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%	103.0 / NA	33	*300* (TAG→TAA)	pgrR	murein peptide degradation regulator
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (18/15);  total (18/15)

AAAAAAAACTGATACGTGTTTTGGATAAATTCACACCAGATTTACCCGGTTATCACCTGTACTATCCACACCGTCGACATGCTGGCTCGGCATTCTCATTATTTATAGATAGGCTGAAGTATAAAGGTGCTGTTTAGCACTACTTGCTGATACATTAATTTAATTCTTCTCTTAACGTATTCTCAGTTCCTTTCAACGTTTTGGTCATTTTTTATTCTTCGTACAATGGCGACAGATGCTGATTATGATACCGAAAACGGGTTTGAACGT  >  NC_000913/1392754‑1393023                                                                                                                                         |                                                                                                                                      aaaaaaaaCTGATACGTGTTTTGGATAAATTCACACCAGATTTACCCGGTTATCACCTGTACTATCCACACCGTCGACATGCTGGCTCGGCATTCTCATTATTTATAGATAGGCTGAAGTATAAAGGTGCTGTTTAACa                                                                                                                                     <  1:1031778/139‑1 (MQ=255)           gATACGTGTTTTGGATAAATTCACACCAGATTTACCCGGTTATCACCTGTACTATCCACACCGTCGACATGCTGGCTCGGCATTCTCATTATTTATAGATAGGCTGAAGTATAAAGGTGCTGTTTAACACTACTTGCTg                                                                                                                           <  2:112341/139‑1 (MQ=255)           gATACGTGTTTTGGATAAATTCACACCAGATTTACCCGGTTATCACCTGTACTATCCACACCGTCGACATGCTGGCTCGGCATTCTCATTATTTATAGATAGGCTGAAGTATAAAGGTGCTGTTTAACACTACTTGCTg                                                                                                                           <  1:801098/139‑1 (MQ=255)                 tgtTTTGGATAAATTCACACCAGATTTACCCGGTTATCACCTGTACTATCCTCACCGTCGACATGCTGGCTCGGCATTCTCATTATTTATAGATAGGCTGAAGTATAAAGGTGCTGTTTAACactact                                                                                                                                <  2:812483/128‑1 (MQ=255)                 tgtTTTGGATAAATTCACACCAGATTTACCCGGTTATCACCTGTACTATCCACACCGTCGACATGCTGGCTCGGCATTCTCATTATTTATAGATAGGCTGAAGTATAAAGGTGCTGTTTAACactact                                                                                                                                >  1:812483/1‑128 (MQ=255)                            aaTTCACACCAGATTTACCCGGTTATCACCTGTACTATCCACACCGTCGACATGCTGGCTCGGCATTCTCATTATTTATAGATAGGCTGAAGTATAAAGGTGCTGTTTAACACTACTTGCTGATACAttaatttaatcc                                                                                                          <  1:645459/139‑3 (MQ=255)                             aTTCACACCAGATTTACCCGGTTATCACCTGTACTATCCACACCGTCGACATGCTGGCTCGGCATTCTCATTATTTATAGATAGGCTGAAGTATAAAGGTGCTGTTTAACACTACTTGCTg                                                                                                                           <  1:514999/121‑1 (MQ=255)                             aTTCACACCAGATTTACCCGGTTATCACCTGTACTATCCACACCGTCGACATGCTGGCTCGGCATTCTCATTATTTATAGATAGGCTGAAGTATAAAGGTGCTGTTTAACACTACTTGCTg                                                                                                                           >  2:514999/1‑121 (MQ=255)                                  cacCAGATTTACCCGGTTATCACCTGTACTATCCACACCGTCGACATGCTGGCTCGGCATTCTCATTATTTATAGATAGGCTGAAGTATAAAGGTGCTGTTTAACACTACTTGCTGATACATTAATTTAATTCTTctct                                                                                                    >  2:564175/1‑139 (MQ=255)                                                  ttATCACCTGTACTATCCACACCGTCGACATGCTGGCGCGGCATTCTCATTATTTATAGATAGGCTGAAGTATAAAGGTGCTGTTTAACACTACTTGCGGATACATTAATTTAATTCTTCTCTTAACGTATTCTCAGtt                                                                                    >  1:758607/1‑139 (MQ=255)                                                                  ccACACCGTCGACATGCTGGCTCGGCATTCTCATTATTTATAGATAGGCTGAAGTATAAAGGTGCTGTTTAACACTACTTGCTGATACATTAATTTAATTCTTCTCTTAACGTATTCTCAGTTCCTTTCAACGTTTTgg                                                                    >  2:390915/1‑139 (MQ=255)                                                                    acacCGTCGACATGCTGGCTCGGCATTCTCATTATTTATAGATAGGCTGAAGTATAAAGGTGCTGTTTAACACTACTTGCTGATACATTAATTTAATTCTTCTCTTAACGTATTCTCAGTTCCTTTCAACGTTTTGGTc                                                                  <  1:390915/139‑1 (MQ=255)                                                                      acCGTCGACATGCTGGCTCGGCATTCTCATTATTTATAGATAGGCTGAAGTATAAAGGTGCTGTTTAACACTACTTGCTGATACATTAATTTAATTCTTCTCTTAACGTATTCTCAGTTCCTTTCAACGTTTTGGTCAt                                                                >  2:724414/1‑139 (MQ=255)                                                                         gTCGACATGCTGGCTCGGCATTCTCATTATTTATAGATAGGCTGAAGTATAAAGGTGCTGTTTAACACTACTTGCTGATACATTAATTTAATTCTTCTCTTAACGTATTCTCAGTTCCTTTCAACGTTTTGGTCAtttt                                                             >  2:21661/1‑139 (MQ=255)                                                                           cGACATGCTGGCTCGGCATTCTCATTATTTATAGATAGGCTGAAGTATAAAGGTGCTGTTTAACACTACTTGCTGATACATTAATTTAATTCTTCTCTTAACGTATtct                                                                                         >  2:553040/1‑109 (MQ=255)                                                                           cGACATGCTGGCTCGGCATTCTCATTATTTATAGATAGGCTGAAGTATAAAGGTGCTGTTTAACACTACTTGCTGATACATTAATTTAATTCTTCTCTTAACGTATtct                                                                                         <  1:553040/109‑1 (MQ=255)                                                                           cGACATGCTGGCTCGGCATTCTCATTATTTATAGATAGGCTGAAGTATAAAGGTGCTGTTTAACACTACTTGCTGATACATTAATTTAATTCTTCTCTTAACGTATTCTCAGTTCCTTTCAACGTTTTGGTCAtttttt                                                           >  1:142181/1‑139 (MQ=255)                                                                                              tctcATTATTTATAGATAGGCTGAAGTATAAAGGTGCTGTTTAACACTACTTGCTGATACATTAATTTAATTCTTCTCTTAACGTATTCTCAGTTCCTTTCAACGTTTTGGTCATTTTTTATTCTTCGTACAATGGCGa                                        <  1:21661/139‑1 (MQ=255)                                                                                               ctcATTATTTATAGATAGGCTGAAGTATAAAGGTGCTGTTTAACACTACTTGCTGATACATTAATTTAATTCTTCTCTTAACGTATTCTCAGTTCCTTTCAACGTTTTGGTCATTTTTTATTCTTCGTACAATGGCGAc                                       <  2:142181/139‑1 (MQ=255)                                                                                                              tagGCTGAAGTATAAAGGTGCTGTTTAACACTACTTGCTGATACATTAATTTAATTCTTCTCTTAACGTATTCTCAGTTCCTTTCAACGTTTTGGTCATTTTTTATTCTTCGTACAATGGCGACAGATGCTGATTATGa                        >  2:944071/1‑139 (MQ=255)                                                                                                                ggCTGAAGTATAAAGGTGCTGTTTAACACTACTTGCTGATACATTAATTTAATTCTTCTCTTAACGTa                                                                                             <  1:546504/68‑1 (MQ=255)                                                                                                                ggCTGAAGTATAAAGGTGCTGTTTAACACTACTTGCTGATACATTAATTTAATTCTTCTCTTAACGTa                                                                                             >  2:546504/1‑68 (MQ=255)                                                                                                                