Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	115,661	T→C	M22V (ATG→GTG)	hofC ←	assembly protein in type IV pilin biogenesis, transmembrane protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	115,661	0	T	C	100.0%	170.0 / NA	47	M22V (ATG→GTG)	hofC	assembly protein in type IV pilin biogenesis, transmembrane protein
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (24/23);  total (24/23)

GTTGATGAATGACTTCCGCGCTTTTATCTCCTCGCCACTGCGCAGAATTGATGGCGATTCGCTTCAGGCTTAGTGGGGTAACCATCTGTTGCTGTAGTGCCATAAGCAGTAAAGTACGGCTCTCTGCCCATAGCATCCCATCTTGCGCATTGCCGTCGCCGGTTATGCCATGCCAGCGCCAGAGTTGCTTACTCGCCATGCGGCATCCCCAGTACGCGGATTAACTCTTCAAAGGTGGTTAAGCCTTGCTCTACGGCC  >  NC_000913/115526‑115783                                                                                                                                        |                                                                                                                           gTTGATGAATGACTTCCGCGCTTTTATCTCCTCGCCACTGCGCAGAATTGATGGCGATTCGCTTCAGGCTTAGTGGGGTAACCATCTGTTGCTGTAGTGCCATAAGCAGTAAAGTACGGCTCTCTGCCCATAGCAcccc                                                                                                                         <  2:760575/139‑1 (MQ=255)       gaatgaCTTCCGCGCTTTTATCTCCTCGCCACTGCGCAGAATTGATGGCGATTCGCTTCAGGCTTAGTGGGGTAACCATCTGTTGCTGTAGTGCCATAAGCAGTAAAGTACGGCTCTCTGCCCATAGCACCCCATCTTg                                                                                                                   >  1:827752/1‑139 (MQ=255)                 cgcgCTTTTATCTCCTCGCCACTGCGCAGAATTGATGGCGATTCGCTTCAGGCTTAGTGGGGTAACCATCTGTTGCTGTAGTGCCATAAGCAGTAAAGTACGGCTCTCTGCCCATAGCACCCCATCTTGCGCATTGCCg                                                                                                         >  2:1358418/1‑139 (MQ=255)                    gcTTTTATCTCCTCGCCACTGCGCAGAATTGATGGCGATTCGCTTCAGGCTTAGTGGGGTAACCATCTGTTGCTGTAGTGCCATAAGCAGTAAAGTACGGCTCTCTGCCCATAGCACCCCATCTTGCGCATTGCCGTCg                                                                                                      <  2:587882/139‑1 (MQ=255)                                         cgcAGAATTGATGGCGATTCGCTTCAGGCTTAGTGGGGTAACCATCTGTTGCTGTAGTGCCATAAGCAGTAAAGTACGGCTCTCTGCCCATAGCACCCCATCTTGCGCATTGCCGTCg                                                                                                      <  1:887244/118‑1 (MQ=255)                                         cgcAGAATTGATGGCGATTCGCTTCAGGCTTAGTGGGGTAACCATCTGTTGCTGTAGTGCCATAAGCAGTAAAGTACGGCTCTATGCCCATAGCACCCCATCTTGCGCATTGCCGTCg                                                                                                      >  2:887244/1‑118 (MQ=255)                                                   aTGGCGATTCGCTTCAGGCTTAGTGGGGTAACCATCTGTTGCTGTAGTGCCATAAGCAGTAAAGTACGGCTCTCTGCCCATAGCACCCCATCTTGCGCATTGCCGTCGCCGGTTATGCCATGCCAGCGCCAGAGTTGCt                                                                       >  2:548855/1‑139 (MQ=255)                                                      gCGATTCGCTTCAGGCTTAGTGGGGTAACCATCTGTTGCTGTAGTGCCATATGCAGTAAAGTACGGCTCTCTGCCGATAGCACCCCATCTTACGCATTGCCGCCGCCGGTTATACCATGCCAGCGCCAGAGTTGCTTAc                                                                    <  2:1063766/139‑1 (MQ=255)                                                      gCGATTCGCTTCAGGCTTAGTGGGGTAACCATCTGTTGCTGTAGTGCCATAAGCAGTAAAGTACGGCTCTCTGCCCATAGCACCCCATCTTGCGCATTGCCGTCGCCGGTTATGCCATGCCAGCGCCAGAGTTGCTTAc                                                                    <  1:548855/139‑1 (MQ=255)                                                        gATTCGCTTCAGGCTTAGTGGGGTAACCATCTGTTGCTGTAGTGCCATAAGCAGTAAAGTACGGCTCTCTGCCCATAGCACCCCATCTTGCGCATTGCCGTTGCCGGTTATAGCATGCCAGCGCCAGAGTTGCTTACTc                                                                  >  1:1063766/1‑139 (MQ=255)                                                        