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%	241.1 / NA	74	pseudogene (34/60 nt)	pbl	pseudogene, peptidoglycan‑binding enzyme family
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (38/36);  total (38/36)

TAACCATTTTTCACGTTGTGGAGTAACGTGGCAATGCCTGGGGACTTATAATGCGGGTTTTGCAATGGATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAGACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGAACATCTAATTTCTTCATGATATTGAGTC  >  NC_000913/2994280‑2994545                                                                                                                                        |                                                                                                                                   taACCATTTTTCACGTTGTGGAGTAACGTGGCAATGCCTGGGGACTTATAATGCGGGTTTTGCAATGGATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACa                                                                                                                                 <  2:1730996/139‑1 (MQ=255)  aaCCATTTTTCACGTTGTGGAGTAACGTGGCAATGCCTGGGGACTTATAATGCGGGTTTTGCAATGGATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACaa                                                                                                                                >  2:1763126/1‑139 (MQ=255)      aTTTTTCACGTTGTGGAGTAACGTGGCAATGCCTGGGGACTTATAATGCGGGTTTTGCAATGGATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGt                                                                                                                            <  1:947291/139‑1 (MQ=255)                ttGTGGAGTAACGTGGCAATGCCTGGGGACTTATAATGCGGGTTTTGCAATGGATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAg                                                                                                                  <  2:1812219/139‑1 (MQ=255)                  gtgGAGTAACGTGGCAATGCCTGGGGACTTATAATGCGGGTTTTGCAATGGATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCa                                                                                                                >  2:155824/1‑139 (MQ=255)                                     ccTGGGGACTTATAATGCGGGTTTTGCAATGGATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGc                                                                                                                       <  1:2039669/113‑1 (MQ=255)                                     ccTGGGGACTTATAATGCGGGTTTTGCAATGGATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGc                                                                                                                       >  2:2039669/1‑113 (MQ=255)                                     ccTGGGGACTTATAATGCGGGTTTTGCAATGGATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCctct                                                                                             <  1:1763126/139‑1 (MQ=255)                                                                   ggATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACg                                                                >  1:1070412/1‑138 (MQ=255)                                                                   ggATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACg                                                                <  2:1070412/138‑1 (MQ=255)                                                                       aaCCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTtata                                                                                   <  2:1028196/115‑1 (MQ=255)                                                                       aaCCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTtata                                                                                   >  1:1028196/1‑115 (MQ=255)                                                                              aaaaGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCctct                                                                                             <  2:171553/98‑1 (MQ=255)                                                                              aaaaGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCctct                                                                                             >  1:171553/1‑98 (MQ=255)                                                                              aaaaGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGtttt                                                    >  2:757342/1‑139 (MQ=255)                                                                                           atatGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATa                                       <  1:155824/139‑1 (MQ=255)                                                                                                   cAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGAt                                                 >  1:1493390/1‑121 (MQ=255)                                                                                                   cAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGAt                                                 <  2:1493390/121‑1 (MQ=255)                                                                                                      aaTATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCctct                                                                                             >  1:1103612/1‑74 (MQ=255)                                                                                                      aaTATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCctct                                                                                             <  2:1103612/74‑1 (MQ=255)                                                                                                               tGTATATACCAGACTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGAACATCTAAttt                   >  1:1981409/1‑139 (MQ=255)                                                                                                                 tatataCCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACt                                  <  2:1573711/122‑1 (MQ=255)                                                                                                                 tatataCCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACt                                  >  1:1573711/1‑122 (MQ=255)                                                                                                                 tatataCCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGAACATCTAATttct                 >  1:1735825/1‑139 (MQ=255)                                                                                                                 tatataCCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGAACATCTAATttct                 >  1:1166230/1‑139 (MQ=255)                                                                                                                  atataCCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCctct                                                                                             >  2:461428/1‑62 (MQ=255)                                                                                                                  atataCCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCctct                                                                                             <  1:461428/62‑1 (MQ=255)                                                                                                                   tataCCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCaaa                                                                          <  1:1567086/80‑1 (MQ=255)                                                                                                                   tataCCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCaaa                                                                          >  2:1567086/1‑80 (MQ=255)                                                                                                                   tataCCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACAccc                                                                     >  1:1704326/1‑85 (MQ=255)                                                                                                                   tataCCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACAccc                                                                     <  2:1704326/85‑1 (MQ=255)                                                                                                                   tataCCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATAc                                      <  2:2037838/116‑1 (MQ=255)                                                                                                                   tataCCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATAc                                      >  1:2037838/1‑116 (MQ=255)                                                                                                                    ataCCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGAACATCTAATTTCTTCa              <  1:1134124/139‑1 (MQ=255)                                                                                                                      aCCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCctct                                                                                             >  1:1214471/1‑58 (MQ=255)                                                                                                                      aCCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCctct                                                                                             <  2:1214471/58‑1 (MQ=255)                                                                                                                        cAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGAACATCTAATTTCTTCa              >  1:1623421/1‑135 (MQ=255)                                                                                                                        cAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGAACATCTAATTTCTTCa              <  2:1623421/135‑1 (MQ=255)                                                                                                                           gCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCctct                                                                                             >  2:1338020/1‑53 (MQ=255)                                                                                                                           gCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCctct                                                                                             <  2:520986/53‑1 (MQ=255)                                                                                                                           gCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCctct                                                                                             <  2:7775/53‑1 (MQ=255)                                                                                                                           gCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCctct                                                                                             >  1:7775/1‑53 (MQ=255)                                                                                                                           gCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCctct                                                                                             <  1:1338020/53‑1 (MQ=255)                                                                                                                           gCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCctct                                                                                             >  1:520986/1‑53 (MQ=255)                                                                                                                           gCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTtata                                                                                   >  2:1192800/1‑63 (MQ=255)                                                                                                                           gCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTtata                                                                                   <  1:1192800/63‑1 (MQ=255)                                                                                                                           gCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACAccc                                                                     <  2:33910/77‑1 (MQ=255)                                                                                                                           gCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACAccc                                                                     >  1:33910/1‑77 (MQ=255)                                                                                                                           gCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATc                                                <  2:1853068/98‑1 (MQ=255)                                                                                                                           gCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATc                                                >  1:1853068/1‑98 (MQ=255)                                                                                                                           gCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATa                                       <  1:1671804/107‑1 (MQ=255)                                                                                                                           gCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATa                                       >  2:1671804/1‑107 (MQ=255)                                                                                                                           gCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATAc                                      <  2:1825536/108‑1 (MQ=255)                                                                                                                           gCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATAc                                      >  1:1825536/1‑108 (MQ=255)                                                                                                                           gCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGAACATCTAATTTCTTCa              >  1:1517851/1‑132 (MQ=255)                                                                                                                           gCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGAACATCTAATTTCTTCa              <  2:1517851/132‑1 (MQ=255)                                                                                                                           gCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGAACATCTAATTTCTTCATGATAtt       >  1:1443144/1‑139 (MQ=255)                                                                                                                           gCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGAACATCTAATTTCTTCATGATAtt       >  1:1568347/1‑139 (MQ=255)                                                                                                                               aaTGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCctct                                                                                             <  1:1269493/49‑1 (MQ=255)                                                                                                                               aaTGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCctct                                                                                             >  2:1269493/1‑49 (MQ=255)                                                                                                                               aaTGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATa                                       >  2:612210/1‑103 (MQ=255)                                                                                                                               aaTGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATa                                       <  1:612210/103‑1 (MQ=255)                                                                                                                               aaTGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGAACATCTAATttct                 <  2:886359/125‑1 (MQ=255)                                                                                                                               aaTGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGAACATCTAATttct                 >  1:886359/1‑125 (MQ=255)                                                                                                                               aaTGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCT‑AAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATa                                       <  2:368163/102‑1 (MQ=255)                                                                                                                               aaTGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCT‑AAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATa                                       >  1:368163/1‑102 (MQ=255)                                                                                                                                aTGAACTAAACAATCGTAAGGCTTCAGTAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATc                                                <  1:1404586/93‑1 (MQ=255)                                                                                                                                aTGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATc                                                >  2:1404586/1‑93 (MQ=255)                                                                                                                                aTGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGAACATCTAATTTCTTCATGATATTGAGTc  >  1:30745/1‑139 (MQ=255)                                                                                                                                     cTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCg                                          <  2:259876/94‑1 (MQ=255)                                                                                                                                     cTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCg                                          >  1:259876/1‑94 (MQ=255)                                                                                                                                     cTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATa                                       >  2:1746951/1‑97 (MQ=255)                                                                                                                                     cTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATa                                       <  1:1746951/97‑1 (MQ=255)                                                                                                                                     cTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTACAAACACCCATACg                                                                <  1:594691/72‑1 (MQ=255)                                                                                                                                        |                                                                                                                                   TAACCATTTTTCACGTTGTGGAGTAACGTGGCAATGCCTGGGGACTTATAATGCGGGTTTTGCAATGGATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAGACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGAACATCTAATTTCTTCATGATATTGAGTC  >  NC_000913/2994280‑2994545

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