ggCTGAAGTATAAAGGTGCTGTTTAACACTACTTGCTGATACATTAATTTAATTCTTCTCTTAACGTATTCTCAGTTCCTTTCAACGTTTTGGTCATTTTTTATTCTTCGTACAATGGCGACAGATGCTGATTATGATa                      >  1:882645/1‑139 (MQ=255)                                                                                                                 gCTGAAGTATAAAGGTGTTGTTTAACACTACTTGCTGATACATTAATTTAATTCTTCTCTTAACGTATTCTCAGTTCCTTTCAACGTTTTGGTCATTTTTTATTCTTCGTACAATGGCGAc                                       >  2:221452/1‑121 (MQ=255)                                                                                                                 gCTGAAGTATAAAGGTGTTGTTTAACACTACTTGCTGATACATTAATTTAATTCTTCTCTTAACGTATTCTCAGTTCCTTTCAACGTTTTGGTCATTTTTTATTCTTCGTACAATGGCGAc                                       <  1:221452/121‑1 (MQ=255)                                                                                                                 gCTGAAGTATAAAGGTGCTGTTTAACACTACTTGCTGATACATTAATTTAATTCTTCTCTTAACGt                                                                                              <  1:596888/66‑1 (MQ=255)                                                                                                                 gCTGAAGTATAAAGGTGCTGTTTAACACTACTTGCTGATACATTAATTTAATTCTTCTCTTAACGt                                                                                              >  2:596888/1‑66 (MQ=255)                                                                                                                          taAAGGTGCTGTTTAACACTACTTGCTGATACATtaatttaatt                                                                                                           >  2:537957/1‑44 (MQ=255)                                                                                                                          taAAGGTGCTGTTTAACACTACTTGCTGATACATtaatttaatt                                                                                                           <  1:537957/44‑1 (MQ=255)                                                                                                                               gTGCTGTTTAACACTACTTGCTGATACATTAATTTAATTCTTCTCTTAACGTATTCTCAGTTCCTTTCAACGTTTTGGTCATTTTTTATTCTTCGTACAATGGCGACAGATGCTGATTATGATACCGAAAACGGGTTTg       >  2:206323/1‑139 (MQ=255)                                                                                                                                  cTGTTTAACACTACTTGCTGATACATTAATTTAATTCTTCTCTTAACGTATTCTCAGTTCCTTTCAACGTTTTGGTCATTTTTTATTCTTCGTACAATGGCGACAGATg                                  <  2:41305/109‑1 (MQ=255)                                                                                                                                  cTGTTTAACACTACTTGCTGATACATTAATTTAATTCTTCTCTTAACGTATTCTCAGTTCCTTTCAACGTTTTGGTCATTTTTTATTCTTCGTACAATGGCGACAGATg                                  >  1:41305/1‑109 (MQ=255)                                                                                                                                    gTTTAACACTACTTGCTGATACATTAATTTAATTCTTCTCTTAACGTATTCTCAGTTCCTTTCAACGTTTTGGTCATTTTTTATTCTTCGTACAATGGCGACAGATGCTGATTATGATACCGAAAACGGGTTTGAACGt  >  2:133452/1‑139 (MQ=255)                                                                                                                                         |                                                                                                                                      AAAAAAAACTGATACGTGTTTTGGATAAATTCACACCAGATTTACCCGGTTATCACCTGTACTATCCACACCGTCGACATGCTGGCTCGGCATTCTCATTATTTATAGATAGGCTGAAGTATAAAGGTGCTGTTTAGCACTACTTGCTGATACATTAATTTAATTCTTCTCTTAACGTATTCTCAGTTCCTTTCAACGTTTTGGTCATTTTTTATTCTTCGTACAATGGCGACAGATGCTGATTATGATACCGAAAACGGGTTTGAACGT  >  NC_000913/1392754‑1393023

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