Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	1	1,555,942	T→C	intergenic (‑25/‑219)	unknown ← / → unknown	Autoinducer 2 (AI‑2) ABC transporter, dimeric ATP‑binding protein/LsrR, transcriptional repressor of lsr operon

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	1	1,555,942	0	T	C	100.0%	91.7 / NA	27	intergenic (‑25/‑219)	unknown/unknown	Autoinducer 2 (AI‑2) ABC transporter, dimeric ATP‑binding protein/LsrR, transcriptional repressor of lsr operon
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (15/12);  total (15/12)

GTCGCACCCCGAACCTCCAGTTCTCCGCTATCTTGCGGCTGAATGCCGGCGATAATTTTCATCAGCGTGGATTTCCCCGCCCCGTTACCGCCGAGCAGTGCGTGCACTTCACCGGCATATAAGGAAAAATCAATGGCTTTCAGCACTTCCACGCCGGAAAACGACTTACCGATGTTTCGAGCGGATATTAAGCATTTTGGCTCTGAAATGTGAGTTTGCATCTTTTACCTGCCGCATAGAATGAATAAATGTATTTAAAAAAAACATTTTTTTAAAATACTAGTCAGGAATGCACAAAATTTCTGAGAACTAGATCACAAATCTGGATAAGATTATCTAAAAATCGCCTTTAATTTTTAAAAAAGTGATCTCCATCATGCTTTTACAAAAAAACGGTAAGAACAATTGATAATAATAAAAAACAAATGAATAATACCCAAAATCAATAAAAACAAATAAATCATATGAACGAATTAATGA  >  1/1555697‑1556176                                                                                                                                                                                                                                                      |                                                                                                                                                                                                                                           gTCGCACCCCGAACCTCCAGTTCTCCGCTATCTTGCGGCTGAATGCCGGCGATAATTTTCATCAGCGTGGATTTCCCCGCCCCGTTACCGCCGAGCAGTGCGTGCACTTCACCGGCATATAAGGAAAAATCAATGGCTTTCAGCACTTCCACGCCGGAAAACGACTTACCGATGTTTCGAGCGGATATTAAGCATTTTGGCTCTGAAATGTGAGTTTGCATCTTTTACCTGCCGCATAGAATGAACAAATg                                                                                                                                                                                                                                       >  1:284326/1‑251 (MQ=255)  tCGCACCCCGAACCTCCAGTTCTCCGCTATCTTGCGGCTGAATGCCGGCGATAATTTTCATCAGCGTGGATTTCCCCGCCCCGTTACCGCCGAGCAGTGCGTGCACTTCACCGGCATATAAGGAAAAATCAATGGCTTTCAGCACTTCCACGCCGGAAAACGACTTACCGATGTTTCGAGCGGATATTAAGCATTTTGGCTCTGAAATGTGAGTTTGCATCTTTTACCTGCCGCATAGAATGAACAAATg                                                                                                                                                                                                                                       <  1:32228/250‑1 (MQ=255)      cccccGAACCTCCAGTTCTGCGCTATCTTGCGGCTGAATGCCGGCGATAATTTTCATCAGCTTGGATTTCCCCGCCCCGTTACCGCCGAGCAGTGCGTGCACTTCACCGGCATATAAGGAAAAATCAATGGCTTTCAGCACTTCCACGCCGGAAAACGACTTACCGATGTTTCGAGCGGATATTAAGCATTTTGGCTCTGAAATGTGAGTTTGCATCTTTTACCTGCCGCATAGAATGAACAAATGTAttt                                                                                                                                                                                                                                  <  1:314817/250‑1 (MQ=255)            aaCCTCCAGTTCTCCGCTATCTTGCGGCTGAATGCCGGCGATAATTTTCATCAGCGTGGATTTCCCCGCCCCGTTACCGCCGAGCAGTGCGTGCACTTCACCGGCATATAAGGAAAAATCAATGGCTTTCAGCACTTCCACGCCGGAAAACGACTTACCGATGTTTCGAGCGGATATTAAGCATTTTGGCTCTGAAATGTGAGTTTGCATCTTTTACCTGCCGCATAGAATGAACAAATGTATTTaaaaaa                                                                                                                                                                                                                            >  1:241813/1‑251 (MQ=255)                 ccAGTTCTCCGCTATCTTGCGGCTGAATGCCGGCGATAATTTTCATCAGCGTGGATTTCCCCGCCCCGTTACCGCCGAGCAGTGCGTGCACTTCACCGGCATATAAGGAAAAATCAATGGCTTTCAGCACTTCCACGCCGGAAAACGACTTACCGATGTTTCGAGCGGATATTAAGCATTTTGGCTCTGAAATGTGAGTTTGCATCTTTTACCTGCCGCATAGAATGAACAAATGTATTTAAAAAAAACAt                                                                                                                                                                                                                       >  1:29688/1‑251 (MQ=255)                              aTCTTGCGGCTGAATGCCGGCGATAATTTTCATCAGCGTGGATTTCCCCGCCCCGTTACCGCCGAGCAGTGCGTGCACTTCACCGGCATATAAGGAAAAATCAATGGCTTTCAGCACTTCCACGCCGGAAAACGACTTACCGATGTTTCGAGCGGATATTAAGCATTTTGGCTCTGAAATGTGAGTTTGCATCTTTTACCTGCCGCATAGAATGAACAAATGt                                                                                                                                                                                                                                      >  1:541616/1‑223 (MQ=255)                                        tGAATGCCGGCGATAATTTTCATCAGCGTGGATTTCCCCGCCCCGTTACCGCCGAGCAGTGCGTGCACTTCACCGGCATATAAGGAAAAATCAATGGCTTTCAGCACTTCCACGCCGGAAAACGACTTACCGATGTTTCGAGCGGATATTAAGCATTTTGGCTCTGAAATGTGAGTTTGCATCTTTTACCTGCCGCATAGAATGAACAAATGTATTTAAAAAAAACATTTTTTTAAAATACTAGTCAGGaa                                                                                                                                                                                                <  1:741126/251‑1 (MQ=255)                                         gAATGCCGGCGATAATTTTCATCAGCGTGGATTTCCCCGCCCCGTTACCGCCGAGCAGTGCGTGCACTTCACCGGCATATAAGGAAAAATCAATGGCTTTCAGCACTTCCACGCCGGAAAACGACTTACCGATGTTTCGAGCGGATATTAAGCATTTTGGCTCTGAAATGTGAGTTTGCATCTTTTACCTGCCGCATAGAATGAACAAATGTATTTAAAAAAAACATTTTTTTAAAATACTAGTCAGGaa                                                                                                                                                                                                >  1:880307/1‑250 (MQ=255)                                                      aaTTTTCATCAGCGTGGATTTCCCCGCCCCGTTACCGCCGAGCAGTGCGTGCACTTCACCGGCATATAAGGAAAAATCAATGGCTTTCAGCACTTCCACGCCGGAAAACGACTTACCGATGTTTCGAGCGGATATTAAGCATTTTGGCTCTGAAATGTGAGTTTGCATCTTTTACCTGCCGCATAGAATGAACAAATGTATTTAAAAAAAACATTTTTTTAAAATACTAGTc                                                                                                                                                                                                     <  1:312919/232‑1 (MQ=255)                                                                       aTTTCCCCGCCCCGTTACCGCCGAGCAGTGCGTGCACTTCACCGGCATATAAGGAAAAATCAATGGCTTTCAGCACTTCCACGCCGGAAAACGACTTACCGATGTTTCGAGCGGATATTAAGCATTTTGGCTCTGAAATGTGAGTTTGCATCTTTTACCTGCCGCATAGAATGAACAAATGTATTTAAAAAAAACATTTTTTTAAAATACTAGTCAGGAATGCACAAAATTTCTGAGAACTAGATCACaa                                                                                                                                                                  <  1:659379/250‑1 (MQ=255)                                                                         