Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,994,415	G→A	pseudogene (34/60 nt)	pbl →	pseudogene, peptidoglycan‑binding enzyme family

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,994,415	0	G	A	100.0%	177.1 / NA	55	pseudogene (34/60 nt)	pbl	pseudogene, peptidoglycan‑binding enzyme family
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (28/27);  total (28/27)

AACCATTTTTCACGTTGTGGAGTAACGTGGCAATGCCTGGGGACTTATAATGCGGGTTTTGCAATGGATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAGACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGAACATCTAATTTCTTCATGATATTG  >  NC_000913/2994281‑2994541                                                                                                                                       |                                                                                                                               aaCCATTTTTCACGTTGTGGAGTAACGTGGCAATGCCTGGGGACTTATAATGCGGGTTTTGCAATGGATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACaa                                                                                                                            >  1:12301/1‑139 (MQ=255)     aTTTTTCACGTTGTGGAGTAACGTGGCAATGCCTGGGGACTTATAATGCGGGTTTTACAATGGATAACCAAAAAAAGAGACAGCAATATGCCCCAAAGTATATATTGTATATACCAGGCTTAATGAACTAAACAATCGt                                                                                                                        <  1:1221126/139‑1 (MQ=255)                          cGTGGCAATGCCTGGGGACTTATAATGCGGGTTTTGCAATGGATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGcc                                                                                                   >  2:194479/1‑139 (MQ=255)                          cGTGGCAATGCCTGGGGACTTATAATGCGGGTTTTGCAATGGATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGcc                                                                                                   >  2:305882/1‑139 (MQ=255)                            tGGCAATGCCTGGGGACTTATAATGCGGGTTTTGCAATGGATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGt                                                                                                                        <  1:943059/116‑1 (MQ=255)                            tGGCAATGCCTGGGGACTTATAATGCGGGTTTTGCAATGGATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGt                                                                                                                        >  2:943059/1‑116 (MQ=255)                                    ccTGGGGACTTATAATGCGGGTTTTGCAATGGATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCctct                                                                                         <  1:305882/139‑1 (MQ=255)                                    ccTGGGGACTTATAATGCGGGTTTTGCAATGGATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCctct                                                                                         <  1:1475672/139‑1 (MQ=255)                                             ttATAATGCGGGTTTTGCAATGGATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTtat                                                                                >  1:696467/1‑139 (MQ=255)                                              tataATGCGGGTTTTGCCATGGATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTtata                                                                               <  1:570470/139‑1 (MQ=255)                                                       ggTTTTGCAATGGATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCaaa                                                                      <  2:12301/139‑1 (MQ=255)                                                                           aaaaaaGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGtt                                                  <  1:194479/139‑1 (MQ=255)                                                                             aaaaGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGt                                                                                                                        >  2:1060793/1‑67 (MQ=255)                                                                             aaaaGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGt                                                                                                                        <  1:1060793/67‑1 (MQ=255)                                                                             aaaaGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCctct                                                                                         >  1:1362045/1‑98 (MQ=255)                                                                             aaaaGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCctct                                                                                         <  2:1362045/98‑1 (MQ=255)                                                                                 gagaCAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATc                                            <  1:116997/139‑1 (MQ=255)                                                                                  agaCAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCctct                                                                                         >  1:344699/1‑93 (MQ=255)                                                                                  agaCAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCctct                                                                                         <  2:344699/93‑1 (MQ=255)                                                                                            atGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCtttttt                                                                                    <  1:662238/88‑1 (MQ=255)                                                                                            atGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCtttttt                                                                                    >  2:662238/1‑88 (MQ=255)                                                                                              gCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCAc                               >  2:1031611/1‑139 (MQ=255)                                                                                                              tGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGAACATCTAAt                 <  1:544600/137‑1 (MQ=255)                                                                                                              tGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGAACATCTAAt                 >  2:544600/1‑137 (MQ=255)                                                                                                              tGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTC‑TTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATAc                                  >  2:263600/1‑119 (MQ=255)                                                                                                              tGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTC‑TTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATAc                                  <  1:263600/119‑1 (MQ=255)                                                                                                                tatataCCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACg                                                            >  1:974980/1‑92 (MQ=255)                                                                                                                tatataCCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACg                                                            <  2:974980/92‑1 (MQ=255)                                                                                                                 