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%	140.7 / NA	44	*300* (TAG→TAA)	pgrR	murein peptide degradation regulator
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (23/21);  total (23/21)

CCCGGTTATCACCTGTACTATCCACACCGTCGACATGCTGGCTCGGCATTCTCATTATTTATAGATAGGCTGAAGTATAAAGGTGCTGTTTAGCACTACTTGCTGATACATTAATTTAATTCTTCTCTTAACGTATTCTCAGTTCCTTTCAACGTTTTGGTCATTTTTTATTCTTCGTACAATGGCGACAGATGCTGATTATGATACCGAAAACGGGTTTGAAC  >  NC_000913/1392798‑1393021                                                                                             |                                                                                                                                    cccGGTTATCACCTGTACTATCCACACCGTCGACATGCTGGCTCGGCATTCTCATTATTTATAGATAGGCTGAAGTATAAAGGTGCTGTTTAACACTACTTGCTGATACATTAATTTAATTCTTCTCtt                                                                                                 >  1:1203271/1‑129 (MQ=255) cccGGTTATCACCTGTACTATCCACACCGTCGACATGCTGGCTCGGCATTCTCATTATTTATAGATAGGCTGAAGTATAAAGGTGCTGTTTAACACTACTTGCTGATACATTAATTTAATTCTTCTCtt                                                                                                 <  2:1203271/129‑1 (MQ=255)                tACTATCCACACCGTCGACATGCTGGCTCGGCATTCTCATTATTTATAGATAGGCTGAAGTATAAAGGTGCTGTTTAACACTACTTGCTGATACATTAATTTAAttctt                                                                                                      >  2:644045/1‑109 (MQ=255)                tACTATCCACACCGTCGACATGCTGGCTCGGCATTCTCATTATTTATAGATAGGCTGAAGTATAAAGGTGCTGTTTAACACTACTTGCTGATACATTAATTTAAttctt                                                                                                      <  1:644045/109‑1 (MQ=255)                tACTATCCACACCGTCGACATGCTGGCTCGGCATTCTCATTATTTATAGATAGGCTGAAGTATAAAGGTGCTGTTTAACACTACTTGCTGATACATTAATTTAAttc                                                                                                        >  1:411937/1‑107 (MQ=255)                tACTATCCACACCGTCGACATGCTGGCTCGGCATTCTCATTATTTATAGATAGGCTGAAGTATAAAGGTGCTGTTTAACACTACTTGCTGATACATTAATTTAAttc                                                                                                        <  2:411937/107‑1 (MQ=255)                          acCGTCGACATGCTGGCTCGGCATTCTCATTATTTATAGATAGGCTGAAGTATAAAGGTGCTGTTTAACACTACTTGCTGATACATTAATTTAATTCTTCTCTTAACGTATTCTCAGTTCCTTTCAACGTTTTGGTCAt                                                              >  1:113496/1‑139 (MQ=255)                            cGTCGACATGCTGGCTCGGCATTCTCATTATTTATAGATAGGCTGAAGTATAAAGGTGCTGTATAACACTACTTGCTGATACATTAATTTAATTCTTCTCTTAACGTATTCTCAGTTCCTTTCAACGTTTAGGTCAttt                                                            >  1:800011/1‑139 (MQ=255)                               cGACATGCTGGCTCGGCATTCTCATTATTTATAGATAGGCTGAAGTATAAAGGTGCTGTTTAACACTACTTGCTGATACAttaatttaa                                                                                                           <  2:1022389/89‑1 (MQ=255)                               cGACATGCTGGCTCGGCATTCTCATTATTTATAGATAGGCTGAAGTATAAAGGTGCTGTTTAACACTACTTGCTGATACAttaatttaa                                                                                                           >  1:1022389/1‑89 (MQ=255)                               cGACATGCTGGCTCGGCATTCTCATTATTTATAGATAGGCTGAAGTATAAAGGTGCTGTTTAACACTACTTGCTGATACATTAATTTAATTCTTCTCTTAACGTATTCTCAGTTCCTTTCAACGTTTTGGTCAtttttt                                                         >  1:1089120/1‑139 (MQ=255)                                 aCATGCTGGCTCGGCATTCTCATTATTTATAGATAGGCTGAAGTATAAAGGTGCTGTTTAACACTACTTGCTGATACATTAATTTAATTCTTCTCTTAACGTATTCTCAGTTCCTTTCAACGTTTTGGTCATTTTTTAt                                                       <  2:113496/139‑1 (MQ=255)                                         gCTCGGCATTCTCATTATTTATAGATAGGCTGAAGTATAAAGGTGCTGTTTAACACTACTTGCTGATACATTAATTTAATTCTTCTCTTAACGTATTCTCAGTTCCTTTCAACGTTTTGGTCAtttttt                                                         >  2:126926/1‑129 (MQ=255)                                         gCTCGGCATTCTCATTATTTATAGATAGGCTGAAGTATAAAGGTGCTGTTTAACACTACTTGCTGATACATTAATTTAATTCTTCTCTTAACGTATTCTCAGTTCCTTTCAACGTTTTGGTCAtttttt                                                         <  1:126926/129‑1 (MQ=255)                                                        tatttatAGATAGGCTGAAGTATAAAGGTGCTGTTTAACACTACTTGCTGATACATTAATTTAATTCTTCTCTTAACGTATTCTCAGTTCCTTTCAACGTTTTGGTCATTTTTTATTCTTCGTACAATGGCGACAGATg                                <  2:1153111/139‑1 (MQ=255)                                                            tataGATAGGCTGAAGTATAAAGGTGCTGTTTAACACTACTTGCTGATACATTAATTTAATTCTTCTCTTAACGt                                                                                            <  2:330555/75‑1 (MQ=255)                                                            tataGATAGGCTGAAGTATAAAGGTGCTGTTTAACACTACTTGCTGATACATTAATTTAATTCTTCTCTTAACGt                                                                                            >  1:330555/1‑75 (MQ=255)                                                             atagatagGCTGAAGTATAAAGGTGCTGTTTAACACTACTTGCTGATACAt                                                                                                                   <  1:1187605/51‑1 (MQ=255)                                                             atagatagGCTGAAGTATAAAGGTGCTGTTTAACACTACTTGCTGATACAt                                                                                                                   >  2:1187605/1‑51 (MQ=255)                                                              tagatagGCTGAAGTATAAAGGTGCTGTTTAACACTACTTGCTGATACATTAATTTAATTCTTCTCTTAACGTATTCTCAGTTCCTTTCAACGTTTTGGTCATTTTTTATTCTTCGTACa                                             <  1:631740/120‑1 (MQ=255)                                                              tagatagGCTGAAGTATAAAGGTGCTGTTTAACACTACTTGCTGATACATTAATTTAATTCTTCTCTTAACGTATTCTCAGTTCCTTTCAACGTTTTGGTCATTTTTTATTCTTCGTACa                                             >  2:631740/1‑120 (MQ=255)                                                                gatagGCTGAAGTATAAAGGTGCTGTTTAACACTACTTGCTGATACATTAATTTAATTCTTCTCTTAACGTATTCTCAGTTCCTTTCAACGTTTTGGTCATTTTTTAttct                                                    >  2:1264770/1‑111 (MQ=255)                                                                gatagGCTGAAGTATAAAGGTGCTGTTTAACACTACTTGCTGATACATTAATTTAATTCTTCTCTTAACGTATTCTCAGTTCCTTTCAACGTTTTGGTCATTTTTTAttct                                                    <  1:1264770/111‑1 (MQ=255)                                                                  tagGCTGAAGTATAAAGGTGCTGTTTAACACTACTTGCTGATACATTAATTTAATTCTTCTCTTAACGTATTCTCAGTTCCTTTCAACGTTTTGGTCATTTTTTATTCTTCGTACAATGGCGACAGATg                                <  2:1096080/129‑1 (MQ=255)                                                                  tagGCTGAAGTATAAAGGTGCTGTTTAACACTACTTGCTGATACATTAATTTAATTCTTCTCTTAACGTATTCTCAGTTCCTTTCAACGTTTTGGTCATTTTTTATTCTTCGTACAATGGCGACAGATg                                >  1:1096080/1‑129 (MQ=255)                                                                    ggCTGAAGTATAAAGGTGCTGTTTAACACTACTTGCTGATACATTAATTTAAttctt                                                                                                      >  1:792473/1‑57 (MQ=255)                                                                    ggCTGAAGTATAAAGGTGCTGTTTAACACTACTTGCTGATACATTAATTTAAttctt                                                                                                      <  2:792473/57‑1 (MQ=255)                                                                    ggCTGAAGTATAAAGGTGCTGTTTAACACTACTTGCTGATACATTAATTTAATTCTTCTCTTAACGTATTCTCAg                                                                                    >  1:889519/1‑75 (MQ=255)                                                                    ggCTGAAGTATAAAGGTGCTGTTTAACACTACTTGCTGATACATTAATTTAATTCTTCTCTTAACGTATTCTCAGTTCCTTTCAACGTTTTGGTCATTTTTTATTCTTCGTACAATGGCGACAGATGCTGATTATGATa                    >  1:689024/1‑139 (MQ=255)                                                                    ggCTGAAGTATAAAGCTGCTGTTTAACACTACTTGCTGATACATTAATTTAATTCTTCTCTTAACGTATTCTCAg                                                                                    <  2:889519/75‑1 (MQ=255)                                                                     gCTGAAGTATAAAGGTGCTGTTTAACACTACTTGCTGATACATTAATTTAATTCTTCTCtt                                                                                                 >  2:386547/1‑61 (MQ=255)                                                                     gCTGAAGTATAAAGGTGCTGTTTAACACTACTTGCTGATACATTAATTTAATTCTTCTCtt                                                                                                 <  1:386547/61‑1 (MQ=255)                                                                     gCTGAAGTATAAAGGTGCTGTTTAACACTACTTGCTGATACATTAATTTAATTCTTCTCTTAACGTATTCTCAGt                                                                                   <  1:396129/75‑1 (MQ=255)                                                                     gCTGAAGTATAAAGGTGCTGTTTAACACTACTTGCTGATACATTAATTTAATTCTTCTCTTAACGTATTCTCAGt                                                                                   >  2:396129/1‑75 (MQ=255)                                                                     gCTGAAGTATAAAGGTGCTGTTTAACACTACTTGCTGATACATTAATTTAATTCTTCTCTTAACGTATTCTCAGTTCCTTTCAACGTTTTGGTCATTTTTTATTCTTCGTACAATGGc                                        >  1:403832/1‑118 (MQ=255)                                                                     gCTGAAGTATAAAGGTGCTGTTTAACACTACTTGCTGATACATTAATTTAATTCTTCTCTTAACGTATTCTCAGTTCCTTTCAACGTTTTGGTCATTTTTTATTCTTCGTACAATGGc                                        <  2:403832/118‑1 (MQ=255)                                                                            tataAAGGTGCTGTTTAACACTACTTGCTGATACATTAATTTAATTCTTCTCTTAACGTATTCTCAGTTCCTTTCAACGTTTTGGTCATTTTTTATTCTTCGTACAATGGCGACAGATGCTGATTATGATACCGAAAAc            <  2:689024/139‑1 (MQ=255)                                                                               aaaGGTGCTGTTTAACACTACTTGCTGATACATTAATTTAATTCTTCTCTTAACGTATTCTCAGTTCCTTTCAACGTTTTGGTCAtttttt                                                         <  1:533657/91‑1 (MQ=255)                                                                               aaaGGTGCTGTTTAACACTACTTGCTGATACATTAATTTAATTCTTCTCTTAACGTATTCTCAGTTCCTTTCAACGTTTTGGTCAtttttt                                                         >  2:533657/1‑91 (MQ=255)                                                                                      cTGTTTAACACTACTTGCTGATACATTAATTTAAttc                                                                                                        <  2:265687/37‑1 (MQ=255)                                                                                      cTGTTTAACACTACTTGCTGATACATTAATTTAAttc                                                                                                        >  1:265687/1‑37 (MQ=255)                                                                                      cTGTTTAACACTACTTGCTGATACATTAATTTAATTCTTCTCTTaa                                                                                               >  2:1218476/1‑46 (MQ=255)                                                                                      cTGTTTAACACTACTTGCTGATACATTAATTTAATTCTTCTCTTaa                                                                                               <  1:1218476/46‑1 (MQ=255)                                                                                      cTGTTTAACACTACTTGCTGATACATTAATTTAATTCTTCTCTTAACGTATTCTCAGTTCCTTTCAACGTTTTGGTCATTTTTTATTCTTCGTACAATGGCGACAGATGCTGATTATGATACCGAAAACGGGTTTGAAc  >  1:1230867/1‑139 (MQ=255)                                                                                             |                                                                                                                                    CCCGGTTATCACCTGTACTATCCACACCGTCGACATGCTGGCTCGGCATTCTCATTATTTATAGATAGGCTGAAGTATAAAGGTGCTGTTTAGCACTACTTGCTGATACATTAATTTAATTCTTCTCTTAACGTATTCTCAGTTCCTTTCAACGTTTTGGTCATTTTTTATTCTTCGTACAATGGCGACAGATGCTGATTATGATACCGAAAACGGGTTTGAAC  >  NC_000913/1392798‑1393021

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