Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	855,796	A→G	intergenic (‑52/‑167)	ldtB ← / → ybiT	L,D‑transpeptidase linking Lpp to murein/ABC‑F family putative regulatory ATPase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	855,796	0	A	G	100.0%	210.2 / NA	59	intergenic (‑52/‑167)	ldtB/ybiT	L,D‑transpeptidase linking Lpp to murein/ABC‑F family putative regulatory ATPase
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (28/31);  total (28/31)

ATAAGTTACCGCAGAGGCGGTACTGCAAAAGCCGACAACAGCGAAGGCCGCTGCGAATAATGTTTTCAATTTCATATTCATGTTAAGCGAGATTTTGTGCCTGGCAGGCCATTGGGTTGAGAATATTAGAGTATTGGAAGCGCATTATAAGTTCATTCCAGCTCACAGTGAAATCAGATGTGTACGAAATCACATTTTTTGCCTTTGGCTTGAGTGTAGACCTTAAGCGAGGAGCAGGATCTTCTTTCAGACTTATGGCATAATGCGC  >  NC_000913/855664‑855931                                                                                                                                     |                                                                                                                                        aTAAGTTACCGCAGAGGCGGTACTGCAAAAGCCGACAACAGCGAAGGCCGCTGCGAATAATGTTTTCAATTTCATATTCATGTTAAGCGAGATTTTGTGCCTGGCAGGCCATTGGGTTGAGAATATTAGAGTGTTGGaa                                                                                                                                   >  1:1000253/1‑139 (MQ=255)    aGTTACCGCAGAGGCGGTACTGCAAAAGCCGACAACAGCGAAGGCCGCTGCGAATAATGTTTTCAATTTCATATTCATGTTAAGCGAGATTTTGTGCCTGGCAGGCCATTGGGTTGAGAATATTAGAGTGTTGGAAgcg                                                                                                                                <  2:359609/139‑1 (MQ=255)     gTTACCGCAGAGGCGGTACTGCAAAAGCCGACAACAGCGAAGGCCGCTGCGAATAATGTTTTCAATTTCATATTCATGTTAAGCGAGATTTTGTGCCTGGCAGGCCATTGGGTTGAGAATATTAGAGTGTTGGAAgcgc                                                                                                                               >  2:1369859/1‑139 (MQ=255)          cGCAGAGGCGGTACTGCAAAAGCCGACAACAGCGAAGGCCGCTGCGAATAATGTTTTCAATTTCATATTCATGTTAAGCGAGATTTTGTGCCTGGCAGGCCATTGGGTTGAGAATATTAGAGTGTTGGAAGCGCATtat                                                                                                                          >  2:878186/1‑139 (MQ=255)               agGCGGTACTGCAAAAGCCGACAACAGCGAAGGCCGCTGCGAATAATGTTTTCAATTTCATATTCATGTTAAGCGAGATTTTGTGCCTGGCAGGCCATTGGGTTGAGAATATTAGAGTGTTGGAAGCGCATTATAAGtt                                                                                                                     <  2:297457/139‑1 (MQ=255)               agGCGGTACTGCAAAAGCCGACAACAGCGAAGGCCGCTGCGAATAATGTTTTCAATTTCATATTCATGTTAAGCGAGATTTTGTGCCTGGCAGGCCATTGGGTTGAGAATATTAGAGTGTTGGAAGCGCATTATAAGtt                                                                                                                     >  1:424650/1‑139 (MQ=255)                    gTACTGCAAAAGCCGACAACAGCGAAGGCCGCTGCGAATAATGTTTTCAATTTCATATTCATGTTAAGCGAGATTTTGTGCCTGGCAGGCCATTGGGTTGAGAATATTAGAGTGTTGGAAGCGCATTATAAGTTCATTc                                                                                                                <  2:38303/139‑1 (MQ=255)                      aCTGCAAAAGCCGACAACAGCGAAGGCCGCTGCGAATAATGTTTTCAATTTCATATTCATGTTAAGCGAGATTTTGTGCCTGGCAGGCCATTGGGTTGAGAATATTAGAGTGTTGGAAGCGCATTATAAGTTCATTCCa                                                                                                              <  1:1341519/139‑1 (MQ=255)                               gCCGACAACAGCGAAGGCCGCTGCGAATAATGTTTTCAATTTCATATTCATGTTAAGCGAGATTTTGTGCCTGGCAGGCCATTGGGTTGAGAATATTAGAGTGTTGGAAGCGCATTATAAGTTCATTCCAGCTCACAGt                                                                                                     <  2:1000253/139‑1 (MQ=255)                               