Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,765,830	G→A	R1216R (CGG→CGA)	rhsA →	rhs element protein RhsA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,765,830	0	G	A	100.0%	51.5 / NA	22	R1216R (CGG→CGA)	rhsA	rhs element protein RhsA
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (10/12);  total (10/12)

CAGCAAGGAAGGGACAACAGAATGGTGCGCAGAATACGATGAATGGGGCAACCTGCTGAATGAAGAGAACCCGCATCAGCTGCAGCAGCTTATCCGCCTGCCGGGGCAGCAGTATGATGAGGAGTCCGGCCTGTATTACAACCGCCACCGCTATTATGACCCGCTGCAGGGGCGGTATATCACTCAGGATCCGATTGGGCTGAAGGGGGGATGGAATTTTTATCAGTATCCGTTGAATCCAGTTACGAATACAGATCCTCTGGGGTTAGAAGTTTTTCCTAGACCATTCCCCTTGCCAATTCCATGGCCCAAAAGCCCTGCACAGCAGCAAGCAGATGATAATGCTGCAAAAGCATTGACAAAATGGTGGAACGATACAGCATCACAAAGAATATTTGACTCTCTAATATTG  >  NC_000913/3765656‑3766067                                                                                                                                                                               |                                                                                                                                                                                                                                              cAGCACGGAAGGGGCAACAGCGTGGTGCGCAGAATATGATGAATGGGGCAACCTGCTGAATTAAGAGAACCCGCATCAGCTGCAGCAGCTTATCCGGCTGCCGGGGCAGCAGTATGATGAGGAGTCCGGCCTGTATTACAACCGCCACCGCTATTATGACCCGCTGCAGGGGCGATATATCACTCAGGATCCGATTGGACTGAAGGGGGGATGGAATTTTTATCAGTATCCGTTGAATCCAGTTACGAATa                                                                                                                                                                   <  1:187898/251‑1 (MQ=11) cAGCACGGAAGGGGCAACAGCGTGGTGCGCAGAATATGATGAATGGGGCAACCTGCTGAATGAAGAGAACCCGCATCAGCTGCAGCAGCTTATCCGGCTGCCGGGGCAGCAGTATGATGAGGAGTCCGGCCTGTATTACAACCGCCACCGCTATTATGACCCGCTGCAGGGGCGATATATCACTCAGGATCCGATTGGACTGAAGGGGGGATGGAATTTTTATCAGTATCCGTTGAATCCAGTTACGAATa                                                                                                                                                                   <  1:179135/251‑1 (MQ=11)                        ggTGCGCAGAATATGATGAATGGGGCAACCTGCTGAATGAAGAGAACCCGCATCAGCTGCAGCAGCTTATCCGGCTGCCGGGGCAGCAGTATGATGAGGAGTCCGGCCTGTATTACAACCGCCACCGCTATTATGACCCGCTGCAGGGGCGATATATCACTCAGGATCCGATTGGACTGAAGGGGGGATGGAATTTTTATCAGTATCCGTTGAATCCAGTTACGAATACAGATCCTCTGGGGTTAGAAGtt                                                                                                                                            <  1:85241/251‑1 (MQ=255)                                 aaTATGATGAATGGGGCAACCTGCTGAATGAAGAGAACCCGCATCAGCTGCAGCAGCTTATCCGGATGCCGGGGCAGCAGTATGATGAGGAGTCCGGCCTGTATTACAACAGCCACCGCTATTATGAACCGCTGCAGGGGCGATATATCACTCATGATCCGATTGGACTGAAGGGGGGATGGAATTTTTATCAGTATCCGTTGAATCAAGTTACGAATAAAAATACTCTGGGATAAGAAGTTTTTCCt                                                                                                                                      >  1:386844/1‑248 (MQ=14)                                    atgATGAATGGGGCAACCTGCTGAATGAAGAGAACCCGCATCAGCTGCAGCAGCTTATCCGGCTGCCGGGGCAGCAGTATGATGAGGAGTCCGGCCTGTATTACAACCGCCACCGCTATTATGACCCGCTGCAGGGGCGATATATCACTCAGGATCCGATTGGACTGAAGGGGGGATGGAATTTTTATCAGTATCCGTTGAATCCAGTTACGAATACAGATCCTCTGGGGTTAGAAGTTTTTCCTAGAcc                                                                                                                                 >  1:215071/3‑250 (MQ=255)                                     tgATGAATGGTGCAACCTGCTGAATGATGAGAAACCGCATCCGCTGCCGCAGCGTATCCGGCTGCCGGGGCAGCAGTATGATGAGGAGTCCGGCCAGTATTACAACCGCCCCCGCTATTATGACCCGCTGCAGGGGCGATATATCACTCAGGATCCGATTGGACTGAAGGGAGGACGGAATTTTTTTCAGTATCAGTTGAATCCAGTTACGACTACAGTTCCTCTGGGGTTTGAACTTTTTCCTAAACCAt                                                                                                                               >  2:57241/2‑251 (MQ=14)                                         gAATGGGGCAACCTGCTGAATGAAGAGAACCCGCATCAGCTGCAGCAGCTTATCCGGCTGCCGGGGCAGCAGTATGATGAGGAGTCCGGCCTGTATTACAACCGCCACCGCTATTATGACCCGCTGCAGGGGCGATATATCACTCAGGATCCGATTGGACTGAAGGGGGGATGGAATTTTTATCAGTATCCGTTGAATCCAGTTACGaa                                                                                                                                                                     <  1:154055/209‑1 (MQ=255)                                         gAATGGGGCAACCTGCTGAATGAAGAGAACCCGCATCAGCTGCAGCAGCTTATCCGGCTGCCGGGGCAGCAGTATGATGAGGAGTCCGGCCTGTATTACAACCGCCACCGCTATTATGACCCGCTGCAGGGGCGATATATAACTCAGGATCCGATTGGACTGACGGGGGGATGGAATTTTTATCAGTATCCGTTGAATCCAGTTACGaa                                                                                                                                                                     >  2:154055/1‑209 (MQ=255)                                                    ccTGCTGAATGAAGAGAACCCGCATCAGCTGCAGCAGCTTATCCGGCTGCCGGGGCAGCAGTATGATGAGGAGTCCGGCCTGTATTACAACCGCCACCGCTATTATGACCCGCTGCAGGGGCGATATATCACTCAGGATCCGATTGGACTGAAGGGGGGATGGAATTTTTATCAGTATCCGTTGAATCCAGTTACGAATACAGATCCTCTGGGGTTAGAAGTTTTTCCTAGACCATTCCCCTTGCCAATTc                                                                                                                <  1:114950/251‑1 (MQ=255)                                                                        ggcatgaggtgaagcagtTTATCCGGCTGCCGGGGAACCAGTAGGGTGAGGAGCCCGGCCGGTATTAAAACCGCCTCCGCTATTATGACCCGCTGCAGGTGCGATATATCACTCAGGATCCGATTGGACTGAAGGGGGGATGGAATTTTTATCAGTATCCGTTGAATCCAGTTACGAATACAGATCCTCTGGGGTTAGAAGTTTCTCCTAGACCATTCCCCTTGCCAATTCCATGGCCCAAAAGCCCTGca                                                                                            <  2:410703/239‑1 (MQ=18)                                                                                  gcagcaGCTTATCCGGCTGCCGGGGCAGCAGTATGATGAGGAGTCCGGCCTGTATTACAACCGCCACCGCTATTATGACCCGCTGCAGGGGCGATATATCACTCAGGATCCGATTGGACTGAAGGGGGGATGGAATTTTTATCAGTATCCGTTGAATCCAGTTACGAATACAGATCCTCTGGGGTTAGAAGTTTTTCCTAGACCATTCCCCTTGCCAATTCCATGGCCCAAAAGCCCTGCACAGCagcaag                                                                                  <  1:441432/251‑1 (MQ=255)                                                                                                   tgacGGGGCAGCAGTATGATGAGGAGTCAGGCCTGTATTACAACCGCCACCGCTATTATGACCCGCTGCAGGGGCGATATATCACTCAGGATCCGATTGGACTGAAGGGGGGATGGAATTTTTATCAGTATCCGTTGAATCCAGTTACGAATACAGATCCTATGGGGTTAGAAGTTTTTCCTAGACCATTCACCTTGCCACTTCAATGGCCCAAAATCCCTGCTCACCAACAAGCAgatgtaaatgatgc                                                                  >  2:302561/4‑240 (MQ=18)                                                                                                    gCCGGGGCAGCAGTATGATGAGGAGTCCGGCCTGTATTACAACCGCCACCGCTATTATGACCCGCTGCAGGGGCGATATATCACTCAGGATCCGATTGGACTGAAGGGGGGATGGAATTTTTATCAGTATCCGTTGAATCCAGTTACGAATACAGATCCTCTGGGGTTAGAAGTTTTTCCTAGACCATTCCCCTTGCCAATTCCATGGCCCAAAAGCCCTGCACAGCAGCAAGCAGATGATAAtgctgc                                                                  <  1:100889/249‑1 (MQ=255)                                                                                                          gcagcaGTATGATGAGGAGTCCGGCCTGTATTACAACCGCCACCGCTATTATGACCCGCTGCAGGGGCGATATATCACTCAGGATCCGATTGGACTGAAGGGGGGATGGAATTTTTATCAGTATCCGTTGAATCCAGTTACGAATACAGATCCTCTGGGGTTAGAAGTTTTTCCTAGACCATTCCCCTTGCCAATTCCATGGCCCAAAAGCCCTGCACAGCAGCAAGCAGATGATAATGCTGCAAAAGCAt                                                          <  1:361985/251‑1 (MQ=255)                                                                                                                   tgatgaGGAGTCCGGCCTGTATTACAACCGCCACCGCTATTATGACCCGCTGCAGGGGCGATATATCACTCAGGATCCGATTGGACTGAAGGGGGGATGGAATTTTTATCAGTATCCGTTGAATCCAGTTACGAATACAGATCCTCTGGGGTTAGAAGTTTTTCCTAGACCATTCCCCTTGCCAATTCCATGGCCCAAAAGCCCTGCACAGCAGCAAGCAGATGATAATGCTGCAAAAGCATTGACAAAAt                                                 >  1:277275/1‑251 (MQ=255)                                                                                                                              ccggccggTATTACAACCTCCACCGCTATTATGACCCGCTGCAGGGGCGATATATCACTCAGGATCCGATTGGACTGAAGGGGGGATGGAATTTTTATCAGTATCCGTTGAATCCAGTTACGAATACAGATCCTCTGGGGTTAGAAGTTTTTCCTAGATCATTCCCCTTGCCAATTCCATGTCCCAAAAGCCCTGCACAGCAGCAAGCAGATGATAATGCTGCAAAAGCATTGACAAAATGGTGGAACGAt                                      <  1:431320/251‑1 (MQ=255)                                                                                                                               cGGCCTGTATTACAACCGCCACCGCTATTATGACCCGCTGCAGGGGCGATATATCACTCAGGATCCGATTGGACTGAAGGGGGGATGGAATTTTTATCAGTATCCGTTGAATCCAGTTACGAATACAGATCCTCTGGGGTTAGAAGTTTTTCCTAGACCATTCCCCTTGCCAATTCCATGGCCCAAAAGCCCTGCACAGCAGCAAGCAGATGATACTGCGGCAAAAGCATTGCCAAAATGGTGGAACggt                                      >  2:180327/1‑248 (MQ=255)                                                                                                                                    