Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,393,269	Δ1 bp	coding (43/1614 nt)	mppA →	murein tripeptide ABC transporter periplasmic binding protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,393,269	0	A	.	100.0%	244.8 / NA	57	coding (43/1614 nt)	mppA	murein tripeptide ABC transporter periplasmic binding protein
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base . (28/29);  total (28/29)

CTTTGTCACTTTTTTGATGGAAGTTGTTTGCATTTCTTTAAGGCGAAACAAATAATTACGCATCAATTTTAATGTCGGTTAGAGGGAAACTTATGAAGCACTCTGTTTCAGTCACGTGTTGTGCGCTGTTGGTCAGCAGCATTTCTCTTTCGTATGCTGCAGAAGTTCCGAGCGGCACAGTACTGGCAGAGAAGCAGGAGCTGGTGCGCCACATTAAAGATGAGCCTGCGTCGCTGGATCCCGCTAAAGCCGTGGGCCTGCCAGAGATT  >  NC_000913/1393135‑1393403                                                                                                                                       |                                                                                                                                       cTTTGTCACTTTTTTGATGGAAGTTGTTTGCATTTCTTTAAGGCGAAACAAATAATTACGCATCAATTTTAATGTCGGTTAGAGGGAAACTTATGAAGCACTCTGTTTCAGTCACGTGTTGTGCGCTGTTGGTC‑gcagca                                                                                                                                  <  1:995864/140‑1 (MQ=255)       cACTTTTTTGATGGAAGTTGTTTGCATTTCTTTAAGGCGAAACAAATAATTACGCATCAATTTTAATGTCGGTTAGAGGGAAACTTATGAAGCACTCTGTTTCAGTCACGTGTTGTGCGCTGTTGGTC‑GCAGCATTtctc                                                                                                                            >  2:37992/1‑140 (MQ=255)          ttttttGATGGAAGTTGTTTGCATTTCTTTAAGGCGAAACAAATAATTACGCATCAATTTTAATGTCGGTTAGAGGGAAACTTATGAAGCACTCTGTTTCAGTCACGTGTTGTGCGCTGTTGGTC‑GCAGCATTTCTCttt                                                                                                                         >  2:884254/1‑140 (MQ=255)                    gAAGTTGTTTGCATTTCTTTAAGGCGAAACAAATAATTACGCATCAATTTTAATGTCGGTTAGAGGGAAACTTATGAAGCACTCTGTTTCAGTCACGTGTTGTGCGCTGTTGGTC‑GCAGCATTTCTCTTTCGTAtgctgc                                                                                                               >  2:641907/1‑140 (MQ=255)                           tttGCATTTCTTTAAGGCGAAACAAATAATTACGCATCAATTTTAATGTCGGTTAGAGGGAAACTTATGAAGCACTCTGTTTCAGTCACGTGTTGTGCGCTGTTGGTC‑GCAGCATTTCTCTTTCGTATGCTGCAGAAGtt                                                                                                        <  1:419150/140‑1 (MQ=255)                                aTTTCTTTAAGGCGAAACAAATAATTACGCATCAATTTTAATGTCGGTTAGAGGGAAACTTATGAAGCACTCTGTTTCAGTCACGTGTTGTGCGCTGTTGGTC‑GCAGCATTTCTCTTTCGTATGCTGCAGAAGTTCCGAg                                                                                                   <  1:783274/140‑1 (MQ=255)                                aTTTCTTTAAGGCGAAACAAATAATTACGCATCAATTTTAATGTCGGTTAGAGGGAAACTTATGAAGCACTCTGTTTCAGTCACGTGTTGTGCGCTGTTGGTC‑GCAGCATTTCTCTTTCGTATGCTGCAGAAGTTCCGAg                                                                                                   <  2:681683/140‑1 (MQ=255)                                