ttCCCCGCCCCGTTACCGCCGAGCAGTGCGTGCACTTCACCGGCATATAAGGAAAAATCAATGGCTTTCAGCACTTCCACGCCGGAAAACGACTTACCGATGTTTCGAGCGGATATTAAGCATTTTGGCTCTGAAATGTGAGTTTGCATCTTTTACCTGCCGCATAGAATGAACAAATGTATTTAAAAAAAACATTTTTTTAAAATACTAGTCAGGAATGCACAAAATTTCTGAGAACTAGATCACAAATc                                                                                                                                                               <  1:770588/251‑1 (MQ=255)                                                                              cgccccgTTACCGCCGAGCAGTGCGTGCACTTCACCGGCATATAAGGAAAAATCAATGGCTTTCAGCACTTCCACGCCGGAAAACGACTTACCGATGTTTCGAGCGGATATTAAGCATTTTGGCTCTGAAATGTGAGTTTGCATCTTTTACCTGCCGCATAGAATGAACAAATGTATTTAAAAAAAACATTTTTTTAAAATACTAGTCAGGAATGCACAAAATTTCTGAGAACTAGATCACAAATCTGGAt                                                                                                                                                          <  1:486868/251‑1 (MQ=255)                                                                                ccccgTTACCGCCGAGCAGTGCGTGCACTTCACCGGCATATAAGGAAAAATCAATGGCTTTCAGCACTTCCACGCCGGAAAACGACTTACCGATGTTTCGAGCGGATATTAAGCATTTTGGCTCTGAAATGTGAGTTTGCATCTTTTACCTGCCGCATAGAATGAACAAATGTATTTAAAAAAAACATTTTTTTAAAATACTAGTc                                                                                                                                                                                                     <  1:822660/206‑1 (MQ=255)                                                                                        ccgccgAGCAGTGCGTGCACTTCACCGGCATATAAGGAAAAATCAATGGCTTTCAGCACTTCCACGCCGGAAAACGACTTACCGATGTTTCGAGCGGATATTAAGCATTTTGGCTCTGAAATGTGAGTTTGCATCTTTTACCTGCCGCATAGAATGAACAAATGTATTTAAAAAAAACATTTTTTTAAAATACTAGTCAGGAATGCACAAAATTTCTGAGAACTAGATCACAAATCTGGATAAGAt                                                                                                                                                     <  1:348258/246‑1 (MQ=255)                                                                                                  gtgcgtgcACTTCACCGGCATATAAGGAAAAATCAATGGCTTTCAGCACTTCCACGCCGGAAAACGACTTACCGATGTTTCGAGCGGATATTAAGCATTTTGGCTCTGAAATGTGAGTTTGCATCTTTTACCTGCCGCATAGAATGAACAAATGTATTTAAAAAAAACATTTTTTTAAAATACTAGTCAGGAATGCACAAAATTTCTGAGAACTAGATCACAAATCTGGATAAGATTATCTAAAAATCGc                                                                                                                                       >  1:837841/1‑250 (MQ=255)                                                                                                   tgcgtgcACTTCACCGGCATATAAGGAAAAATCAATGGCTTTCAGCACTTCCACGCCGGAAAACGACTTACCGATGTTTCGAGCGGATATTAAGCATTTTGGCTCTGAAATGTGAGTTTGCATCTTTTACCTGCCGCATAGAATGAACAAATGTATTTAAAAAAAACATTTTTTTAAAATACTAGTCAgg                                                                                                                                                                                                  >  1:151273/1‑190 (MQ=255)                                                                                                         cACTTCACCGGCATATAAGGAAAAATCAATGGCTTTCAGCACTTCCACGCCGGAAAACGACTTACCGATGTTTCGAGCGGATATTAAGCATTTTGGCTCTGAAATGTGAGTTTGCATCTTTTACCTGCCGCATAGAATGAACAAATGTATTTAAAAAAAACATTTTTTTAAAATACTAGTCAGGAATGCACAAAATTTCTGAGAACTAGATCACAAATCTGGATAAGATTATCTAAAAATCGCCTTTAAtt                                                                                                                               <  1:328985/251‑1 (MQ=255)                                                                                                                   gCATATAAGGAAAAATCAATGGCTTTCAGCACTTCCACGCCGGAAAACGACTTACCGATGTTTCGAGCGGATATTAAGCATTTTGGCTCTGAAATGTGAGTTTGCATCTTTTACCTGCCGCATAGAATGAACAAATGTATTTAAAAAAAACATTTTTTTAAAATACTAGTCAGGAATGCACAAAATTTCTGAGAACTAGATCACAAATCTGGATAAGATTATCTaaaaa                                                                                                                                           >  1:391742/1‑229 (MQ=255)                                                                                                                                       ggCTTTCAGCACTTCCACGCCGGAAAACGACTTACCGATGTTTCGAGCGGATATTAAGCATTTTGGCTCTGAAATGTGAGTTTGCATCTTTTACCTGCCGCATAGAATGAACAAATGTATTTAAAAAAAACATTTTTTTAAAATACTAGTCAGGAATGCACAAAATTTCTGAGAACTAGATCACAAATCTGGATAAGAt                                                                                                                                                     >  1:208877/1‑199 (MQ=255)                                                                                                                                                                 aCGACTTACCGATGTTTCGAGCGGATATTAAGCATTTTGGCTCTGAAATGTGAGTTTGCATCTTTTACCTGCCGCATAGAATGAACAAATGTATTTAAAAAAAACATTTTTTTAAAATACTAGTCAGGAATGCACAAAATTTCTGAGAACTAGATCACAAATCTGGATAAGATTATCTAAAAATCGCCTTTAATTTTTAAAAAAGTGATCTCCATCATGCTTTTACAAAAAAACGGTAAGAACAATTGata                                                                       <  1:840746/251‑1 (MQ=255)                                                                                                                                                                                  cGAGCGGATATTAAGCATTTTGGCTCTGAAATGTGAGTTTGCATCTTTTACCTGCCGCATAGAATGAACAAATGTATTTAAAAAAAACATTTTTTTAAAATACTAGTCAGGAATGCACAAAATTTCTGAGAACTAGATCACAAATCTGGATAAGATTATCTAAAAATCGCCTTTAATTTTTAAAAAAGTGATCTCCATCATGCTTTTACAAAAAAACGGTAAGAACAATTGATAATAATAAAAAACAAATg                                                      <  1:296625/251‑1 (MQ=255)                                                                                                                                                                                        gATATTAAGCATTTTGGCTCTGAAATGTGAGTTTGCATCTTTTACCTGCCGCATAGAATGAACAAATGTATTTAAAAAAAACATTTTTTTAAAATACTAGTCAGGAATGCACAAAATTTCTGAGAACTAGATCACAAATCTGGATAAGATTATCTAAAAATCGCCTTTAGTTTTTAAAAAAGTGATCTCCATCATGCTTTTACAAAAAAACGGTAAGAACAATTg                                                                          >  1:454612/1‑225 (MQ=255)                                                                                                                                                                                         atatTAAGCATTTTGGCTCTGAAATGTGAGTTTGCATCTTTTACCTGCCGCATAGAATGAACAAATGTATTTAAAAAAAACATTTTTTTAAAATACTAGTCAGGAATGCACAAAATTTCTGAGAACTAGATCACAAATCTGGATAAGAt                                                                                                                                                     >  1:680055/1‑149 (MQ=255)                                                                                                                                                                                         