gATTCGCTTCAGGCTTAGTGGGGTAACCATCTGTTGCTGTAGTGCCATAAGCAGTAAAGTACGGCTCTCTGCCCATAGCACCCCATCTTGCGCATTGCCGTCGCCGGTTATGCCATGCCAGCGCCAGAGTTGCTTACTc                                                                  >  1:1006388/1‑139 (MQ=255)                                                          ttCGCTTCAGGCTTAGTGGGGTAACCATCTGTTGCTGTAGTGCCATAAGCAGTAAAGTACGGCTCTCTGCCCATAGCAcccc                                                                                                                         >  1:1390246/1‑82 (MQ=255)                                                          ttCGCTTCAGGCTTAGTGGGGTAACCATCTGTTGCTGTAGTGCCATAAGCAGTAAAGTACGGCTCTCTGCCCATAGCAcccc                                                                                                                         <  2:1390246/82‑1 (MQ=255)                                                               ttCAGGCTTAGTGGGGTAACCATCTGTTGCTGTAGTGCCATAAGCAGTAAAGTACGGCTCTCTGCCCATAGCACCCCATCTTGCGCATTGCCGTCGCCGGTTATGCCATGCCAGCGCCAGAGTTGCTTACTCGCCATGc                                                           <  2:827752/139‑1 (MQ=255)                                                                    gCTTAGTGGGGTAACCATCTGTTGCTGTAGTGCCATAAGCAGTAAAGTACGGCTCTCTGCCCATAGCACCCCATCTTGCGCATTGCCGTCGCCGGTTATGCCATGCCAGCGCCAGAGTTGCTTACTCGCCATGCGGCAt                                                      <  1:120177/139‑1 (MQ=255)                                                                              gTAACCATCTGTTGCTGTAGTGCCATAAGCAGTAAAGTACGGCTCTCTGCCCATAGCACCCCATCTTGCGCATTGCCGTCGCCGGTTATGCCATGCCAGCGCCAGAGTTGCTTACTCGCCATGCGGCATCCCCAGTAcg                                            >  1:165367/1‑139 (MQ=255)                                                                                      cTGTTGCTGTAGTGCCATAAGCAGTAAAGTACGGCTCTCTGCCCATAGCACCCCATCTTGCGCATTGCCGTCGCCGGTTATGCCATGCCAGCGCCAGAGTTGCTTACTCGCCATGCGGCATCCCCAGTACGCGGATTaa                                    <  1:1358418/139‑1 (MQ=255)                                                                                      cTGTTGCTGTAGTGCCATAAGCAGTAAAGTACGGCTCTCTGCCCATAGCACCCCATCTTGCGCATTGCCGTCGCCGGTTATGCCATGCCAGCGCCAGAGTTGCTTACTCGCCATGCGGCATCCCCAGTACGCGGATTaa                                    <  2:1006388/139‑1 (MQ=255)                                                                                       tGTTGCTGTAGTGCCATAAGCAGTAAAGTACGGCTCTCTGCCCATAGCACCCCATCTTGCGCATTg                                                                                                            <  1:188109/66‑1 (MQ=255)                                                                                       tGTTGCTGTAGTGCCATAAGCAGTAAAGTACGGCTCTCTGCCCATAGCACCCCATCTTGCGCATTg                                                                                                            >  2:188109/1‑66 (MQ=255)                                                                                       tGTTGCTGTAGTGCCATAAGCAGTAAAGTACGGCTCTCTGCCCATAGCACCCCATCTTGCGCATTGCCGTCGCCGGTTATGCCATGCCAGCGCCAGAGTTGCTTACTCGCCATGCGGCATCCCCAGTACGCGGATTAAc                                   >  1:660607/1‑139 (MQ=255)                                                                                           acTGTAGTGCCATAAGCAGTAAAGTACGGCTCTCTGCCCATAGCACCCCATCTTGCGCATTGCCGTCg                                                                                                      >  2:306594/2‑68 (MQ=255)                                                                                           acTGTAGTGCCATAAGCAGTAAAGTACGGCTCTCTGCCCATAGCACCCCATCTTGCGCATTGCCGTCg                                                                                                      <  1:306594/67‑1 (MQ=255)                                                                                                    ccATAAGCAGTAAAGTACGGCTCTCTGCCCATAGCACCCCATCTTGCGCATTGCCGTCGCCGGTTATGCCATGCCAgcgc                                                                                 >  1:815740/1‑80 (MQ=255)                                                                                                    