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%	180.4 / NA	55	*109* (TAG→TAA)	ynfA	UPF0060 family inner membrane protein
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (28/27);  total (28/27)

ATCGAAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGAATACCTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCCTACGTGCGCCCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTCCAGTCATAAAGAGTCAGTTTCACGCCATCCACAACGCGCAGCCACATCAACGCCGTGCAGACATAAACGCC  >  NC_000913/1655215‑1655481                                                                                                                                     |                                                                                                                                       aTCGAAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGAATACCTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTg                                                                                                                                  >  2:94366/1‑139 (MQ=255)      aaaaaGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGAATACCTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCGccc                                                                                                                             <  1:1574549/139‑1 (MQ=255)                aGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGAATACCTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGcaa                                                                                                                  <  1:1634202/139‑1 (MQ=255)                aGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGAATACCTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGcaa                                                                                                                  <  1:681688/139‑1 (MQ=255)                aGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGAATACCTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGcaa                                                                                                                  <  1:13427/139‑1 (MQ=255)                  tGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGAATACCTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGcaaca                                                                                                                <  2:582597/139‑1 (MQ=255)                  tGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGAATACCTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGcaaca                                                                                                                <  2:713553/139‑1 (MQ=255)                         aaaaaaaGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGAATACCTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCa                                                                                                         <  1:80361/139‑1 (MQ=255)                                   gTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGAATACCTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCa                                                                                               >  2:991171/1‑139 (MQ=255)                                               tgtgAATGGTTGACAAAAGATGAAATAGAATACCTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCaa                                                                                   <  2:1182550/139‑1 (MQ=255)                                                 tgAATGGTTGACAAAAGATGAAATAGAATACCTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCGccccagcc                                                                                                                        <  2:1040593/101‑5 (MQ=255)                                                 tgAATGGTTGACAAAAGATGAAATAGAATACCTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCGccccagcc                                                                                                                        >  1:1040593/1‑97 (MQ=255)                                                         tGACAAAAGATGAAATAGAATACCTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTc                                                                         <  2:464913/139‑1 (MQ=255)                                                           aCAAAAGATGAAATAGAATACCTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGcaaca                                                                                                                >  1:1540522/1‑98 (MQ=255)                                                           aCAAAAGATGAAATAGAATACCTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGcaaca                                                                                                                <  2:1540522/98‑1 (MQ=255)                                                           aCAAAAGATGAAATAGAATACCTTTTGTCAGCTGACAC‑TCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTCCAg                                                                      >  1:78868/1‑139 (MQ=255)                                                                            aTACCTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTc                                                                         <  2:461953/120‑1 (MQ=255)                                                                            aTACCTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTc                                                                         >  1:461953/1‑120 (MQ=255)                                                                                cTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCGccccagcc                                                                                                                        >  2:857851/1‑66 (MQ=255)                                                                                cTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCGccccagcc                                                                                                                        <  1:857851/70‑5 (MQ=255)                                                                                cTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGcaaca                                                                                                                <  2:837670/77‑1 (MQ=255)                                                                                cTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGcaaca                                                                                                                >  1:837670/1‑77 (MQ=255)                                                                                  tttGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCa                                                                                               <  1:79599/92‑1 (MQ=255)                                                                                  tttGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCa                                                                                               >  2:79599/1‑92 (MQ=255)                                                                                  tttGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTCCAGTCATAAAGAGTCAGTTTCACGc                                                >  1:1174733/1‑139 (MQ=255)                                                                                   ttGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACg                                                                                 <  1:1177543/105‑1 (MQ=255)                                                                                   ttGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACg                                                                                 >  2:1177543/1‑105 (MQ=255)                                                                                    tGTCAGCTGACAC‑TCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTCCAGTCATAAAGAGTCAGTTTCACGCCAt                                             <  2:78868/139‑1 (MQ=255)                                                                                     gTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGt                                                                                                                                   >  2:329986/1‑54 (MQ=255)                                                                                     gTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGt                                                                                                                                   <  1:329986/54‑1 (MQ=255)                                                                                     gTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCAc                                                                              <  1:528020/106‑1 (MQ=255)                                                                                     gTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCAc                                                                              >  2:528020/1‑106 (MQ=255)                                                                                          cTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCg                                                                                                                     <  2:343247/62‑1 (MQ=255)                                                                                          cTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCg                                                                                                                     >  1:343247/1‑62 (MQ=255)                                                                                          cTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTCCAGTCATAAAGAGTCAGTTTCACg                                                 <  1:109528/130‑1 (MQ=255)                                                                                          cTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTCCAGTCATAAAGAGTCAGTTTCACg                                                 >  2:109528/1‑130 (MQ=255)                                                                                          cTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTCCAGTCATAAAGAGTCAGTTTCACGCCATCcaca                                        >  2:368971/1‑139 (MQ=255)                                                                                             acacTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCa                                                                               <  1:1330931/97‑1 (MQ=255)                                                                                             acacTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCa                                                                               >  2:1330931/1‑97 (MQ=255)                                                                                                   ccTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCGccc                                                                                                                             <  2:1184607/46‑1 (MQ=255)                                                                                                   ccTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCGccc                                                                                                                             >  1:1184607/1‑46 (MQ=255)                                                                                                       ttatcttatTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTCCAGTCATAAAGAGTCAGTTTCACGCCATCCACAACGCGCAGCcaca                           >  1:709151/1‑139 (MQ=255)                                                                                                           cttatTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACACGCCGCAAAGCGCAATCAACGCACCCGTCCAGTCATAAAGAGTCAGTTTCACGCCATCCACAACGCGCAGCCACATCaa                       >  2:981105/1‑139 (MQ=255)                                                                                                             tatTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTCCAGTCATAAAGAGTCAGTTTCACGCCATCCACAACGCGCAGCCACATCAACg                     >  1:1476906/1‑139 (MQ=255)                                                                                                              atTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGcaa                                                                                                                  >  2:200602/1‑45 (MQ=255)                                                                                                              atTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGcaa                                                                                                                  <  1:200602/45‑1 (MQ=255)                                                                                                              atTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTCCAGTCATAAAGAGTCAGTTTCACGCCATCCACAACGCGCAGCCACATCAACGc                    >  1:499693/1‑139 (MQ=255)                                                                                                               ttGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTCCAGTCATAAAGAGTCAGTTTCACGCCATCCACAACGCGCAGCCACATCAACg                     >  2:666738/1‑137 (MQ=255)                                                                                                               ttGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTCCAGTCATAAAGAGTCAGTTTCACGCCATCCACAACGCGCAGCCACATCAACg                     <  1:666738/137‑1 (MQ=255)                                                                                                               ttGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTCCAGTCAT‑AAGAGTCAGTTTCACGCCATCCACAACGCGCAGCCACATCAACGCCg                  >  2:396706/1‑139 (MQ=255)                                                                                                                    aaaaTGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTCCAGTCATAAAGAGTCAGTTTCACGCCATCCACAACGCGCAGCCACATCAACGCCGTGCa              >  1:557766/1‑139 (MQ=255)                                                                                                                            tttATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTCCAGTCATAAAGAGTCAGTTTCACGCCATCCACAACGCGCAGCCACATCAACGCCGTGCAGACATaaa      >  1:680835/1‑139 (MQ=255)                                                                                                                              tATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTCCAGTCATAAAGAGTCAGTTTCACGGCATCCACAACGCGCAGCCACATCAACGCCGTGCAGACATAAACg    <  2:1174733/139‑1 (MQ=255)                                                                                                                               aTGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTCCAGTCATAAAGAGTCAGTTTCACGCCATCCACAACGCGCAGCCACATCAACGCCGTGCAGACATAAACGc   <  1:367229/139‑1 (MQ=255)                                                                                                                                tGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTCCAGTCATAAAGAGTCAGTTTCACGCCATCCACAACGCGCAGCCACATCAACGCCGTGCAGACATAAACGcc  >  2:679271/1‑139 (MQ=255)                                                                                                                                     |                                                                                                                                       ATCGAAAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGAATACCTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCCTACGTGCGCCCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTCCAGTCATAAAGAGTCAGTTTCACGCCATCCACAACGCGCAGCCACATCAACGCCGTGCAGACATAAACGCC  >  NC_000913/1655215‑1655481

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