tGTATTACAACCGCCACCGCTATTATGACCCGATGCAGGGGCGATATATCACTCAGGATCCGATTGGACTGAAGGGGGGATGGAATTTTTATCAGTATCCGTTGAATCCAGTTACGAATACAGATCCTCTGGGGTTAGAAGTTTTTCCTAGACCATTCCCCTTGCCAATTCCATGGCCCCAAAGCCCTGCACAGCAGCAAGCAGATGATAATGCTGCCAAAGCATTGACAAAATGGAGGAACGATAAAGc                                 >  1:114630/1‑250 (MQ=37)                                                                                                                                       aTTACAACCGCCACCGCTATTATGACCCGCTGCAGGGGCGATATATCACTCAGGATCCGATTGGACTGAAGGGGGGATGGAATTTTTATCAGTATCCGTTGAATCCAGTTACGAATACAGATCCTCTGGGGTTAGAAGTTTTTCCTAGACCATTCCCCTTGCCAATTCCATGGCCCAAAAGCCCTGCACAGCAGCAAGCAGATGATAATGCTGCAAAAGCATTGACAACATGGTGGAACGATACAGCATc                              >  1:230965/1‑250 (MQ=255)                                                                                                                                            aaCCGCCACCGCTATTATGACCCGCTGCAGGGGCGATATATCACTCAGGATCCGATTGGACTGAAGGGGGGATGGAATTTTTATCAGTATCCGTTGAATCCAGTTACGAATACAGATCCTCTGGGGTTAGAAGTTTTTCCTAGACCATTCCCCTTGCCAATTCCATGGCCCAAAAGCCCTGCACAGCAGCAAGCAGATGATAATGCTGCAAAAGCATTGACAAAATGGTGGAACGATACAGCATCACAAAg                        <  1:180327/251‑1 (MQ=255)                                                                                                                                                                 ccGCTTCAGGGGAGATATATAACTCAGGATCCGAGTGGACTGAAGGGGGGATGGAATTTTTATCAGTATCCGGTGAATCCAGTCACGAATAAAGATCATATGGGGTTAGAAGTTTTTCCTAGACCATTCCCTTTGACCATTCAATGGCCCACAAGCCCTACAAGGCAGCAAGCAGATAATAATGATGAAAAAGCATTGACAAATTGGTGGAACGATAAAGAATCACAAAGAatcatggaatatataatatt   >  2:261287/1‑233 (MQ=16)                                                                                                                                                                  cGCTGCAGGGGCGATATATCACTCAGGATCCGATTGGACTGAAGGGGGGATGGAATTTTTATCAGTATCCGTTGAATCCAGTTACGAATACAGATCCTCTGGGGTTAGAAGTTTTTCCTAGACCATTCCCCTTGCCAATTCCATGGCCCAAAAGCCCTGCACAGCAGCAAGCAGATGATAATGCTGCAAAAGCATTGACAAAATGGTGGAACGATACAGCATCACAAAGAATATTTGACTCTCTAATATTg  <  1:136141/251‑1 (MQ=255)                                                                                                                                                                               |                                                                                                                                                                                                                                              CAGCAAGGAAGGGACAACAGAATGGTGCGCAGAATACGATGAATGGGGCAACCTGCTGAATGAAGAGAACCCGCATCAGCTGCAGCAGCTTATCCGCCTGCCGGGGCAGCAGTATGATGAGGAGTCCGGCCTGTATTACAACCGCCACCGCTATTATGACCCGCTGCAGGGGCGGTATATCACTCAGGATCCGATTGGGCTGAAGGGGGGATGGAATTTTTATCAGTATCCGTTGAATCCAGTTACGAATACAGATCCTCTGGGGTTAGAAGTTTTTCCTAGACCATTCCCCTTGCCAATTCCATGGCCCAAAAGCCCTGCACAGCAGCAAGCAGATGATAATGCTGCAAAAGCATTGACAAAATGGTGGAACGATACAGCATCACAAAGAATATTTGACTCTCTAATATTG  >  NC_000913/3765656‑3766067

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