Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,655,360	(C)5→4	coding (314/327 nt)	ynfA ←	UPF0060 family inner membrane protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,655,356	0	C	.	100.0%	178.2 / NA	43	coding (318/327 nt)	ynfA	UPF0060 family inner membrane protein
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base . (23/20);  total (23/20)

AAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGAATACCTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCCTACGTGCGCCCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTCCAGTCATAAAGAGTCAGTTTCACGCCATCCACAACGCGCAGCCACATCAACGCCGTGCAGACATAAACG  >  NC_000913/1655220‑1655479                                                                                                                                         |                                                                                                                            aaaaaGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGAATACCTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCGccc                                                                                                                           >  2:511964/1‑139 (MQ=255)   aaaGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGAATACCTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCGcccca                                                                                                                         <  1:304264/139‑2 (MQ=255)          gAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGAATACCTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGca                                                                                                                 >  2:624611/1‑139 (MQ=255)           aGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGAATACCTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGcaa                                                                                                                <  1:511964/139‑1 (MQ=255)                       aaaaGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGAATACCTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACa                                                                                                    >  1:599926/1‑139 (MQ=255)                        aaaGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGAATACCTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACAt                                                                                                   <  2:599926/139‑1 (MQ=255)                                            tgAATGGTTGACAAAAGATGAAATAGAATACCTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACg                                                                               >  2:74252/1‑139 (MQ=255)                                                    tGACAAAAGATGAAATAGAATACCTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTc                                                                       <  1:74252/139‑1 (MQ=255)                                                     gACAAAAGATGAAATAGAATACCTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTcc                                                                      >  1:991565/1‑139 (MQ=255)                                                      aCAAAAGATGAAATAGAATACCTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCGcccca                                                                                                                         <  1:1104203/88‑2 (MQ=255)                                                      aCAAAAGATGAAATAGAATACCTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCGcccca                                                                                                                         >  2:1104203/1‑87 (MQ=255)                                                      aCAAAAGATGAAATAGAATACCTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTCCa                                                                     >  1:167081/1‑139 (MQ=255)                                                        aaaaGATGAAATAGAATACCTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTCCAGt                                                                   <  2:991565/139‑1 (MQ=255)                                                                             tttGTCAGCTGACACTTCCTCTTATCATATTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTCCAGTCATAAAGAGTCAGTTTCACGc                                              >  1:1337130/1‑139 (MQ=255)                                                                               tGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTCCAGTCAt                                                                <  1:1267687/119‑1 (MQ=255)                                                                               tGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTCCAGTCAt                                                                >  2:1267687/1‑119 (MQ=255)                                                                               tGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTCCAGTCATAAAGAGTCAGTTTCACGCCa                                            >  1:907285/1‑139 (MQ=255)                                                                                gTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAAc                                                                                                     >  1:20543/1‑81 (MQ=255)                                                                                gTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAAc                                                                                                     <  2:20543/81‑1 (MQ=255)                                                                                           cTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCATCCAGTCATAAAGAGCCAGTTTCACGCCATCCACAACgcgc                                >  1:1068159/1‑139 (MQ=255)                                                                                            ttCCTCTTATCTTATTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTCCAGTCATAAAGAGTCAGTTTCACGCCATCCACAACGCGCa                               <  2:167081/139‑1 (MQ=255)                                                                                                    atcttatTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTCCAGTCATAAAGAGTCAGTTTCACGCCATCCACAACGCGCAGc                             <  2:527838/133‑1 (MQ=255)                                                                                                    atcttatTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTCCAGTCATAAAGAGTCAGTTTCACGCCATCCACAACGCGCAGc                             >  1:527838/1‑133 (MQ=255)                                                                                                        tatTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGc                                                                                              <  1:656057/64‑1 (MQ=255)                                                                                                        tatTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGc                                                                                              >  2:656057/1‑64 (MQ=255)                                                                                                        tatTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTCCAGTCATAAAGAGTCAGTTTCACGCCATCCACAACGCGCAGCCACATCAACg                   <  2:907285/139‑1 (MQ=255)                                                                                                         atTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGcaaca                                                                                                              <  1:735424/47‑1 (MQ=255)                                                                                                         atTGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGcaaca                                                                                                              >  2:735424/1‑47 (MQ=255)                                                                                                          ttGATAAAATGGATTTATGTTCTTACGTGCGcccca                                                                                                                         <  2:372940/36‑2 (MQ=255)                                                                                                          ttGATAAAATGGATTTATGTTCTTACGTGCGcccca                                                                                                                         >  1:372940/1‑35 (MQ=255)                                                                                                          ttGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGcaa                                                                                                                <  1:254708/44‑1 (MQ=255)                                                                                                          ttGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGcaa                                                                                                                >  2:254708/1‑44 (MQ=255)                                                                                                          ttGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTc                                                                       >  1:441900/1‑85 (MQ=255)                                                                                                          ttGATAAAATGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTc                                                                       <  2:441900/85‑1 (MQ=255)                                                                                                               aaaaTGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACAt                                                                                                   >  1:326485/1‑52 (MQ=255)                                                                                                               aaaaTGGATTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACAt                                                                                                   <  2:326485/52‑1 (MQ=255)                                                                                                                      aTTTATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTCCAGTCATAAAGAGTCAGTTTCACGCCATCCACAACGCGCAGCCACATCAACGCCGTGCAGACATaa     >  1:1047012/1‑139 (MQ=255)                                                                                                                        ttATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTCCAGTCATAAAGAGTCAGTTTCACGCCATCCACAACGCGCAGCCACATCAACGCCGTGCAGACATAAAc   >  1:535077/1‑139 (MQ=255)                                                                                                                         tATGTTCTTACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTCCAGTCATAAAGAGTCAGTTTCACGCCATCCACAACGCGCAGCCACATCAACGCCGTGCAGACATAAACg  <  2:535077/139‑1 (MQ=255)                                                                                                                               cttACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCa                                                                             <  2:818203/56‑1 (MQ=255)                                                                                                                               cttACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCa                                                                             >  1:818203/3‑58 (MQ=255)                                                                                                                               cttACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCAc                                                                            <  2:535310/57‑1 (MQ=255)                                                                                                                               cttACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCAc                                                                            >  1:535310/3‑59 (MQ=255)                                                                                                                               cttACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTCCa                                                                     <  2:1339535/64‑1 (MQ=255)                                                                                                                               cttACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTCCa                                                                     >  1:1339535/3‑66 (MQ=255)                                                                                                                               cttACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTCCAGTCATAAAGAGTCAGTTTCACGCCATCCACAAcgc                                  <  2:844405/99‑1 (MQ=255)                                                                                                                               cttACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTCCAGTCATAAAGAGTCAGTTTCACGCCATCCACAACGCGCAGCCACATCAACGCCGTGCa            <  1:991312/121‑1 (MQ=255)                                                                                                                               cttACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTCCAGTCATAAAGAGTCAGTTTCACGCCATCCACAACGCGCAGCCACATCAACGCCGTGCa            >  2:991312/3‑123 (MQ=255)                                                                                                                               cttACGTGCG‑CCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATAAACGCACCCGTCCAGTCATAAAGAGTCAGTTTCACGCCATCCACAAcgc                                  >  1:844405/3‑101 (MQ=255)                                                                                                                                         |                                                                                                                            AAAAAGCCGGAGTGATCACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAAAAGATGAAATAGAATACCTTTTGTCAGCTGACACTTCCTCTTATCTTATTGATAAAATGGATTTATGTTCCTACGTGCGCCCCCAGCCCGCAACAATGATCAACATGCCGCAAAGCGCAATCAACGCACCCGTCCAGTCATAAAGAGTCAGTTTCACGCCATCCACAACGCGCAGCCACATCAACGCCGTGCAGACATAAACG  >  NC_000913/1655220‑1655479

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: ‑