Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,655,347	C→T	*109* (TAG→TAA)	ynfA ←	UPF0060 family inner membrane protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,655,347	0	C	T	100.0%	86.1 / NA	28	*109* (TAG→TAA)	ynfA	UPF0060 family inner membrane protein
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (16/12);  total (16/12)

AAAGATCGAAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGAATACCTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCCTACGTGCGCCCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTCCAGTCATAAAGAGTCAGTTTCACGCCATCCACAACGCGCAGCCACATCAACGCCGTGC  >  NC_000913/1655211‑1655468                                                                                                                                         |                                                                                                                          aaaGATCGAAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGAATACCTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTa                                                                                                                         >  2:126595/1‑139 (MQ=255)                                    ggCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGAATACCTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGcc                                                                                     >  1:501246/1‑139 (MQ=255)                                                      gAATGGTTGACAAAAGATGAAATAGAATACCTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGc                                                                   >  2:608731/1‑139 (MQ=255)                                                               aCAAAAGATGAAATAGAATACCTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTCCa                                                          >  2:412492/1‑139 (MQ=255)                                                               aCAAAAGATGAAATAGAATACCTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTCCa                                                          >  1:403381/1‑139 (MQ=255)                                                                      aTGAAATAGAATACCTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCa                                                                  >  2:40568/1‑124 (MQ=255)                                                                      aTGAAATAGAATACCTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCa                                                                  <  1:40568/124‑1 (MQ=255)                                                                                    cTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTc                                                            <  1:874264/116‑1 (MQ=255)                                                                                    cTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTc                                                            >  2:874264/1‑116 (MQ=255)                                                                                    cTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTCCAGTCATAAAGAGt                                              >  2:148059/1‑130 (MQ=255)                                                                                    cTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTCCAGTCATAAAGAGt                                              <  1:148059/130‑1 (MQ=255)                                                                                              cTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGcaaca                                                                                                   <  1:717254/67‑1 (MQ=255)                                                                                              cTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGcaaca                                                                                                   >  2:717254/1‑67 (MQ=255)                                                                                                   acTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTCCAGTCATAAAGAGTCAGTTTCACGCCATCCACAAcgcg                      <  1:536603/139‑1 (MQ=255)                                                                                                       ccTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCg                                                                                                        >  2:189485/1‑53 (MQ=255)                                                                                                       ccTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCg                                                                                                        <  1:189485/53‑1 (MQ=255)                                                                                                       ccTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTCCAGTCATAAAGAGTCAGTTTCACGCCATCCACAACGCGCAGc                  <  1:412492/139‑1 (MQ=255)                                                                                                       ccTCTTATATTATAGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGAAACAGTGAACAACATGCCGCATAGCGCAATCAACGCACCCGTCCAGTCATAAAGCGTCAGTTTAACGCCCTCCACAACGCGCAGc                  >  2:711543/1‑139 (MQ=255)                                                                                                        ctctTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTc                                                            <  2:1065675/96‑1 (MQ=255)                                                                                                        ctctTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTc                                                            >  1:1065675/1‑96 (MQ=255)                                                                                                                  atTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCg                                                                                                        >  1:220351/1‑42 (MQ=255)                                                                                                                  atTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCg                                                                                                        <  2:220351/42‑1 (MQ=255)                                                                                                                   ttGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTCCAGTCATAAAGAGTCAGTTTCACGCCATCCACAACGCGCAGCCACATCAACGcc      >  2:391230/1‑139 (MQ=255)                                                                                                                       tAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTCCAGTCATAAAGAGTCAGTTTCACGCCATCCACAACGCGCAGCCACATCAACGCCGTGc  <  1:126595/139‑1 (MQ=255)                                                                                                                        aaaaTGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTCCAGTCATa                                                    <  2:306456/88‑1 (MQ=255)                                                                                                                        aaaaTGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTCCAGTCATa                                                    >  1:306456/1‑88 (MQ=255)                                                                                                                          aaTGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTc                                                            <  1:914087/78‑1 (MQ=255)                                                                                                                          aaTGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTc                                                            >  2:914087/1‑78 (MQ=255)                                                                                                                                         |                                                                                                                          AAAGATCGAAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGAATACCTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCCTACGTGCGCCCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTCCAGTCATAAAGAGTCAGTTTCACGCCATCCACAACGCGCAGCCACATCAACGCCGTGC  >  NC_000913/1655211‑1655468

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