atataCCAGGCTTAATGAACTAAACAGTCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCCTACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGCACAt                      >  1:1634052/1‑129 (MQ=255)                                                                                                                 atataCCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGAACAt                      <  2:1634052/129‑1 (MQ=255)                                                                                                                  tataCCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCaaa                                                                      <  1:783165/80‑1 (MQ=255)                                                                                                                  tataCCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCaaa                                                                      >  2:783165/1‑80 (MQ=255)                                                                                                                   ataCCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGAACATCTAATTTCTTCa          <  2:696467/139‑1 (MQ=255)                                                                                                                   ataCAAGCCTTAATCAACTAATCAATCTAAAGCGTTCGGCAAAATGGGCCTAAAG‑CTATTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGAACATCTAATTTCTTCAt         <  1:34499/139‑1 (MQ=255)                                                                                                                       cAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGAACATCTAATTTCTTCATGat      >  2:112240/1‑139 (MQ=255)                                                                                                                       cAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGAACATCTAATTTCTTCATGat      >  2:502644/1‑139 (MQ=255)                                                                                                                       cAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTC‑TTTTTTTATTTTATGCAAACAACCATACGTAAAGCTGTTTTTAACCAATTCATTCCCCCTTGAAACTCTAATTTCTTCATtata     >  2:34499/1‑139 (MQ=255)                                                                                                                         ggCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGAACATCTAATTTCTTCATGatat    >  1:173056/1‑139 (MQ=255)                                                                                                                          gCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGc                                                                                             <  1:891169/49‑1 (MQ=255)                                                                                                                          gCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGc                                                                                             >  2:891169/1‑49 (MQ=255)                                                                                                                          gCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCaa                                                                       <  2:57319/71‑1 (MQ=255)                                                                                                                          gCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCaa                                                                       >  1:57319/1‑71 (MQ=255)                                                                                                                          gCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCaa                                          >  2:1008909/1‑100 (MQ=255)                                                                                                                          gCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCaa                                          <  1:1008909/100‑1 (MQ=255)                                                                                                                          gCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGAACATCTAATTTCTTCATGATAtt   >  1:429262/1‑139 (MQ=255)                                                                                                                           cTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGAACATCTAATTTCTTCATGATATTg  <  2:173056/139‑1 (MQ=255)                                                                                                                              aaTGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCct                                                                                           >  2:130725/1‑47 (MQ=255)                                                                                                                              aaTGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCct                                                                                           <  1:130725/47‑1 (MQ=255)                                                                                                                              aaTGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCaaa                                                                      >  2:1461953/1‑68 (MQ=255)                                                                                                                              aaTGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCaaa                                                                      <  1:1461953/68‑1 (MQ=255)                                                                                                                               aTGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGa                                     <  1:319676/100‑1 (MQ=255)                                                                                                                               aTGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGa                                     >  2:319676/1‑100 (MQ=255)                                                                                                                                   aCTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAg                                                                            <  2:1057057/57‑1 (MQ=255)                                                                                                                                   aCTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAg                                                                            >  1:1057057/1‑57 (MQ=255)                                                                                                                                    cTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCctct                                                                                         <  2:760372/43‑1 (MQ=255)                                                                                                                                    cTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCctct                                                                                         >  1:760372/1‑43 (MQ=255)                                                                                                                                       |                                                                                                                               AACCATTTTTCACGTTGTGGAGTAACGTGGCAATGCCTGGGGACTTATAATGCGGGTTTTGCAATGGATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAGACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGAACATCTAATTTCTTCATGATATTG  >  NC_000913/2994281‑2994541

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