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%	186.3 / NA	58	pseudogene (34/60 nt)	pbl	pseudogene, peptidoglycan‑binding enzyme family
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (34/24);  total (34/24)

CGTGGCAATGCCTGGGGACTTATAATGCGGGTTTTGCAATGGATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAGACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGAACATCTAATTTCTTCATGATATTGAGTCTATGA  >  NC_000913/2994306‑2994550                                                                                                              |                                                                                                                                        cGTGGCAATGCCTGGGGACTTATAATGCGGGTTTTGCAATGGATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGcc                                                                                                            >  2:1013349/1‑139 (MQ=255)   tGGCAATGCCTGGGGACTTATAATGCGGGTTTTGCAATGGATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTa                                                                                                          >  1:130815/1‑139 (MQ=255)     gCAATGCCTGGGGACTTATAATGCGGGTTTTGCAATGGATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTaaa                                                                                                        >  2:162596/1‑139 (MQ=255)      cAATGCCTGGGGACTTATAATGCGGGTTTTGCAATGGATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAg                                                                                                       >  1:799194/1‑139 (MQ=255)           ccTGGGGACTTATAATGCGGGTTTTGCAATGGATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCctct                                                                                                  <  2:799194/139‑1 (MQ=255)           ccTGGGGACTTATAATGCGGGTTTTGCAATGGATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCctct                                                                                                  <  2:130815/139‑1 (MQ=255)           ccTGGGGACTTATAATGCGGGTTTTGCAATGGATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCctct                                                                                                  <  2:32207/139‑1 (MQ=255)           ccTGGGGACTTATAATGCGGGTTTTGCAATGGATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCctct                                                                                                  <  1:3809/139‑1 (MQ=255)           ccTGGGGACTTATAATGCGGGTTTTGCAATGGATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCctct                                                                                                  <  1:1013349/139‑1 (MQ=255)             tGGGGACTTATAATGCGGGTTTTGAAATGGATAAGCAAAAAAAGAGACAGCAATATGCCCCCAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAACTGAGCCTAAAGCCTCttt                                                                                                <  2:542894/139‑1 (MQ=255)                     tataATGCGGGTTTTGCAATGGATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCt                                                                                                                           <  2:427781/104‑1 (MQ=255)                     tataATGCGGGTTTTGCAATGGATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCt                                                                                                                           >  1:427781/1‑104 (MQ=255)                     tataATGCGGGTTTTGCAATGGATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTtata                                                                                        >  1:74230/1‑139 (MQ=255)                              ggTTTTGCAATGGATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCaaa                                                                               <  1:162596/139‑1 (MQ=255)                                                             aGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTc                                                >  2:245270/1‑139 (MQ=255)                                                                  tatGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATAc                                           <  2:41844/139‑1 (MQ=255)                                                                       cccAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATa                                            <  2:494139/133‑1 (MQ=255)                                                                       cccAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATa                                            >  1:494139/1‑133 (MQ=255)                                                                                     tGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGAACATCTAAttt                        >  2:536927/1‑139 (MQ=255)                                                                                      gTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCctct                                                                                                  >  1:229304/1‑64 (MQ=255)                                                                                      gTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCctct                                                                                                  <  2:229304/64‑1 (MQ=255)                                                                                      gTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGAACATCTAATttc                       >  1:352339/1‑139 (MQ=255)                                                                                       tatataCCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGaa                                  <  2:969227/127‑1 (MQ=255)                                                                                       tatataCCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGaa                                  >  1:969227/1‑127 (MQ=255)                                                                                       tatataCCAGGCTGAATGAACTAAACAATCGTAAGGCTTCATCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGAACATCTAAtttgt                      <  2:74230/139‑3 (MQ=255)                                                                                        atataCCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCctct                                                                                                  >  2:151724/1‑62 (MQ=255)                                                                                        atataCCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCctct                                                                                                  <  1:151724/62‑1 (MQ=255)                                                                                         tataCCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAg                                                                                     >  2:20195/1‑74 (MQ=255)                                                                                         tataCCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAg                                                                                     <  1:20195/74‑1 (MQ=255)                                                                                         tataCCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGAACATCTAATttcttc                    >  1:948592/1‑139 (MQ=255)                                                                                         tataCCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGAACATCTAATttctt                     <  2:915575/138‑1 (MQ=255)                                                                                         tataCCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGAACATCTAATttctt                     >  1:915575/1‑138 (MQ=255)                                                                                            aCCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGAACATCTAATTTCTTCATg                 >  1:97266/1‑139 (MQ=255)                                                                                            aCCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGAACATCTAATTTCTTCATg                 >  1:802224/1‑139 (MQ=255)                                                                                                ggCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGAACATCTAATTTCTTCATGatat             >  2:421710/1‑139 (MQ=255)                                                                                                 gCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGa                                                                                                               >  2:167765/1‑40 (MQ=255)                                                                                                 gCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGa                                                                                                               <  1:167765/40‑1 (MQ=255)                                                                                                 gCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTACAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATAcc                                          <  2:687515/109‑1 (MQ=255)                                                                                                 gCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCctct                                                                                                  >  1:334837/1‑53 (MQ=255)                                                                                                 gCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCctct                                                                                                  >  2:445384/1‑53 (MQ=255)                                                                                                 gCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCctct                                                                                                  <  2:334837/53‑1 (MQ=255)                                                                                                 gCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCctct                                                                                                  <  1:445384/53‑1 (MQ=255)                                                                                                 gCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATAcc                                          >  1:687515/1‑109 (MQ=255)                                                                                                 gCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCAc                                        <  2:487460/111‑1 (MQ=255)                                                                                                 gCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCAc                                        >  1:487460/1‑111 (MQ=255)                                                                                                 gCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACtgt                                     <  1:400404/114‑1 (MQ=255)                                                                                                 gCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACtgt                                     >  2:400404/1‑114 (MQ=255)                                                                                                 gCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGAACATCTAATTTCTTCATGATAtt            >  1:125054/1‑139 (MQ=255)                                                                                                 gCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGAACATCTAATTTCTTCATGATAtt            >  1:1004310/1‑139 (MQ=255)                                                                                                 gCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGAACATCTAATTTCTTCATGATAtt            >  1:950411/1‑139 (MQ=255)                                                                                                 gCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGAACATCTAATTTCTTCATGATAtt            >  1:1009953/1‑139 (MQ=255)                                                                                                 gCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGAACATCTAATTTCTTCATGATAtt            >  2:795930/1‑139 (MQ=255)                                                                                                 gCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGAACATCTAATTTCTTCATGATAtt            >  1:914361/1‑139 (MQ=255)                                                                                                     aaTGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCctct                                                                                                  >  1:490298/1‑49 (MQ=255)                                                                                                     aaTGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCctct                                                                                                  <  2:490298/49‑1 (MQ=255)                                                                                                      aTGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGAACATCTAATTTCTTCATGATATTGAGTc       >  2:877178/1‑139 (MQ=255)                                                                                                        gAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGAACATCTAATTTCTTCATGATATTGAGTCTa     <  2:352339/139‑1 (MQ=255)                                                                                                           cTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGAACATCTAATTTCTTCATGATATTGAGTCTATGa  >  2:96706/1‑139 (MQ=255)                                                                                                              |                                                                                                                                        CGTGGCAATGCCTGGGGACTTATAATGCGGGTTTTGCAATGGATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAGACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGAACATCTAATTTCTTCATGATATTGAGTCTATGA  >  NC_000913/2994306‑2994550

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