aTTTCTTTAAGGCGAAACAAATAATTACGCATCAATTTTAATGTCGGTTAGAGGGAAACTTATGAAGCACTCTGTTTCAGTCACGTGTTGTGCGCTGTTGGTC‑GCAGCATTTCTCTTTCGTATGCTGCAGAAGTTCCGAg                                                                                                   <  1:496049/140‑1 (MQ=255)                                    cTTTAAGGCGAAACAAATAATTACGCATCAATTTTAATGTCGGTTAGAGGGAAACTTATGAAGCACTCTGTTTCAGTCACGTGTTGTGCGCTGTTGGTC‑GCAGCATTTCTCTTTCGTATGCTGCAGAAGTTCCGAGCGGc                                                                                               <  2:214016/140‑1 (MQ=255)                                     tttAAGGCGAAACAAATAATTACGCATCAATTTTAATGTCGGTTAGAGGGAAACTTATGAAGCACTCTGTTTCAGTCACGTGTTGTGCGCTGTTGGTC‑GCAGCATTTCTCTTTCGTATGCTGCAGAAGTTCCGAGCGGca                                                                                              <  2:427926/140‑1 (MQ=255)                                              aaaCAAATAATTACGCATCAATTTTAATGTCGGTTAGAGGGAAACTTATGAAGCACTCTGTTTCAGTCACGTGTTGTGCGCTGTTGGTC‑GCAGCATTTCTCTTTCGTATGCTGCAGAAGTTCCGAg                                                                                                   <  2:569072/126‑1 (MQ=255)                                              aaaCAAATAATTACGCATCAATTTTAATGTCGGTTAGAGGGAAACTTATGAAGCACTCTGTTTCAGTCACGTGTTGTGCGCTGTTGGTC‑GCAGCATTTCTCTTTCGTATGCTGCAGAAGTTCCGAg                                                                                                   >  1:569072/1‑126 (MQ=255)                                               aaCAAATAATTACGCATCAATTTTAATGTCGGTTAGAGGGAAACTTATGAAGCACTCTGTTTCAGTCACGTGTTGTGCGCTGTTGGTC‑GCAGCATTTCTCTTTCGTATGCTGCAGAAGTTCCGAGCGGCACAGTACTGGc                                                                                    >  1:240302/1‑140 (MQ=255)                                                           cGCATCAATTTTAATGTCGGTTAGAGGGAAACTTATGAAGCACTCTGTTTCAGTCACGTGTTGTGCGCTGTTGGTC‑GCAGCATTTCTCTTTCGTATGCTGCAGAAGTTCCGAGCGGCACAGTACTGGCAGAGAAGCAGGa                                                                        >  1:296183/1‑140 (MQ=255)                                                            gCATCAATTTTAATGTCGGTTAGAGGGAAACTTATGAAGCACTCTGTTTCAGTCACGTGTTGTGCGCTGTTGGTC‑GCAGCATTTCTCTTTCGTATGCTGCAGAAGTTCCGAGCGGCACAGTACTGGCAGAGAAGCAGGAg                                                                       >  1:323907/1‑140 (MQ=255)                                                               tCAATTTTAATGTAGGTTAGAGGGAAACTTATGAAGCACTCTGTTTCAGTCACGTGTTGTGCGCTGTTGGTC‑GCAGCATTTCTCTTTCGTATGCTGCAGAAGTTCCGAGCGGCACAGTACTGGCAGAGAAGCAGGAGCTg                                                                    >  2:697843/1‑140 (MQ=255)                                                                     ttAATGTCGGTTAGAGGGAAACTTATGAAGCACTCTGTTTCAGTCACGTGTTGTGCGCTGTTGGTC‑GCAGCATTTCTCTTTCGTATGCTGCAGAAGTTCCGAGCGGCACAGTACTGGCAGAGAAGCAGGAGCTGGTgcgc                                                              <  2:284183/140‑1 (MQ=255)                                                                     ttAATGTCGGTTAGAGGGAAACTTATGAAGCACTCTGTTTCAGTCACGTGTTGTGCGCTGTTGGTC‑GCAGCATTTCTCTTTCGTATGCTGCAGAAGTTCCGAGCGGCACAGTACTGGCAGAGAAGCAGGAGCTGGTgcgc                                                              <  1:641907/140‑1 (MQ=255)                                                                     ttAATGTCGGTTAGAGGGAAACTTATGAAGCACTCTGTTTCAGTCACGTGTTGTGCGCTGTTGGTC‑GCAGCATTTCTCTTTCGTATGCTGCAGAAGTTCCGAGCGGCACAGTACTGGCAGAGAAGCAGGAGCTGGTgcgc                                                              <  2:237964/140‑1 (MQ=255)                                                                       aaTGTCGGTTAGAGGGAAACTTATGAAGCACTCTGTTTCAGTCACGTGTTGTGCGCTGTTGGTC‑GCAGCATTTCTCTTTCGTATGCTGCAGAAGTTCCGAGCGGCACAGTACTGGCAGAGAAGCAGGAGCTGGTGCGCca                                                            <  2:323907/140‑1 (MQ=255)                                                                        aTGTCGGTTAGAGGGAAACTTATGAAGCACTCTGTTTCAGTCACGTGTTGTGCGCTGTTGGTC‑GCAGCATTTCTCTTTCGTATGCTGCAGAAGTTCCGAGCGGCACAGTACTGGCAGAGAAGCAGGAGCTGGTGCGCcac                                                           >  1:77332/1‑140 (MQ=255)                                                                         tGTCGGTTAGAGGGAAACTTATGAAGCACTCTGTTTCAGTCACGTGTTGTGCGCTGTTGGTC‑GCAGCATTTCTCTTTCGTATGCTGCAGAAGTTCCGAGCGGCACAGTACTGGCAGAGAAGCAGGAGCTGGTGCGCcaca                                                          >  1:39149/1‑140 (MQ=255)                                                                         tGTCGGTTAGAGGGAAACTTATGAAGCACTCTGTTTCAGTCACGTGTTGTGCGCTGTTGGTC‑GCAGCATTTCTCTTTCGTATGCTGCAGAAGTTCCGAGCGGCACAGTACTGGCAGAGAAGCAGGAGCTGGTGCGCcaca                                                          <  1:9086/140‑1 (MQ=255)                                                                           tCGGTTAGAGGGAAACTTATGAAGCACTCTGTTTCAGTCACGTGTTGTGCGCTGTTGGTC‑GCAGCATTTCTCTTTCGTATGCTGCAGAAGTTCCGAGCGGCACAGTACTGGCAGAGAAGCAGGAGCTGGTGCGCCACAtt                                                        <  2:655160/140‑1 (MQ=255)                                                                           tCGGTTAGAGGGAAACTTATGAAGCACTCTGTTTCAGTCACGTGTTGTGCGCTGTTGGTC‑GCAGCATTTCTCTTTCGTATGCTGCAGAAGTTCCGAGCGGCACAGTACTGGCAGAGAAGCAGGAGCTGGTGCGCCACAtt                                                        <  2:240302/140‑1 (MQ=255)                                                                                        aaCTTATGAAGCACTCTGTTTCAGTCACGTGTTGTGCGCTGTTGGTC‑GCAGCATTTCTCTTTCGTATGCTGCAGAAGTTCCGAGCGGCACAGTACTGGCAGAGAAGCAGGAGCTGGTGCGCCACATTAAAGATGAGCCTg                                           >  1:1115852/1‑140 (MQ=255)                                                                                             aTGAAGCACTCTGTTTCAGTCACGTGTTGTGCGCTGTTGGTC‑GCAGCATTTCTCTTTCGTATGCTTCAGAAGTTCCGAGCGGCACAGTACTGGCAGAGAAGCAGGAGCTGGTGCGCCACATTAAAg                                                    <  2:108490/126‑1 (MQ=255)                                                                                             aTGAAGCACTCTGTTTCAGTCACGTGTTGTGCGCTGTTGGTC‑GCAGCATTTCTCTTTCGTATGCTTCAGAAGTTCCGAGCGGCACAGTACTGGCAGAGAAGCAGGAGCTGGTGCGCCACATTAAAg                                                    >  1:108490/1‑126 (MQ=255)                                                                                               