atatTAAGCATTTTGGCTCTGAAATGTGAGTTTGCATCTTTTACCTGCCGCATAGAATGAACAAATGTATTTAAAAAAAACATTTTTTTAAAATACTAGTCAGGAATGCACAAAATTTCTGAGAACTAGATCACAAATCTGGATAAGATTATCTAAAAATCGCCTTTAATTTTTAAAAAAGTGATCTCCATCATGCTTTTACAAAAAAACGGTAAGAACAATTg                                                                          >  1:743085/1‑224 (MQ=255)                                                                                                                                                                                                                      gTTTGCATCTTTTACCTGCCGCATAGAATGAACAAATGTATTTAAAAAAAACATTTTTTTAAAATACTAGTCAGGAATGCACAAAATTTCTGAGAACTAGATCACAAATCTGGATAAGATTATCTAAAAATCGCCTTTAATTTTTAAAAAAGTGATCTCCATCATGCTTTTACAAAAAAACGGTAAGAACAATTGATAATAATAAAAAACAAATGAATAATACCCAAAATCAATAAAAACAAATAAATCat                  >  1:724181/1‑251 (MQ=255)                                                                                                                                                                                                                             tCTTTTACCTGCCGCATAGAATGAACAAATGTATTTAAAAAAAACATTTTTTTAAAATACTAGTCAGGAATGCACAAAATTTCTGAGAACTAGATCACAAATCTGGATAAGATTATCTAAAAATCGCCTTTAATTTTTAAAAAAGTGATCTCCATCATGCTTTTACAAAAAAACGGTAAGAACAATTGATAATAATAAAAAACAAATGAATAATACCCAAAATCAATAAAAACAAATAAATCATATGAACg           >  1:809428/1‑251 (MQ=255)                                                                                                                                                                                                                                       gCCGCATAGAATGAACAAATGTATTTAAAAAAAACATTTTTTTAAAATACTAGTCAGGAATGCACAAAATTTCTGAGAACTAGATCACAAATCTGGATAAGATTATCTAAAAATCGCCTTTAATTTTTAAAAAAGTGATCTCCATCATGCTTTTACAAAAAAACGGTAAGAACAATTGATAATAATAAAAAACAAATGAATAATACCCAAAATCAATAAAAACAAATAAATCATATGAACGAATTAATGa  >  1:645428/1‑250 (MQ=255)                                                                                                                                                                                                                                               gaatgaacAAATGTATTTAAAAAAAACATTTTTTTAAAATACTAGTCAGGAATGCACAAAATTTCTGAGAACTAGATCACAAATCTGGATAAGATTATCTAAAAATCGCCTTTAATTTTTAAAAAAGTGATCTCCATCATGCTTTTACAAAAAAACGGTAAGAACAATTGATAATAATAAAAAACAAATGAATAATACCCAAAATCAATAAAAACAAATAAATCa                   <  1:653878/225‑1 (MQ=255)                                                                                                                                                                                                                                                      |                                                                                                                                                                                                                                           GTCGCACCCCGAACCTCCAGTTCTCCGCTATCTTGCGGCTGAATGCCGGCGATAATTTTCATCAGCGTGGATTTCCCCGCCCCGTTACCGCCGAGCAGTGCGTGCACTTCACCGGCATATAAGGAAAAATCAATGGCTTTCAGCACTTCCACGCCGGAAAACGACTTACCGATGTTTCGAGCGGATATTAAGCATTTTGGCTCTGAAATGTGAGTTTGCATCTTTTACCTGCCGCATAGAATGAATAAATGTATTTAAAAAAAACATTTTTTTAAAATACTAGTCAGGAATGCACAAAATTTCTGAGAACTAGATCACAAATCTGGATAAGATTATCTAAAAATCGCCTTTAATTTTTAAAAAAGTGATCTCCATCATGCTTTTACAAAAAAACGGTAAGAACAATTGATAATAATAAAAAACAAATGAATAATACCCAAAATCAATAAAAACAAATAAATCATATGAACGAATTAATGA  >  1/1555697‑1556176

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