gCCGACAACAGCGAAGGCCGCTGCGAATAATGTTTTCAATTTCATATTCATGTTAAGCGAGATTTTGTGCCTGGCAGGCCATTGGGTTGAGAATATTAGAGTGTTGGAAGCGCATTATAAGTTCATTCCAGCTCACAGt                                                                                                     <  2:79607/139‑1 (MQ=255)                                 cGACAACAGCGAAGGCCGCTGCGAATAATGTTTTCAATTTCATATTCATGTTAAGCGAGATTTTGTGCCTGGCAGGCCATTGGGTTGAGAATATTAGAGTGTTGGAAgcg                                                                                                                                <  1:1181145/110‑1 (MQ=255)                                 cGACAACAGCGAAGACCGCTGCGAATAATGTTTTCAATTTCATATTCATGTTAAGCGAGATTTTGTGCCTGGCAGGCCATTGGGTTGAGAATATTAGAGTGTTGGAAgcg                                                                                                                                >  2:1181145/1‑110 (MQ=255)                                    caacaGCGAAGGCCGCTGCGAATAATGTTTTCAATTTCATATTCATGTTAAGCGAGATTTTGTGCCTGGCAGGCCATTGGGTTGAGAATATTAGAGTGTTGGAAg                                                                                                                                  >  2:93513/1‑105 (MQ=255)                                    caacaGCGAAGGCCGCTGCGAATAATGTTTTCAATTTCATATTCATGTTAAGCGAGATTTTGTGCCTGGCAGGCCATTGGGTTGAGAATATTAGAGTGTTGGAAg                                                                                                                                  <  1:93513/105‑1 (MQ=255)                                       caGCGAAGGCCGCTGCGAATAATGTTTTCAATTTCATATTCATGTTAAGCGAGATTTTGTGCCTGGCAGGCCATTGGGTTGAGAATATTAGAGTGTTGGAAGCGCATTATAAGTTCATTCCAGCTCACAGTGAAATCAg                                                                                             <  2:1127243/139‑1 (MQ=255)                                              ggCCGCTGCGAATAATGTTTTCAATTTCATATTCATGTTAAGCGAGATTTTGTGCCTGGCAGGCCATTGGGTTGAGAATATTAGAGTGTTGGAAGCGCATTATAAGTTCATTCCAGCTCACAGTGAAATCAGATGTGTa                                                                                      >  1:761776/1‑139 (MQ=255)                                                ccGCTGCGAATAATGTTTTCAATTTCATATTCATGTTAAGCGAGATTTTGTGCCTGGCAGGCCATTGGGTTGAGAATATTAGAGTGTTGGAAGCGCATTATAAGTTCATTCCAGCTCACAGTGAAATCAGATGTGTACg                                                                                    <  2:424650/139‑1 (MQ=255)                                                   cTGCGAATAATGTTTTCAATTTCATATTCATGTTAAGCGAGATTTTGTGCCTGGCAGGCCATTGGGTTGAGAATATTAGAGTGTTGGAAGCGCATTATAAGTTCATTCCAGCTCACAGt                                                                                                     <  2:909245/119‑1 (MQ=255)                                                   cTGCGAATAATGTTTTCAATTTCATATTCAAGTTAAGCGAGATTTTGTGCCTGGCAGGCCATTGGGTTGAGAATATTAGAGTGTTGGAAGCGCATTATAAGTTCATTCCAGCTCACAGt                                                                                                     >  1:909245/1‑119 (MQ=255)                                                        aataatGTTTTCAATTTCATATTCATGTTAAGCGAGATTTTGTGCCTGGCAGGCCATTGGGTTGAGAATATTAGAGTGTTGGAAGCGCATTATAAGTTCATTCCAGCTCACAGTGAAATCAGATGTGTACGAAATcaca                                                                            >  2:498927/1‑139 (MQ=255)                                                         ataatGTTTTCAATTTCATATTCATGTTAAGCGAGATTTTGTGCCTGGCAGGCCATTGGGTTGAGAATATTAGAGTGTTGGAAGCGCATTATAAGTTCATTCCAGCTCACAGTGAAATCAGATGTGTACGAAATCACAt                                                                           >  2:1076999/1‑139 (MQ=255)                                                                 ttCAATTTCATATTCATGTTAAGCGAGATTTTGTGCCTGGCAGGCCATTGGGTTGAGAATATTAGAGTGTTGGAAGCGCATTATAAGTTCATTCCAGCTCACAGTGAAATCAGATGTGTACGAAATCACATTTTTTGcc                                                                   <  1:498927/139‑1 (MQ=255)                                                                  