ccATAAGCAGTAAAGTACGGCTCTCTGCCCATAGCACCCCATCTTGCGCATTGCCGTCGCCGGTTATGCCATGCCAgcgc                                                                                 <  2:815740/80‑1 (MQ=255)                                                                                                       tAAGCAGTAAAGTACGGCTCTCTGCCCATAGCACCCCATCTTGCGCATTGCCGTCGCCGGt                                                                                                 >  1:1498315/1‑61 (MQ=255)                                                                                                       tAAGCAGTAAAGTACGGCTCTCTGCCCATAGCACCCCATCTTGCGCATTGCCGTCGCCGGt                                                                                                 <  2:1498315/61‑1 (MQ=255)                                                                                                         aGCAGTAAAGTACGGCTCTCTGCCCATAGCACCCCATCTTGCGCATTGCCGTCGCCGGTTATGCCATGCCAGCGCCAGAGTTGCTTACTCGCCATGCGGCATCCCCAGTACGCGGAtt                                      >  2:834320/1‑118 (MQ=255)                                                                                                         aGCAGTAAAGTACGGCTCTCTGCCCATAGCACCCCATCTTGCGCATTGCCGTCGCCGGTTATGCCATGCCAGCGCCAGAGTTGCTTACTCGCCATGCGGCATCCCCAGTACGCGGAtt                                      <  1:834320/118‑1 (MQ=255)                                                                                                              tAAAGTACGGCTCTCTGCCCATAGCACCCCATCTTGCGCATTGCCGTCGCCGGt                                                                                                 <  2:1041146/54‑1 (MQ=255)                                                                                                              tAAAGTACGGCTCTCTGCCCATAGCACCCCATCTTGCGCATTGCCGTCGCCGGt                                                                                                 >  1:1041146/1‑54 (MQ=255)                                                                                                              tAAAGTACGGCTCTCTGCCCATAGCACCCCATCTTGCGCATTGCCGTCGCCGGTTatgccatgc                                                                                       >  2:1670221/1‑64 (MQ=255)                                                                                                              tAAAGTACGGCTCTCTGCCCATAGCACCCCATCTTGCGCATTGCCGTCGCCGGTTatgccatgc                                                                                       <  1:1670221/64‑1 (MQ=255)                                                                                                              tAAAGTACGGCTCTCTGCCCATAGCACCCCATCTTGCGCATTGCCGTCGCCGGTTATGCCATGCCAGCGCCAGAGTTGCTTACTCGCCAt                                                             >  2:1525832/1‑90 (MQ=255)                                                                                                              tAAAGTACGGCTCTCTGCCCATAGCACCCCATCTTGCGCATTGCCGTCGCCGGTTATGCCATGCCAGCGCCAGAGTTGCTTACTCGCCAt                                                             <  1:1525832/90‑1 (MQ=255)                                                                                                              tAAAGTACGGCTCTCTGCCCATAGCACCCCATCTTGCGCATTGCCGTCGCCGGTTATGCCATGCCAGCGCCAGAGTTGCTTACTCGCCATGCGGCATCCCCAGTACGCGGATTAACTCTTCAAAg                          >  1:790542/1‑125 (MQ=255)                                                                                                              tAAAGTACGGCTCTCTGCCCATAGCACCCCATCTTGCGCATTGCCGTCGCCGGTTATGCCATGCCAGCGCCAGAGTTGCTTACTCGCCATGCGGCATCCCCAGTACGCGGATTAACTCTTCAAAg                          <  2:790542/125‑1 (MQ=255)                                                                                                                   tACGGCTCTCTGCCCATAGCACCCCATCTTGCGCATTGCCGt                                                                                                        <  2:1309077/42‑1 (MQ=255)                                                                                                                   