Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	AM260479	1,240,057	+T	intergenic (‑57/‑218)	h16_A1136 ← / → grpE	conserved hypothetical protein/molecular chaperone GrpE

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	AM260479	1,240,053	1	.	T	100.0%	164.1 / NA	43	intergenic (‑53/‑222)	h16_A1136/grpE	conserved hypothetical protein/molecular chaperone GrpE
Reads supporting (aligned to +/- strand):  ref base . (0/0);  new base T (22/21);  total (22/21)

AAGACGGTCATGACCGCCAATGCGGCCACAAGGCAGAGTGTCACGACTGGCAGCTTATGCATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCA‑TTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAAGGCGTCGATTGCATATGCCTGGCCTTTGTAACCGTGTGTTTCCGCGTCACGCCAGCGC  >  AM260479/1239939‑1240166                                                                                                                    |                                                                                                                  aaGACGGTCATGACCGCCAATGCGGCCACAAGGCAGAGTGTCACGACTGGCAGCTTATGCATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTttatta                                                                                                  <  2:247042/133‑1 (MQ=255) aaGACGGTCATGACCGCCAATGCGGCCACAAGGCAGAGTGTCACGACTGGCAGCTTATGCATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTttatta                                                                                                  <  2:277784/133‑1 (MQ=255)        tCATGACCGCCAATGCGGCCACAAGGCAGAGTGTCACGACTGGCAGCTTATGCATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAAt                                                                                          >  2:827232/1‑134 (MQ=255)            gACCGCCAATGCGGCCACAAGGCAGAGTGTCACGACTGGCAGCTTATGCATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCt                                                                                        >  1:785950/1‑132 (MQ=255)            gACCGCCAATGCGGCCACAAGGCAGAGTGTCACGACTGGCAGCTTATGCATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCt                                                                                        >  2:341025/1‑132 (MQ=255)              ccGCCAATGCGGCCACAAGGCAGAGTGTCACGACTGGCAGCTTATGCATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCAtt                                                                                                         <  2:205854/113‑1 (MQ=255)              ccGCCAATGCGGCCACAAGGCAGAGTGTCACGACTGGCAGCTTATGCATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCAtt                                                                                                         >  1:205854/1‑113 (MQ=255)                     tGCGGCCACAAGGCAGAGTGTCACGACTGGCAGCTTATGCATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGc                                                                              >  2:160950/1‑133 (MQ=255)                      gCGGCCACAAGGCAGAGTGTCACGACTGGCAGCTTATGCATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGa                                                                            >  1:1083360/1‑134 (MQ=255)                      gCGGCCACAAGGCAGAGTGTCACGACTGGCAGCTTATGCATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGa                                                                            >  2:490893/1‑134 (MQ=255)                         gCCACAAGGCAGAGTGTCACGACTGGCAGCTTATGCATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATgc                                                                         <  1:695458/134‑1 (MQ=255)                                           aCGACTGGCAGCTTATGCATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAAGGCg                                                        <  1:248160/133‑1 (MQ=255)                                           aCGACTGGCAGCTTATGCATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAAGGCg                                                        <  2:785950/133‑1 (MQ=255)                                           aCGACTGGCAGCTTATGCATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAAGGCGt                                                       >  1:206489/1‑134 (MQ=255)                                           aCGACTGGCAGCTTATGCATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAAGGCGt                                                       >  1:421312/1‑134 (MQ=255)                                            cGACTGGCAGCTTATGCATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAAGGCGTc                                                      >  2:195515/1‑134 (MQ=255)                                               cTGGCAGCTTATGCATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAAGGCGTCGAt                                                   <  1:1062353/134‑1 (MQ=255)                                                tGGCAGCTTATGCATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAAGGCGTCGAt                                                   <  1:178533/133‑1 (MQ=255)                                                tGGCAGCTTATGCATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAAGGCGTCGAt                                                   >  2:178533/1‑133 (MQ=255)                                                         aTGCATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAAGGCGTCGATTGCATATg                                           <  1:938505/132‑1 (MQ=255)                                                          tGCATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAAGGCGTCGATTGCATATGcc                                         <  2:206489/133‑1 (MQ=255)                                                          tGCATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAAGGCGTCGATTGCATATGcc                                         <  1:827232/133‑1 (MQ=255)                                                          tGCATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAAGGCGTCGATTGCATATGcc                                         <  2:421312/133‑1 (MQ=255)                                                                     ccTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAAGGCGTCGATTGCATATg                                           >  2:671765/1‑120 (MQ=255)                                                                     ccTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAAGGCGTCGATTGCATATg                                           <  1:671765/120‑1 (MQ=255)                                                                        tCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAAGGCGTCGATTGCATATGCCTGGCCTTTGTAACCg                          >  1:793891/1‑134 (MQ=255)                                                                              agagGCACAAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAAGGCGTCGATTGCATATGCCTGGCCTTTGTAACCGTGTGtt                    >  2:538253/1‑134 (MQ=255)                                                                                     caAAGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAAGGCGTCGATTGCATATGCCTGGCCTTTGTAACCGTGTGTTTCCGCGt             >  1:94518/1‑134 (MQ=255)                                                                                      aaaGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATgc                                                                         <  1:989852/73‑1 (MQ=255)                                                                                      aaaGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATgc                                                                         >  2:989852/1‑73 (MQ=255)                                                                                      aaaGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAAGGCGTCGATTGCATATGCCTGGCCTTTGTAACCGTGTGTTTCCGCGTc            <  1:195515/134‑1 (MQ=255)                                                                                       aaGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTttat                                                                                                    <  1:503791/45‑1 (MQ=38)                                                                                       aaGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTttat                                                                                                    >  2:503791/1‑45 (MQ=38)                                                                                        aGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAAGGCGTCGAt                                                   <  2:446089/93‑1 (MQ=255)                                                                                        aGATGAACCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAAGGCGTCGAt                                                   >  1:446089/1‑93 (MQ=255)                                                                                              aCCATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAAGGCGTCGATTGCATATGCCTGGCCTTTGTAACCGTGTGTTTCCGCGTCACGCCAgc    <  1:490893/134‑1 (MQ=255)                                                                                                cATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAAGGCGTCGAt                                                   >  1:537996/1‑85 (MQ=255)                                                                                                cATCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAAGGCGTCGAt                                                   <  2:537996/85‑1 (MQ=255)                                                                                                 aTCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAAGGCGTCGATTGCATATGCCTGGCCTTTGTAACCGTGTGTTTCCGCGTCACGCCAgcgc  >  1:387666/1‑133 (MQ=255)                                                                                                 aTCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAAGGCGTCGATTGCATATGCCTGGCCTTTGTAACCGTGTGTTTCCGCGTCACGCCAgcg   >  1:88636/1‑132 (MQ=255)                                                                                                 aTCTCCACAACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAAGGCGTCGATTGCATATGCCTGGCCTTTGTAACCGTGTGTTTCCGCGTCACGCCAgcg   <  2:88636/132‑1 (MQ=255)                                                                                                        caACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAAGGCGTCGATTGCata                                             >  1:750899/1‑83 (MQ=255)                                                                                                        caACCCCCGGCATTTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAAGGCGTCGATTGCata                                             <  2:750899/83‑1 (MQ=255)                                                                                                                    |                                                                                                                  AAGACGGTCATGACCGCCAATGCGGCCACAAGGCAGAGTGTCACGACTGGCAGCTTATGCATGGCCAACCTTCCGGAAGAGGCACAAAGATGAACCATCTCCACAACCCCCGGCA‑TTTTGTCATTTTTATTACTGGGAATCTTAGTGATTGCGATGCAGCAAAGCAATAAGGCGTCGATTGCATATGCCTGGCCTTTGTAACCGTGTGTTTCCGCGTCACGCCAGCGC  >  AM260479/1239939‑1240166

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