tCAATTTCATATTCATGTTAAGCGAGATTTTGTGCCTGGCAGGCCATTGGGTTGAGAATATTAGAGTGTTGGAAGCGCATTATAAGTTCATTCCAGCTCACAGTGAAATCAGAt                                                                                           >  2:1132611/1‑114 (MQ=255)                                                                  tCAATTTCATATTCATGTTAAGCGAGATTTTGTGCCTGGCAGGCCATTGGGTTGAGAATATTAGAGTGTTGGAAGCGCATTATAAGTTCATTCCAGCTCACAGTGAAATCAGAt                                                                                           <  1:1132611/114‑1 (MQ=255)                                                                       ttCATATTCATGTTAAGCGAGATTTTGTGCCTGGCAGGCCATTGGCTTGAGAATATTAGAGTGCTGGAAGCGCATTATAAGTTCATTCCAGCTCACAGTGAAATCAGATGTGTACGAAATCACATTTTTTGCCTTTGGc                                                             <  1:878186/139‑1 (MQ=255)                                                                         cATATTCATGTTAAGCGAGATTTTGTGCCTGGCAGGCCATTGGGTTGAGAATATTAGAGTGTTGGAAGCGCATTATAAGTTCATTCCAGCTCACAGt                                                                                                     >  2:464996/1‑97 (MQ=255)                                                                         cATATTCATGTTAAGCGAGATTTTGTGCCTGGCAGGCCATTGGGTTGAGAATATTAGAGTGTTGGAAGCGCATTATAAGTTCATTCCAGCTCACAGt                                                                                                     <  1:464996/97‑1 (MQ=255)                                                                              tCATGTTAAGCGAGATTTTGTGCCTGGCAGGCCATTGGGTTGAGAATATTAGAGTGTTGGAAGCGCATTATAAGTTCATTCCAGCTCACAGTGAAATCAGATGTGTACGAAATCACATTTTTTGCCTTTGGCTTGAgtg                                                      <  1:1052244/139‑1 (MQ=255)                                                                                  gTTAAGCGAGATTTTGTGCCTGGCAGGCCATTGGGTTGAGAATATTAGAGTGTTGGAAGCGCATTATAAGTTCATTCCAGCTCACAGTGAAATCAGATGTGTACGAAATCACATTTTTTGCCTTTGGCTTg                                                          >  2:163444/1‑131 (MQ=255)                                                                                  gTTAAGCGAGATTTTGTGCCTGGCAGGCCATTGGGTTGAGAATATTAGAGTGTTGGAAGCGCATTATAAGTTCATTCCAGCTCACAGTGAAATCAGATGTGTACGAAATCACATTTTTTGCCTTTGGCTTg                                                          <  1:163444/131‑1 (MQ=255)                                                                                     aaGCGAGATTTTGTGCCTGGCAGGCCATTGGGTTGAGAATATTAGAGTGTTGGAAGCGCATTATAAGTTCATTCCAGCTCACAGTGAAATCAGATGTGTACGAAATCACATTTTTTGCCTTTGGCTTGAGTGTAGACCt                                               >  1:1332661/1‑139 (MQ=255)                                                                                      aGCGAGATTTTGTGCCTGGCAGGCCATTGGGTTGAGAATATTAGAGTGTTGGAAGCGCATTATAAGTTCATTCCAGCTCACAGTGAAATCAGATGTGTACGAAATCACATTTTTTGCCTTTGGCtt                                                           >  1:149439/1‑126 (MQ=255)                                                                                      aGCGAGATTTTGTGCCTGGCAGGCCATTGGGTTGAGAATATTAGAGTGTTGGAAGCGCATTATAAGTTCATTCCAGCTCACAGTGAAATCAGATGTGTACGAAATCACATTTTTTGCCTTTGGCtt                                                           <  2:149439/126‑1 (MQ=255)                                                                                       gCGAGATTTTGTGCCTGGCAGGCCATTGGGTTGAGAATATTAGAGTGTTGGAAGCGCATTATAAGtt                                                                                                                     <  2:955578/67‑1 (MQ=255)                                                                                       gCGAGATTTTGTGCCTGGCAGGCCATTGGGTTGAGAATATTAGAGTGTTGGAAGCGCATTATAAGtt                                                                                                                     >  1:955578/1‑67 (MQ=255)                                                                                        