tACGGCTCTCTGCCCATAGCACCCCATCTTGCGCATTGCCGt                                                                                                        >  1:1309077/1‑42 (MQ=255)                                                                                                                   tACGGCTCTCTGCCCATAGCACCCCATCTTGCGCATTGCCGTCg                                                                                                      >  2:513324/1‑44 (MQ=255)                                                                                                                   tACGGCTCTCTGCCCATAGCACCCCATCTTGCGCATTGCCGTCg                                                                                                      <  1:513324/44‑1 (MQ=255)                                                                                                                        ctctctGCCCATAGCACCCCATCTTGCGCATTGCCGTCGCCGGTTATGCCATGCTAGCGCCa                                                                               <  1:1095845/62‑1 (MQ=255)                                                                                                                        ctctctGCCCATAGCACCCCATCTTGCGCATTGCCGTCGCCGGTTATGCCATGCCAGCGCCa                                                                               >  2:1095845/1‑62 (MQ=255)                                                                                                                        ctctctGCCCATAGCACCCCATCTTGCGCATTGCCGTCGCCGGTTATGCCATGCCAGCGCCa                                                                               <  2:667685/62‑1 (MQ=255)                                                                                                                        ctctctGCCCATAGCACCCCATCTTGCGCATTGCCGTCGCCGGTTATGCCATGCCAGCGCCa                                                                               >  1:667685/1‑62 (MQ=255)                                                                                                                        ctctctGCCCATAGCACCCCATCTTGCGCATTGCCGTCGCCGGTTATGCCATGCCAGCGCCAGAGTTGCTTACTCGCCATGCGGCATCCCCAGTACGCGGATTaa                                    <  2:305338/105‑1 (MQ=255)                                                                                                                        ctctctGCCCATAGCACCCCATCTTGCGCATTGCCGTCGCCGGTTATGCCATGCCAGCGCCAGAGTTGCTTACTCGCCATGCGGCATCCCCAGTACGCGGATTaa                                    >  1:305338/1‑105 (MQ=255)                                                                                                                        ctctctGCCCATAGCACCCCATCTTGCGCATTGCCGTCGCCGGTTATGCCATGCCAGCGCCAGAGTTGCTTACTCGCCATGCGGCATCCCCAGTACGCGGATTAACTCTTCAAAGGTGGTTAAGCCTTGCTCTACGGcc  >  1:298465/1‑139 (MQ=255)                                                                                                                             tGCCCATAGCACCCCATCTTGCGCATTGCCGTCGCCGGt                                                                                                 >  2:500585/1‑39 (MQ=38)                                                                                                                             tGCCCATAGCACCCCATCTTGCGCATTGCCGTCGCCGGt                                                                                                 <  1:500585/39‑1 (MQ=38)                                                                                                                                        |                                                                                                                           GTTGATGAATGACTTCCGCGCTTTTATCTCCTCGCCACTGCGCAGAATTGATGGCGATTCGCTTCAGGCTTAGTGGGGTAACCATCTGTTGCTGTAGTGCCATAAGCAGTAAAGTACGGCTCTCTGCCCATAGCATCCCATCTTGCGCATTGCCGTCGCCGGTTATGCCATGCCAGCGCCAGAGTTGCTTACTCGCCATGCGGCATCCCCAGTACGCGGATTAACTCTTCAAAGGTGGTTAAGCCTTGCTCTACGGCC  >  NC_000913/115526‑115783

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