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%	227.6 / NA	71	pseudogene (34/60 nt)	pbl	pseudogene, peptidoglycan‑binding enzyme family
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (37/34);  total (37/34)

GTGGAGTAACGTGGCAATGCCTGGGGACTTATAATGCGGGTTTTGCAATGGATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAGACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTC‑TTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGAACATCTAATTTCTTCATGATATTGAGTC  >  NC_000913/2994297‑2994545                                                                                                                       |                                                                                                                                    gtgGAGTAACGTGGCAATGCCTGGGGACTTATAATGCGGGTTTTGCAATGGATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCa                                                                                                                 >  1:579879/1‑139 (MQ=255)                    ccTGGTGACTTATAATGCGTGTTTTGCAATGGATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCctc‑t                                                                                             <  2:834073/139‑1 (MQ=255)                    ccTGGGGACTTATAATGCGGGTTTTGCAATGGATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCctc‑t                                                                                             <  2:6106/139‑1 (MQ=255)                    ccTGGGGACTTATAATGCGGGTTTTGCAATGGATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTCAATGAACTAAACAATCGTAACGCTTCAGCAAAATGAGCCTAAAGCctc‑t                                                                                             <  2:602217/139‑1 (MQ=255)                           aCTTATAATGCGGGTTTTGCAATGGATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTC‑tttttttt                                                                                      <  2:579879/139‑1 (MQ=255)                              tataATGCGGGTTTTGCAATGGATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCctc‑t                                                                                             <  2:5603/129‑1 (MQ=255)                              tataATGCGGGTTTTGCAATGGATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCATAAGGCTTCAGCAAAAGGAGCCTAAAGCctc‑t                                                                                             >  1:5603/1‑129 (MQ=255)                                       ggTTTTGCAATGGATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTATTGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTC‑tttttt                                                                                        <  1:627906/125‑1 (MQ=255)                                       ggTTTTGCAATGGATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCctc‑t                                                                                             >  2:215553/1‑120 (MQ=255)                                       ggTTTTGCAATGGATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCctc‑t                                                                                             <  1:215553/120‑1 (MQ=255)                                       ggTTTTGCAATGGATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTC‑tttttt                                                                                        >  2:627906/1‑125 (MQ=255)                                          ttggaaaTGGATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAAATAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTC‑TTTTTTTTATATAGTGCAAacac                                                                       <  1:758633/134‑1 (MQ=255)                                                      aaCCAAAAAAAGAGACAGCAATATGCCCGAAAATGTATATTGTATATACTAGGCTTAATGAGCTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTC‑TTTTTTTTATATAGTGCAAACACCCATACGTAAAg                                                           >  2:602143/1‑139 (MQ=255)                                                             aaaaGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCctc‑t                                                                                             <  1:385508/98‑1 (MQ=255)                                                             aaaaGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCctc‑t                                                                                             >  2:385508/1‑98 (MQ=255)                                                                agagACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTC‑TTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGAt                                                 <  2:552817/139‑1 (MQ=255)                                                                           tatGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTCTTTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATa                                       <  1:803977/139‑1 (MQ=255)                                                                                       tatatatTGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTC‑TTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGAACAt                          <  1:210599/139‑1 (MQ=255)                                                                                              tGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTC‑TTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATa                                       >  1:646147/1‑119 (MQ=255)                                                                                              tGTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTC‑TTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATa                                       <  2:646147/119‑1 (MQ=255)                                                                                               gTATATACCAGGCTTAATGAACTAAACAATCGTAAGGCTACAGCAACATGAGACTATAGCCTG‑TTTTTATTCTATAGTGCCAACTCCCATAAGTATAGCCGTCTTAATCATCTCGATACCACTATGAACATCTTTTttc                  >  2:256637/1‑139 (MQ=255)                                                                                                tatataCCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCctc‑t                                                                                             <  2:863644/63‑1 (MQ=255)                                                                                                tatataCCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCctc‑t                                                                                             >  1:863644/1‑63 (MQ=255)                                                                                                tatataCCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTC‑TTTTTTTTATATAGTGCAAACACCCATACGTAAAg                                                           <  1:283887/97‑1 (MQ=255)                                                                                                tatataCCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTC‑TTTTTTTTATATAGTGCAAACACCCATACGTAAAg                                                           >  2:283887/1‑97 (MQ=255)                                                                                                tatataCCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTC‑TTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGAACATCTAATttct                 <  2:110112/139‑1 (MQ=255)                                                                                                 atataCCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTC‑TTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGAACATCTAATttctt                >  1:691465/1‑139 (MQ=255)                                                                                                  tataCCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTC‑TTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCaa                                              >  1:160367/1‑108 (MQ=255)                                                                                                  tataCCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTC‑TTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCaa                                              <  2:160367/108‑1 (MQ=255)                                                                                                  tataCCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTC‑TTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGAACATCTAATttcttc               >  2:785217/1‑139 (MQ=255)                                                                                                   ataCCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCctc‑t                                                                                             <  1:671747/60‑1 (MQ=255)                                                                                                   ataCCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCctc‑t                                                                                             >  2:671747/1‑60 (MQ=255)                                                                                                     aCCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCctc‑t                                                                                             <  1:677375/58‑1 (MQ=255)                                                                                                     aCCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCctc‑t                                                                                             >  2:677375/1‑58 (MQ=255)                                                                                                     aCCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTC‑TTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATc                                                <  2:520102/103‑1 (MQ=255)                                                                                                     aCCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTC‑TTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATc                                                >  1:520102/1‑103 (MQ=255)                                                                                                     aCCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTC‑TTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGAACATCTAATTTCTTCATg            >  2:7075/1‑139 (MQ=255)                                                                                                     aCCAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTC‑TTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGAACATCTAATTTCTTCATg            >  2:909614/1‑139 (MQ=255)                                                                                                       cAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCctc‑t                                                                                             <  2:776637/56‑1 (MQ=255)                                                                                                       cAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCctc‑t                                                                                             >  1:776637/1‑56 (MQ=255)                                                                                                       cAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTC‑TTTTTTTTATATAGTGCa                                                                            >  2:295983/1‑73 (MQ=255)                                                                                                       cAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTC‑TTTTTTTTATATAGTGCa                                                                            <  1:295983/73‑1 (MQ=255)                                                                                                       cAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTC‑TTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACt                                            >  2:254256/1‑105 (MQ=255)                                                                                                       cAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTC‑TTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACt                                            <  1:254256/105‑1 (MQ=255)                                                                                                       cAGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTC‑TTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGAACATCTAATTTCTTCATGat          >  2:878060/1‑139 (MQ=255)                                                                                                        aGGCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTC‑TTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGAACATCTAATTTCTTCATGata         <  2:296136/139‑1 (MQ=255)                                                                                                          gCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCctc‑t                                                                                             >  2:812450/1‑53 (MQ=255)                                                                                                          gCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCctc‑t                                                                                             >  2:43806/1‑53 (MQ=255)                                                                                                          gCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCctc‑t                                                                                             <  1:43806/53‑1 (MQ=255)                                                                                                          gCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCctc‑t                                                                                             <  1:812450/53‑1 (MQ=255)                                                                                                          gCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTC‑ttt                                                                                           >  2:357265/1‑55 (MQ=255)                                                                                                          gCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTC‑ttt                                                                                           >  2:380290/1‑55 (MQ=255)                                                                                                          gCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTC‑ttt                                                                                           <  1:380290/55‑1 (MQ=255)                                                                                                          gCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTC‑ttt                                                                                           <  1:357265/55‑1 (MQ=255)                                                                                                          gCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTC‑TTTTTTTTATATAGTGCaaa                                                                          >  2:316166/1‑72 (MQ=255)                                                                                                          gCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTC‑TTTTTTTTATATAGTGCaaa                                                                          >  2:860174/1‑72 (MQ=255)                                                                                                          gCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTC‑TTTTTTTTATATAGTGCaaa                                                                          <  1:860174/72‑1 (MQ=255)                                                                                                          gCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTC‑TTTTTTTTATATAGTGCaaa                                                                          <  1:316166/72‑1 (MQ=255)                                                                                                          gCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTC‑TTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGAAc                            <  2:374475/118‑1 (MQ=255)                                                                                                          gCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTC‑TTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGAAc                            >  1:374475/1‑118 (MQ=255)                                                                                                          gCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTC‑TTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGAACATCTAATTTCTTCATGATAtt       >  2:93482/1‑139 (MQ=255)                                                                                                          gCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTC‑TTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGAACATCTAATTTCTTCATGATAtt       >  1:786470/1‑139 (MQ=255)                                                                                                          gCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTC‑TTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGAACATCTAATTTCTTCATGATAtt       <  1:7075/139‑1 (MQ=255)                                                                                                          gCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTC‑TTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGAACATCTAATTTCTTCATGATAtt       >  1:448131/1‑139 (MQ=255)                                                                                                          gCTTAATGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTC‑TTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGAACATCTAATTTCTTCATGATAtt       >  1:225990/1‑139 (MQ=255)                                                                                                              aaTGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCctc‑t                                                                                             >  2:175739/1‑49 (MQ=255)                                                                                                              aaTGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCctc‑t                                                                                             <  1:175739/49‑1 (MQ=255)                                                                                                              aaTGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTC‑TTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGAACATCTAATTTCTTCATGATATTGAGt   >  1:312306/1‑139 (MQ=255)                                                                                                               aTGAACTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTC‑TTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGAACATCTAATTTCTTCATGATATTGAGTc  >  1:72120/1‑139 (MQ=255)                                                                                                                    cTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTC‑TTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGAACATCTAATttct                 >  1:909478/1‑119 (MQ=255)                                                                                                                    cTAAACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTC‑TTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGAACATCTAATttct                 <  2:909478/119‑1 (MQ=255)                                                                                                                       |                                                                                                                                    GTGGAGTAACGTGGCAATGCCTGGGGACTTATAATGCGGGTTTTGCAATGGATAACCAAAAAAAGAGACAGCAATATGCCCCAAAATATATATTGTATATACCAGGCTTAATGAACTAGACAATCGTAAGGCTTCAGCAAAATGAGCCTAAAGCCTC‑TTTTTTTTATATAGTGCAAACACCCATACGTAAAGCTGTTTTGATCAACTCGATACCACTGTGAACATCTAATTTCTTCATGATATTGAGTC  >  NC_000913/2994297‑2994545

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: ‑