cGAGATTTTGTGCCTGGCAGGCCATTGGGTTGAGAATATTAGAGTGTTGGAAGCGCATtat                                                                                                                          >  1:257101/1‑61 (MQ=255)                                                                                        cGAGATTTTGTGCCTGGCAGGCCATTGGGTTGAGAATATTAGAGTGTTGGAAGCGCATtat                                                                                                                          <  2:257101/61‑1 (MQ=255)                                                                                        cGAGATTTTGTGCCTGGCAGGCCATTGGGTTGAGAATATTAGAGTGTTGGAAGCGCATTATAAGTTCATTCCAGCTCACAGTGAAATCAGATGTGTACGAAATCACATTTTTTGCCTTTGGCTTGAGTGTAGACCTTaa                                            >  2:115303/1‑139 (MQ=255)                                                                                            aTTTTGTGCCTGGCAGGCCATTGGGTTGAGAATATTAGAGTGTTGGAAGCGCATTATAAGTTCATTCCAGCTc                                                                                                          >  2:816176/1‑73 (MQ=255)                                                                                            aTTTTGTGCCTGGCAGGCCATTGGGTTGAGAATATTAGAGTGTTGGAAGCGCATTATAAGTTCATTCCAGCTc                                                                                                          <  1:816176/73‑1 (MQ=255)                                                                                            aTTTTGTGCCTGGCAGGCCATTGGGTTGAGAATATTAGAGTGTTGGAAGCGCATTATAAGTTCATTCCAGCTCACAGt                                                                                                     <  1:421512/78‑1 (MQ=255)                                                                                            aTTTTGTGCCTGGCAGGCCATTGGGTTGAGAATATTAGAGTGTTGGAAGCGCATTATAAGTTCATTCCAGCTCACAGt                                                                                                     >  2:421512/1‑78 (MQ=255)                                                                                            aTTTTGTGCCTGGCAGGCCATTGGGTTGAGAATATTAGAGTGTTGGAAGCGCATTATAAGTTCATTCCAGCTCACAGTGAAATCAGATGTGTACGAAATcac                                                                             >  1:1036369/1‑102 (MQ=255)                                                                                            aTTTTGTGCCTGGCAGGCCATTGGGTTGAGAATATTAGAGTGTTGGAAGCGCATTATAAGTTCATTCCAGCTCACAGTGAAATCAGATGTGTACGAAATcac                                                                             <  2:1036369/102‑1 (MQ=255)                                                                                                tgtgCCTGGCAGGCCATTGGGTTGAGAATATTAGAGTGTTGGAAGCGCATTATAAGTTCATTCCAGCTCACAGTGAAATCAGATGTGTACGAAATCACATTTTTTGCCTTTGGCTTGAGTGTAGACCTTAAGCgaggag                                    >  2:849005/1‑139 (MQ=255)                                                                                                   gCCTGGCAGGCCATTGGGTTGAGAATATTAGAGTGTTGGAAGCGCATTATAAGTTCATTCCAGCTCACAGTGAAATCAGATGTGTACGAAATCACATTTTTTGCCTTTGGCTTGAGTGTAGACCTTAAGCGAGGAGCAg                                 <  1:1369859/139‑1 (MQ=255)                                                                                                     cTGGCAGGCCATTGGGTTGAGAATATTAGAGTGTTGGAAGCGCATTATAAGTTCATTCCAGCTCACAGTGAAATCAGATGTGTACGAAATca                                                                              <  1:918490/92‑1 (MQ=255)                                                                                                     cTGGCAGGCCATTGGGTTGAGAATATTAGAGTGTTGGAAGCGCATTATAAGTTCATTCCAGCTCACAGTGAAATCAGATGTGTACGAAATca                                                                              >  2:918490/1‑92 (MQ=255)                                                                                                       