Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,392,890	G→A	*300* (TAG→TAA)	pgrR →	murein peptide degradation regulator

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,392,890	0	G	A	100.0%	126.4 / NA	40	*300* (TAG→TAA)	pgrR	murein peptide degradation regulator
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (21/19);  total (21/19)

AAAAACTGATACGTGTTTTGGATAAATTCACACCAGATTTACCCGGTTATCACCTGTACTATCCACACCGTCGACATGCTGGCTCGGCATTCTCATTATTTATAGATAGGCTGAAGTATAAAGGTGCTGTTTAGCACTACTTGCTGATACATTAATTTAATTCTTCTCTTAACGTATTCTCAGTTCCTTTCAACGTTTTGGTCATTTTTTATTCTTCGTACAATGGCGACAGATGCTGATTATGATACCGAAAACGGGTTTGAAC  >  NC_000913/1392757‑1393021                                                                                                                                      |                                                                                                                                    aaaaaCTGATACGTGTTTTGGATAAATTCACACCAGATTTACCCGGTTATCACCTGTACTATCCACACCGTCGACATGCTGGCTCGGCATTCTCATTATTTATAGATAGGCTGAAGTATAAAGGTGCTGTTTAACacta                                                                                                                                <  2:597484/139‑1 (MQ=255)              tgtTTTGGATAAATTCACACCAGATTTACCCGGTTATCACCTGTACTATCCACACCGTCGACATGCTGGCTCGGCATTCTCATTATTTATAGATAGGCTGAAGTATAAAGGTGCTGTTTAACACTACTTGCTGATACAt                                                                                                                   <  1:748093/139‑1 (MQ=255)                                              gTTATCACCTGTACTATCCACACCGTCGACATGCTGGCTCGGCATTCTCATTATTTATAGATAGGCTGAAGTATAAAGGTGCTGTTTAACACTACTTGCTGATACATTAATTTAATTCTTCTCTTAACGTATTCTCAGt                                                                                   <  1:874768/139‑1 (MQ=255)                                                         tACTATCCACACCGTCGACATGCTGGCTCGGCATTCTCATTATTTATAGATAGGCTGAAGTATAAAGGTGCTGTTTAACACTACTTGCTGATACATTAATTTAATTCTTCTCTTAACGTATTCTCAGTTCCTTTCAACg                                                                        >  2:440581/1‑139 (MQ=255)                                                                cacaCCGTCGACATGCTGGCTCGGCATTCTCATTATTTATAGATAGGCTGAAGTATAAAGGTGCTGTTTAACACTACTTGCTGATACATTAATTTAATTCTTCTCTTAACGTATTCTCAGt                                                                                   <  2:8215/121‑1 (MQ=255)                                                                cacaCCGTCGACATGCTGGCTCGGCATTCTCATTATTTATAGATAGGCTGAAGTATAAAGGTGCTGTTTAACACTACTTGCTGATACATTAATTTAATTCTTCTCTTAACGTATTCTCAGt                                                                                   >  1:8215/1‑121 (MQ=255)                                                                 acacCGTCGACATGCTGGCTCGGCATTCTCATTATTTATAGATAGGCTGAAGTATAAAGGTGCTGTTTAACACTACTTGCTGATACATTAATTTAATTCTTCTCTTAACGTATTCTCAGTTCCTTTCAACGTTTTGGTc                                                                <  1:440581/139‑1 (MQ=255)                                                                 acacCGTCGACATGCTGGCTCGGCATTCTCATTATTTATAGATAGGCTGAAGTATAAAGGTGCTGTTTAACACTACTTGCTGATACATTAATTTAATTCTTCTCTTAACGTATTCTCAGTTCCTTTCAACGTTTTGGTc                                                                <  1:989890/139‑1 (MQ=255)                                                                   acCGTCGACATGCTGGCTCGGCATTCTCATTATTTATAGATAGGCTGAAGTATAAAGGTGCTGTTTAACACTACTTGCTGATACAt                                                                                                                   <  1:439453/86‑1 (MQ=255)                                                                   acCGTCGACATGCTGGCTCGGCATTCTCATTATTTATAGATAGGCTGAAGTATAAAGGTGCTGTTTAACACTACTTGCTGATACAt                                                                                                                   >  2:439453/1‑86 (MQ=255)                                                                     cGTCGACATGCTGGCTCGGCATTCTCATTATTTATAGATAGGCTGAAGTATAAAGGTGCTGTTTAACacta                                                                                                                                >  2:849019/1‑71 (MQ=255)                                                                     cGTCGACATGCTGGCTCGGCATTCTCATTATTTATAGATAGGCTGAAGTATAAAGGTGCTGTTTAACacta                                                                                                                                <  1:849019/71‑1 (MQ=255)                                                                     cGTCGACATGCTGGCTCGGCATTCTCATTATTTATAGATAGGCTGAAGTATAAAGGTGCTGTTTAACACTACTTGCTGATACATTAATTTAATTCTTCTCTTAACGTATTCTCAGTTCCTTTCAACGTTTTGGTCAttt                                                            >  1:894187/1‑139 (MQ=255)                                                                      gTCGACATGCTGGCTCGGCATTCTCATTATTTATAGATAGGCTGAAGTATAAAGGTGCTGTTTAACACTACTTGCTGATACATtaatttaatt                                                                                                         >  2:1031458/1‑93 (MQ=255)                                                                      gTCGACATGCTGGCTCGGCATTCTCATTATTTATAGATAGGCTGAAGTATAAAGGTGCTGTTTAACACTACTTGCTGATACATtaatttaatt                                                                                                         <  1:1031458/93‑1 (MQ=255)                                                                        cGACATGCTGGCTCGGCATTCTCATTATTTATAGATAGGCTGAAGTATAAAGGTGCTGTTTAACACTACTTGCTGATACATTAATTTAATTCTTCTCTTAACGTATTCTCAGTTCCTTTCAACGTTTTGGTCAtttttt                                                         <  1:443671/139‑1 (MQ=255)                                                                        cGACATGCTGGCTCGGCATTCTCATTATTTATAGATAGGCTGAAGTATAAAGGTGCTGTTTAACACTACTTGCTGATACATTAATTTAATTCTTCTCTTAACGTATTCTCAGTTCCTTTCAACGTTTTGGTCAtttttt                                                         >  2:443671/1‑139 (MQ=255)                                                                               cTGGCTCGGCATTCTCATTATTTATAGATAGGCTGAAGTATAAAGGTGCTGTTTAACACTACTTGCTGATACATTAATTTAAttcttc                                                                                                     <  1:365413/88‑1 (MQ=255)                                                                               cTGGCTCGGCATTCTCATTATTTATAGATAGGCTGAAGTATAAAGGTGCTGTTTAACACTACTTGCTGATACATTAATTTAAttcttc                                                                                                     >  2:365413/1‑88 (MQ=255)                                                                               cTGGCTCGGCATTCTCATTATTTATAGATAGGCTGAAGTATAAAGGTGCTGTTTAACACTACTTGCTGATACATTAATTTAATTCTTCTCTTAACGTATTCTCAGTTCCTTTCAACGTTTTGGTc                                                                >  1:233792/1‑125 (MQ=255)                                                                               cTGGCTCGGCATTCTCATTATTTATAGATAGGCTGAAGTATAAAGGTGCTGTTTAACACTACTTGCTGATACATTAATTTAATTCTTCTCTTAACGTATTCTCAGTTCCTTTCAACGTTTTGGTc                                                                <  2:233792/125‑1 (MQ=255)                                                                                 ggCTCGGCATTCTCATTATTTATAGATAGGCTGAAGTATAAAGGTGCTGTTTAACACTACTTGCTGATACATTAATTTAATTCTTCTCTTAACGTATTCTCAGTTCCTTTCAACGTTTTGGTCATTTTTTATTCTTCGt                                                >  1:1001848/1‑139 (MQ=255)                                                                                                   tttatAGATAGGCTGAAGTATAAAGGTGCTGTTTAACACTACTTGCTGATACATTAATTTAATTCTTCTCTTAACGTATTCTCAGTTCCTTTCAACGTTTTGGTCATTTTTTATTCTTCGTACCATGGCGACAGATGCt                              <  2:744343/139‑1 (MQ=255)                                                                                                           tagGCTGAAGTATAAAGGTGCTGTTTAACACTACTTGCTGATACATTAATTTAATTCTTCTCTTAACGTATTCTCAGTTCCTTTCAACGTTTTGGTCATTTTTTATTCTTCGTACAATGGCGACAGATGCTGATTATGa                      >  2:1079783/1‑139 (MQ=255)                                                                                                             ggCTGAAGTATAAAGGTGCTGTTTAACACTACTTGCTGATACATTAATTTAATTCTTCTCTTAACGTATTCTCAGTTCCTTTCAACGTTTTGGTCATTTTTTATTCTTCGTACAATg                                          >  2:590811/1‑117 (MQ=255)                                                                                                             ggCTGAAGTATAAAGGTGCTGTTTAACACTACTTGCTGATACATTAATTTAATTCTTCTCTTAACGTATTCTCAGTTCCTTTCAACGTTTTGGTCATTTTTTATTCTTCGTACAATg                                          <  1:590811/117‑1 (MQ=255)                                                                                                             ggCTGAAGTATAAAGGTGCTGTTTAACACTACTTGCTGATACATTAATTTAATTCTTCTCTTAACGTATTCTCAGTTCCTTTCAACGTTTTGGTCATTTTTTATTCTTCGTACAATGGCGACAGATGCTGATTATGATa                    >  2:882254/1‑139 (MQ=255)                                                                                                             ggCTGAAGTATAAAGGTGCTGTTTAACACTACTTGCTGATACATTAATTTAATTCTTCTCTTAACGTATTCTCAGTTCCTTTCAACGTTTTGGTCATTTTTTATTCTTCGTACAATGGCGACAGATGCTGATTATGATa                    >  1:49319/1‑139 (MQ=255)                                                                                                              gCTGAAGTATAAAGGTGCTGTTTAACACTACTTGCTGATACATTAATTTAATTCTTCTCTTAACGTATTCTCAGTTCCTTTCAACGTTTTGGTc                                                                >  2:1030143/1‑94 (MQ=255)                                                                                                              gCTGAAGTATAAAGGTGCTGTTTAACACTACTTGCTGATACATTAATTTAATTCTTCTCTTAACGTATTCTCAGTTCCTTTCAACGTTTTGGTc                                                                <  1:1030143/94‑1 (MQ=255)                                                                                                                              gCTGTTTAACACTACTTGCTGATACATTAATTTAATTCTTCTCTTAACGTATTCTCAGTTCCTTTCAACGTTTTGGTCATTTTTTATTCTTCGTACAATGGCGACAGATGCTGATTATGATACCGAAAACGGGTTTGaa   <  1:882254/139‑1 (MQ=255)                                                                                                                               cTGTTTAACACTACTTGCTGTTACATTAAGTTAATTCTTCTCTTAACGTATTCTCAGTTCCTTTCa                                                                           >  2:653346/1‑66 (MQ=255)                                                                                                                               cTGTTTAACACTACTTGCTGATACATTAATTTAATTCTTCTCTTAACGTATTCTCAGTTCCTTTCa                                                                           <  1:653346/66‑1 (MQ=255)                                                                                                                               cTGTTTAACACTACTTGCTGATACATTAATTTAATTCTTCTCTTAACGTATTCTCAGTTCCTTTCAACGTTTTGGTCATTTTTTATTCTTCGTACAATGGCGACAGATg                                <  2:188858/109‑1 (MQ=255)                                                                                                                               cTGTTTAACACTACTTGCTGATACATTAATTTAATTCTTCTCTTAACGTATTCTCAGTTCCTTTCAACGTTTTGGTCATTTTTTATTCTTCGTACAATGGCGACAGATg                                >  1:188858/1‑109 (MQ=255)                                                                                                                               cTGTTTAACACTACTTGCTGATACATTAATTTAATTCTTCTCTTAACGTATTCTCAGTTCCTTTCAACGTTTTGGTCATTTTTTATTCTTCGTACAATGGCGACAGATGCt                              >  2:11654/1‑111 (MQ=255)                                                                                                                               cTGTTTAACACTACTTGCTGATACATTAATTTAATTCTTCTCTTAACGTATTCTCAGTTCCTTTCAACGTTTTGGTCATTTTTTATTCTTCGTACAATGGCGACAGATGCt                              <  1:11654/111‑1 (MQ=255)                                                                                                                               cTGTTTAACACTACTTGCTGATACATTAATTTAATTCTTCTCTTAACGTATTCTCAGTTCCTTTCAACGTTTTGGTCATTTTTTATTCTTCGTACAATGGCGACAGATGCTGATTATGATACCGAAAACGGGTTTGAAc  >  2:338909/1‑139 (MQ=255)                                                                                                                               cTGTTTAACACTACTTGCTGATACATTAATTTAATTCTTCTCTTAACGTATTCTCAGTTCCTTTCAACGTTTTGGTCATTTTTTATTCTTCGTACAATGGCGACAGATGCTGATTATGATACCGAAAACGGGTTTGAAc  >  2:366057/1‑139 (MQ=255)                                                                                                                               cTGTTTAACACTACTTGCTGATACATTAATTTAATTCTTCTCTTAACGTATTCTCAGTTCCTTTCAACGTTTTGGTCATTTTTTATTCTTCGTACAATGGCGACAGATGCTGATTATGATACCGAAAACGGGTTTGAAc  >  1:436818/1‑139 (MQ=255)                                                                                                                                      |                                                                                                                                    AAAAACTGATACGTGTTTTGGATAAATTCACACCAGATTTACCCGGTTATCACCTGTACTATCCACACCGTCGACATGCTGGCTCGGCATTCTCATTATTTATAGATAGGCTGAAGTATAAAGGTGCTGTTTAGCACTACTTGCTGATACATTAATTTAATTCTTCTCTTAACGTATTCTCAGTTCCTTTCAACGTTTTGGTCATTTTTTATTCTTCGTACAATGGCGACAGATGCTGATTATGATACCGAAAACGGGTTTGAAC  >  NC_000913/1392757‑1393021

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