gAAGCACTCTGTTTCAGTCACGTGTTGTGCGCTGTTGGTC‑GCAGCATTTCTCTTTCGTATGCTGCAGAAGTTCCGAGCGGCACAGTACTGGCAGAGAAGCAGGAGCTGGTGCGCCACATTAAAGATGAGCCTGCGTCGCt                                    >  1:693907/1‑140 (MQ=255)                                                                                                     ctctGTTTCAGTCACGTGTTGTGCGCTGTTGGTC‑GCAGCATTTCTCTTTCGTATGCTGCAGAAGTTCCGAGCGGCACAGTACTGGCAGAGAAGCAGGAGCTGGTGCGCCACATTAAAGATGAGCCTg                                           >  2:627373/1‑127 (MQ=255)                                                                                                     ctctGTTTCAGTCACGTGTTGTGCGCTGTTGGTC‑GCAGCATTTCTCTTTCGTATGCTGCAGAAGTTCCGAGCGGCACAGTACTGGCAGAGAAGCAGGAGCTGGTGCGCCACATTAAAGATGAGCCTg                                           <  1:627373/127‑1 (MQ=255)                                                                                                     ctctGTTTCAGTCACGTGTTGTGCGCTGTTGGTC‑GCAGCATTTCTCTTTCGTATGCTGCAGAAGTTCCGAGCGGCACAGTACTGGCAGAGAAGCAGGAGCTGGTGCGCCACATTAAAGATGAGCCTGCGTCGCTGGATcc                              >  1:427267/1‑140 (MQ=255)                                                                                                        tGTTTCAGTCACGTGTTGTGCGCTGTTGGTC‑GCAGCATTTCTCTTTCGTATGCTGCAGAAGTTCCGAGCGGCACAGTACTGGCAGAGAAGCAGGAGCTGGTGCGCCACATTAAAGATGAGCCTGCGTCGCTGGATCCCGc                           >  2:1108016/1‑140 (MQ=255)                                                                                                          tttCAGTCACGTGTTGTGCGCTGTTGGTC‑GCAGCATTTCTCTTTCGTATGCTGCAGAAGTTCCGAGCGGCACAGTACTGGCAGAGAAGCAGGAGCTGGTGCGCTACATTAAAGATGAGCCTGCGTCGCTGGATCCCGCTa                         <  2:190033/140‑1 (MQ=255)                                                                                                          tttCAGTCACGTGTTGTGCGCTGTTGGTC‑GCAGCATTTCTCTTTCGTATGCTGCAGAAGTTCCGAGCGGCACAGTACTGGCAGAGAAGCAGGAGCTGGTGCGCCACATTAAAGATGAGCCTGCGTCGCTGGATCCCGCTa                         >  2:535274/1‑140 (MQ=255)                                                                                                          tttCAGTCACGTGTTGTGCGCTGTTGGTC‑GCAGCATTTCTCTTTCGTATGCTGCAGAAGTTCCGAGCGGCACAGTACTGGCAGAGAAGCAGGAGCTGGTGCGCCACATTAAAGATGAGCCTGCGTCGCTGGATCCCGCTa                         <  1:188934/140‑1 (MQ=255)                                                                                                               gTCACGTGTTGTGCGCTGTTGGTC‑GCAGCATTTCTCTTTCGTATGCTGCAGAAGTTCCGAGCGGCACAGTACTGGCAGAGAAGCAGGAGCTGGTGCGCCACATTAAAGATGAGCCTGCGTCGCTGGATCCCGCTAAAGcc                    >  2:1125264/1‑140 (MQ=255)                                                                                                                tCACGTGTTGTGCGCTGTTGGTC‑GCAGCATTTCTCTTTCGTATGCTGCAGAAGTTCCGAGCGGCACAGTACTGGCAGAGAAGCAGGAGCTGGTGCGCCACATTAAAGATGAGCCTGCGTCGCTGGATCCCGCTAAAGCCg                   >  2:543122/1‑140 (MQ=255)                                                                                                                tCACGTGTTGTGCGCTGTTGGTC‑GCAGCATTTCTCTTTCGTATGCTGCAGAAGTTCCGAGCGGCACAGTACTGGCAGAGAAGCAGGAGCTGGTGCGCCACATTAAAGATGAGCCTGCGTCGCTGGATCCCGCTAAAGCCg                   >  1:1114002/1‑140 (MQ=255)                                                                                                                    gtgtTGTGCGCTGTTGGTC‑GCAGCATTTCTCTTTCGTATGCTGCAGAAGTTCCGAGCGGCACAGTACTGGCAGAGAAGCAGGAGCTGGTGCGCCACATTAAAGATGAGCCTGCGTCGCTGGATCCCGCTAAAGCCGt                  >  2:718716/1‑137 (MQ=255)                                                                                                                    gtgtTGTGCGCTGTTGGTC‑GCAGCATTTCTCTTTCGTATGCTGCAGAAGTTCCGAGCGGCACAGTACTGGCAGAGAAGCAGGAGCTGGTGCGCCACATTAAAGATGAGCCTGCGTCGCTGGATCCCGCTAAAGCCGt                  >  2:517309/1‑137 (MQ=255)                                                                                                                    gtgtTGTGCGCTGTTGGTC‑GCAGCATTTCTCTTTCGTATGCTGCAGAAGTTCCGAGCGGCACAGTACTGGCAGAGAAGCAGGAGCTGGTGCGCCACATTAAAGATGAGCCTGCGTCGCTGGATCCCGCTAAAGCCGt                  <  1:517309/137‑1 (MQ=255)                                                                                                                    gtgtTGTGCGCTGTTGGTC‑GCAGCATTTCTCTTTCGTATGCTGCAGAAGTTCCGAGCGGCACAGTACTGGCAGAGAAGCAGGAGCTGGTGCGCCACATTAAAGATGAGCCTGCGTCGCTGGATCCCGCTAAAGCCGt                  <  1:718716/137‑1 (MQ=255)                                                                                                                       ttgtGCGCTGTTGGTC‑GCAGCATTTCTCTTTCGTATGCTGCAGAAGTTCCGAGCGGCACAGTACTGGCAGAGAAGCAGGAGCTGGTGCGCCACATTAAAGATGAGCCTGCGTCGCTGGATCCCGCTAAAGCCGTGGGCCt            <  2:217355/140‑1 (MQ=255)                                                                                                                          tgCGCTGTTGGTC‑GCAGCATTTCTCTTTCGTATGCTGCAGAAGTTCCGAGCGGCACAGTACTGGCAGAGAAGCAGGAGCTGGTGCGCCACATTAAAGATGAGCCTGCGTCGCTGGATCCCGCTAAAGCCGt                  >  2:678273/1‑131 (MQ=255)                                                                                                                          tgCGCTGTTGGTC‑GCAGCATTTCTCTTTCGTATGCTGCAGAAGTTCCGAGCGGCACAGTACTGGCAGAGAAGCAGGAGCTGGTGCGCCACATTAAAGATGAGCCTGCGTCGCTGGATCCCGCTAAAGCCGt                  <  1:678273/131‑1 (MQ=255)                                                                                                                          tgCGCTGTTGGTC‑GCAGCATTTCTCTTTCGTATGCTGCAGAAGTTCCGAGCGGCACAGTACTGGCAGAGAAGCAGGAGCTGGTGCGCCACATTAAAGATGAGCCTGCGTCGCTGGATCCCGCTAAAGCCGTGGGc              >  2:918511/1‑135 (MQ=255)                                                                                                                          tgCGCTGTTGGTC‑GCAGCATTTCTCTTTCGTATGCTGCAGAAGTTCCGAGCGGCACAGTACTGGCAGAGAAGCAGGAGCTGGTGCGCCACATTAAAGATGAGCCTGCGTCGCTGGATCCCGCTAAAGCCGTGGGc              <  1:918511/135‑1 (MQ=255)                                                                                                                          tgCGCTGTTGGTC‑GCAGCATTTCTCTTTCGTATGCTGCAGAAGTTCCGAGCGGCACAGTACTGGCAGAGAAGCAGGAGCTGGTGCGCCACATTAAAGATGAGCCTGCGTCGCTGGATCCCGCTAAAGCCGTGGGCCTGcc         <  1:652277/140‑1 (MQ=255)                                                                                                                           