ggCAGGCCATTGGGTTGAGAATATTAGAGTGTTGGAAGCGCATTATAAGTTCATTCCAGCTc                                                                                                          <  1:217220/62‑1 (MQ=255)                                                                                                       ggCAGGCCATTGGGTTGAGAATATTAGAGTGTTGGAAGCGCATTATAAGTTCATTCCAGCTc                                                                                                          >  2:217220/1‑62 (MQ=255)                                                                                                        gCAGGCCATTGGGTTGAGAATATTAGAGTGTTGGAAGCGCATTATAAGTTCATTCCAGCTCACAGTGAAATCAGATGTGTACGAAATCACAttttt                                                                       <  1:891034/96‑1 (MQ=255)                                                                                                        gCAGGCCATTGGGTTGAGAATATTAGAGTGTTGGAAGCGCATTATAAGTTCATTCCAGCTCACAGTGAAATCAGATGTGTACGAAATCACAttttt                                                                       >  2:891034/1‑96 (MQ=255)                                                                                                                  gggTTGAGAATATTAGAGTGTTGGAAGCGCATTATAAGTTCATTCCAGCTCACAGTGAAATCAGATGTGTACGAAATCACATTTTTTGCCTTTGGCTTGAGTGTAGACCTTAAGCGAGGAGCAGGa                               >  2:462076/1‑126 (MQ=255)                                                                                                                  gggTTGAGAATATTAGAGTGTTGGAAGCGCATTATAAGTTCATTCCAGCTCACAGTGAAATCAGATGTGTACGAAATCACATTTTTTGCCTTTGGCTTGAGTGTAGACCTTAAGCGAGGAGCAGGa                               <  1:462076/126‑1 (MQ=255)                                                                                                                  gggTTGAGAATATTAGAGTGTTGGAAGCGCATTATAAGTTCATTCCAGCTCACAGTGAAATCAGATGTGTACGAAATCACATTTTTTGCCTTTGGCTTGAGTGTAGACCTTAAGCGAGGAGCAGGATCTTCTTTCAGAc                  <  2:1075609/139‑1 (MQ=255)                                                                                                                        agaATATTAGAGTGTTGGAAGCGCATTATAAGTTCATTCCAGCTCACAGTGAAATCAGATGTGTACGAAATCACATTTTTTGCCTTTGGCTTGAGTGTAGACCTTAAGCGAGGAGCAGGATCTTCTTTCAGACTTATgg            >  2:1358895/1‑139 (MQ=255)                                                                                                                                 gagTGTTGGAAGCGCATTATAAGTTCATTCCAGCTCACAGTGAAATCAGATGTGTACGAAATCACATTTTTTGCCTTTGGCTTGAGTGTAGACCTTAAGCGAGGAGCAGGATCTTCTTTCAGACTTATGGCATAATgcg   <  2:761776/139‑1 (MQ=255)                                                                                                                                 gagTGTTGGAAGCGCATTATAAGTTCATTCCAGCTCACAGTGAAATCAGATGTGTACGAAATCACATTTTTTGCCTTTGGCTTGAGTGTAGACCTTAAGCGAGGAGCAGGATCTTCTTTCAGACTTATGGCATAATgcg   <  2:1332661/139‑1 (MQ=255)                                                                                                                                  agTGTTGGAAGCGCATTATAAGTTCATTCCAGCTCACAGTGAAATCAGATGTGTACGAAATCACATTTTTTGCCTTTGGCTTGAGTGTAGACCTTAAGCGAGGAGCAGGATCTTCTTTCAGACTTATGGCATAATgcgc  >  2:1213406/1‑139 (MQ=255)                                                                                                                                     |                                                                                                                                        ATAAGTTACCGCAGAGGCGGTACTGCAAAAGCCGACAACAGCGAAGGCCGCTGCGAATAATGTTTTCAATTTCATATTCATGTTAAGCGAGATTTTGTGCCTGGCAGGCCATTGGGTTGAGAATATTAGAGTATTGGAAGCGCATTATAAGTTCATTCCAGCTCACAGTGAAATCAGATGTGTACGAAATCACATTTTTTGCCTTTGGCTTGAGTGTAGACCTTAAGCGAGGAGCAGGATCTTCTTTCAGACTTATGGCATAATGCGC  >  NC_000913/855664‑855931

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: ‑