGTAAGCAAAAATTCGAGACATAGTGAGGCTCTATACGAAATTGGTGTTCATATCATAATGCATCTCAGAAAATAATTATGATTAttttt                                               <  2:222751/133‑1 (MQ=255)                                                      cGTTGATTTTCGGTGGTCTGATCCAGCGTTGATATCCGACAGTAAGCAAAAATTCGAGACATAGTGAGGCTCTATACGAAATTGGTGTTCATATCATAATGCATCTCAGAAAATAATTATGATTATTTTtgtg                                            <  1:453050/133‑1 (MQ=17)                                                                                cGTTGATATCCGACAGTAAGCAAAAATTCGAGACATAGTGAGGCTCTATACGAAATTGGTGTTCATATCATAATGCATCTCAGAAAATAATTATGATTATTTTTGTGCATATTTGTATGTACACGTTCGaaaa                  >  1:260483/1‑133 (MQ=18)                                                                                cGTTGATATCCGACAGTAAGCAAAAATTCGAGACATAGTGAGGCTCTATACGAAATTGGTGTTCATATCATAATGCATCTCAGAAAATAATTATGATTATTTTTGTGCATATTTGTATGTACACGTTCGaaaa                  >  2:8575/1‑133 (MQ=18)                                                                                    gATATCCGACAGTAAGCAAAAATTCGAGACATAGTGAGGCTCTATACGAAATTGGTGTTCATATCATAATGCATCTCAGAAAATAATTATGATTATTTTTGTGCATATTTGTATGTACACGTTCGAGAATaaa              >  1:438054/1‑133 (MQ=16)                                                                                     atatCCGACAGTAAGCAAAAATTCGAGACATAGTGAGGCTCTATACGAAATTGGGGTTCATATCATAATGCATCTCAGAAAATAATTATGATTATTTTTGTGCATATTTGTATGTACACGTTCGAAAATAAAc             >  1:11918/1‑133 (MQ=17)                                                                                      tatCCGACAGTAAGCAAAAATTCGAGACATAGTGAGGCTCTATACGAAATTGGTGTTCATATCATAATGCATCTCAGAAAATAATTATGATTATTTTTGTGCATATTTGTATGTACACGTTCGAGAATAAACg            <  2:438054/133‑1 (MQ=17)                                                                                       atCCGACAGTAAGCAAAAATTCGAGACATAGTGAGGCTCTATACGAAATTGGTGTTCATATCATAATGCATCTCAGAAAATAATTATGATTATTTTTGTGCATATTTGTATGTACACGTTCGAAAATAAACGa           <  2:50983/133‑1 (MQ=17)                                                                                         ccGACAGTAAGCAAAGATGCGAGACATAGTGAGGCTCTATACGAAATTGGTGTTCATATCATAATGCATCTCAGAAAATAATTATGATTATTTTTGTGCATATTTGTATGTACACGTTCGAAAATAAACGAAt         <  1:198411/133‑1 (MQ=12)                                                                                                tAAGCAAAAATTCGAGACATAGTGAGGCTCTATACGAAATTGGTGTTCATATCATAATGCATCTCAGAAAATAATTATGATTATTTTTGTGCATATTTGTATGTACACGTTCGAAAATAAACGAATGCGTATg  >  2:257000/1‑133 (MQ=18)                                                                                                                          |                                                                                                           CTTCGATTATTTGCTGAGGTTTGATTTTAAAACCTGCACTTTCGATTTCCCGGCGTTGATTTTCGGTGGTCTGATCCAGCGTTGATATCCGACAGTAAGCAAAAATTCGAGACATAGTGAGACTCTATACGAAATTGGTGTTCATATCATAATGCATCTCAGAAAATAATTATGATTATTTTTGTGCATATTTGTATGTACACGTTCGAAAATAAACGAATGCGTATG  >  NC_000913/1433560‑1433787

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