gcgcTGTTGGTC‑GCAGCATTTCTCTTTCGTATGCTGCAGAAGTTCCGAGCGGCACAGTACTGGCAGAGAAGCAGGAGCTGGTGCGCCACATTAAAGATGAGCCTGCGTCGCTGGATCCCGCTAAAGCCGTGGGCCTGCCa        <  1:884254/140‑1 (MQ=255)                                                                                                                           gcgcTGTTGGTC‑GCAGCATTTCTCTTTCGTATGCTGCAGAAGTTCCGAGCGGCACAGTACTGGCAGAGAAGCAGGAGCTGGTGCGCCACATTAAAGATGAGCCTGCGTCGCTGGATCCCGCTAAAGCCGTGGGCCTGCCa        <  2:693907/140‑1 (MQ=255)                                                                                                                           gcgcTGTTGGTC‑GCAGCATTTCTCTTTCGTATGCTGCAGAAGTTCCGAGCGGCACAGTACTGGCAGAGAAGCAGGAGCTGGTGCGCCACATTAAAGATGAGCCTGCGTCGCTGGATCCCGCTAAAGCCGTGGGCCTGCCa        <  1:925105/140‑1 (MQ=255)                                                                                                                            cgcTGTTGGTC‑GCAGCATTTCTCTTTCGTATGCTGCAGAAGTTCCGAGCGGCACAGTACTGGCAGAGAAGCAGGAGCTGGTGCGCCACATTAAAGATGAGCCTGCGTCGCTGGATCCCGCTAAAGCCGTGGGCCTGCCag       >  1:542772/1‑140 (MQ=255)                                                                                                                            cgcTGTTGGTC‑GCAGCATTTCTCTTTCGTATGCTGCAGAAGTTCCGAGCGGCACAGTACTGGCAGAGAAGCAGGAGCTGGTGCGCCACATTAAAGATGAGCCTGCGTCGCTGGATCCCGCTAAAGCCGTGGGCCTGCCag       <  2:77332/140‑1 (MQ=255)                                                                                                                                 ttGGTC‑GCAGCATTTCTCTTTCGTATGCTGCAGAAGTTCCGAGCGGCACAGTACTGGCAGAGAAGCAGGAGCTGGTGCGCCACATTAAAGATGAGCCTGCGTCGCTGGATCCCGCTAAAGCCGTGGGCCTGCCa        >  1:256957/1‑134 (MQ=255)                                                                                                                                 ttGGTC‑GCAGCATTTCTCTTTCGTATGCTGCAGAAGTTCCGAGCGGCACAGTACTGGCAGAGAAGCAGGAGCTGGTGCGCCACATTAAAGATGAGCCTGCGTCGCTGGATCCCGCTAAAGCCGTGGGCCTGCCa        <  2:256957/134‑1 (MQ=255)                                                                                                                                 ttGGTC‑GCAGCATTTCTCTTTCGTATGCTGCAGAAGTTCCGAGCGGCACAGTACTGGCAGAGAAGCAGGAGCTGGTGCGCCACATTAAAGATGAGCCTGCGTCGCTGGATCCCGCTAAAGCCGTGGGCCTGCCAGAGAtt  >  2:755001/1‑140 (MQ=255)                                                                                                                                 ttGGTC‑GCAGCATTTCTCTTTCGTATGCTGCAGAAGTTCCGAGCGGCACAGTACTGGCAGAGAAGCAGGAGCTGGTGCGCCACATTAAAGATGAGCCTGCGTCGCTGGATCCCGCTAAAGCCGTGGGCCTGCCAGAGAtt  >  1:1132039/1‑140 (MQ=255)                                                                                                                                       |                                                                                                                                       CTTTGTCACTTTTTTGATGGAAGTTGTTTGCATTTCTTTAAGGCGAAACAAATAATTACGCATCAATTTTAATGTCGGTTAGAGGGAAACTTATGAAGCACTCTGTTTCAGTCACGTGTTGTGCGCTGTTGGTCAGCAGCATTTCTCTTTCGTATGCTGCAGAAGTTCCGAGCGGCACAGTACTGGCAGAGAAGCAGGAGCTGGTGCGCCACATTAAAGATGAGCCTGCGTCGCTGGATCCCGCTAAAGCCGTGGGCCTGCCAGAGATT  >  NC_000913/1393135‑1393403

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