Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,535,441	C→T	pseudogene (439/1029 nt)	yjhR →	pseudogene, helicase family, putative frameshift suppressor

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,535,441	0	C	T	100.0%	209.9 / NA	65	pseudogene (439/1029 nt)	yjhR	pseudogene, helicase family, putative frameshift suppressor
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (31/34);  total (31/34)

CTCTTTTCTCCTGTCTACTCAAAACATGAAGATGGCAGGTTTCTTGATAGCAACAGCACTATCCTCAATGTTGCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGCCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTCAGAAACGACAGGATTTAATTTCCGCACATACACAAATTTCAACGCTGCATGGTGTGGAG  >  NC_000913/4535306‑4535575                                                                                                                                        |                                                                                                                                       ctctTTTCTCCTGTCTACTCAAAACATGAAGATGGCAGGTTTCTTGATAGCAACAGCACTATCCTCAATGTTGCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCg                                                                                                                                     >  2:1029332/1‑139 (MQ=255)              tCTACTCAAAACATGAAGATGGCAGGTTTCTTGATAGCAACAGCACTATCCTCAATGTTGCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCcgcg                                                                                                                        <  1:676932/139‑1 (MQ=255)                       aaCATGAAGATGGCAGGTTTCTTGATAGCAACAGCACTATCCTCAATGTTGCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACTTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTAtt                                                                                                               >  1:66071/1‑139 (MQ=255)                        aCATGAAGATGGCAGGTTTCTTGATAGCAACAGCACTATCCTCAATGTTGCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTg                                                                                                              >  2:1138009/1‑139 (MQ=255)                        aCATGAAGATGGCAGGTTTCTTGATAGCAACAGCACTATCCTCAATGTTGCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTg                                                                                                              >  1:777408/1‑139 (MQ=255)                                    cAGGTTTCTTGATAGCAACAGCACTATCCTCAATGTTGCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTAt                                                                                                                >  2:201456/1‑125 (MQ=255)                                    cAGGTTTCTTGATAGCAACAGCACTATCCTCAATGTTGCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTAt                                                                                                                <  1:201456/125‑1 (MQ=255)                                          tCTTGATAGCAACAGCACTATCCTCAATGTTGCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTttct                                                                                            <  1:733958/139‑1 (MQ=255)                                          tCTTGATAGCAACAGCACTATCCTCAATGTTGCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTttct                                                                                            <  1:339963/139‑1 (MQ=255)                                             tGATAGCAACAGCACTATCCTCAATGTTGCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCa                                                                                         <  2:1406913/139‑1 (MQ=255)                                                  gCAACAGCACTATCCTCAATGTTGCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCAGataa                                                                                    <  2:928744/139‑1 (MQ=255)                                                  gCAACAGCACTATCCTCAATGTTGCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCAGataa                                                                                    >  2:1455365/1‑139 (MQ=255)                                                   cAACAGCACTATCCTCAATGTTGCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCtt                                                                                                <  2:1087104/126‑1 (MQ=255)                                                   cAACAGCACTATCCTCAATGTTGCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCtt                                                                                                >  1:1087104/1‑126 (MQ=255)                                                         cACTATCCTCAATGTTGCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTcgc                                                                                                                            <  1:195539/92‑1 (MQ=255)                                                         cACTATCCTCAATGTTGCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTcgc                                                                                                                            >  2:195539/1‑92 (MQ=255)                                                                cTCAATGTTGCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCAAt                                                                      >  2:606556/1‑139 (MQ=255)                                                                        tGCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTttct                                                                                            <  2:1077048/109‑1 (MQ=255)                                                                        tGCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTttct                                                                                            >  1:1077048/1‑109 (MQ=255)                                                                        tGCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGttt                                                              >  1:345547/1‑139 (MQ=255)                                                                         gCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTc                                                             >  1:1410657/1‑139 (MQ=255)                                                                          cTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGa                                                                                                                       >  2:457881/1‑80 (MQ=255)                                                                          cTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGa                                                                                                                       <  1:457881/80‑1 (MQ=255)                                                                            gTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTttct                                                                                            >  1:589792/1‑105 (MQ=255)                                                                            gTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTttct                                                                                            <  2:589792/105‑1 (MQ=255)                                                                            gTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTCAGa                                                          <  2:1410657/139‑1 (MQ=255)                                                                                       tAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTCAGAAACGACAGGAt                                               <  1:741365/139‑1 (MQ=255)                                                                                       tAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTCAGAAACGACAGGAt                                               <  2:345547/139‑1 (MQ=255)                                                                                         aaGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTcgccg                                                                                                                          >  1:720147/1‑62 (MQ=255)                                                                                         aaGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTcgccg                                                                                                                          <  2:720147/62‑1 (MQ=255)                                                                                               gTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTCAGAAACGACAGGATTTAATTTc                                       <  2:66071/139‑1 (MQ=255)                                                                                               gTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTCAGAAACGACAGGACTTAATTTc                                       <  1:1455365/139‑1 (MQ=255)                                                                                                 tttCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTCAGAAACGACAGGAt                                               <  1:144997/129‑1 (MQ=255)                                                                                                 tttCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTCAGAAACGACAGGAt                                               >  2:144997/1‑129 (MQ=255)                                                                                                   tCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCAGa                                                                                       <  1:1151339/87‑1 (MQ=255)                                                                                                   tCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCAGa                                                                                       >  2:1151339/1‑87 (MQ=255)                                                                                                     tGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGa                                                                                                                       >  2:986954/1‑53 (MQ=255)                                                                                                     tGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGa                                                                                                                       <  1:986954/53‑1 (MQ=255)                                                                                                     tGGTATTTGGCGATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTCAGAAACGACAGGATTTAATTTCCGcaca                                 >  2:991873/1‑139 (MQ=255)                                                                                                                gATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTCAGAAACGACAGGATTTAATTTCCGCACATACACAAAttt                      <  2:1263314/139‑1 (MQ=255)                                                                                                                gATATGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTCAGAAACGACAGGATTTAATTTCCGCACATACACAAAttt                      <  2:777408/139‑1 (MQ=255)                                                                                                                 atatGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTGTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTCAGAAACGACATGATTTAATTTCCGCACATACACAAATTTc                     >  1:949605/1‑139 (MQ=255)                                                                                                                  tatGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCAg                                                                                        >  1:3684/1‑71 (MQ=255)                                                                                                                  tatGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCAg                                                                                        <  2:3684/71‑1 (MQ=255)                                                                                                                  tatGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTCAGAAACGACAGGATTTAATTTCCGCACATACACAAATTTCa                    >  2:1024400/1‑139 (MQ=255)                                                                                                                    tGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTttctt                                                                                           <  2:1238008/66‑1 (MQ=255)                                                                                                                    tGGACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTttctt                                                                                           >  1:1238008/1‑66 (MQ=255)                                                                                                                     ggACCTTATCGAGATGCAGTCCGCATTTTCGCCGCGAGGNNTATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTCAGAAACGACAGGATTTAATTTCCGCACATACACAAATTTCAACg                 <  2:231010/139‑1 (MQ=255)                                                                                                                          ttATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTCAGAAACGACAGGATTTAATTTCCGCACATACACAAATTTCAACGCTGCa            <  1:606556/139‑1 (MQ=255)                                                                                                                          ttATCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTCAGAAACGACAGGATTTAATTTCCGCACATACACAAATTTCAACGCTGCa            <  1:1024400/139‑1 (MQ=255)                                                                                                                            aTCGAGATGCAGTTCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTCAGAAACGACAGGATTTAATTTCCGca                                   <  2:371878/114‑1 (MQ=255)                                                                                                                            aTCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTttct                                                                                            >  1:132426/1‑57 (MQ=255)                                                                                                                            aTCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTttct                                                                                            <  2:132426/57‑1 (MQ=255)                                                                                                                            aTCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCa                                                                                         >  1:1195604/1‑60 (MQ=255)                                                                                                                            aTCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCa                                                                                         <  2:1195604/60‑1 (MQ=255)                                                                                                                            aTCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTCAGAAACGACAGGAtt                                              >  1:1085750/1‑103 (MQ=255)                                                                                                                            aTCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTCAGAAACGACAGGAtt                                              <  2:1085750/103‑1 (MQ=255)                                                                                                                            aTCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTCAGAAACGACAGGATTTAATTTCCGca                                   >  1:371878/1‑114 (MQ=255)                                                                                                                            aTCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTCAGAAACGACAGGATTTAATTTCCGCACATACACAAATTTCAACGCTGCATg          >  2:882689/1‑139 (MQ=255)                                                                                                                             tCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGGAAAATATCTCTTTTGTACAGATAATAATGCGTTGCAATTTGAGTTTCAGAAACGAc                                                    >  1:970697/1‑96 (MQ=255)                                                                                                                             tCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTCAGAAACGAc                                                    <  2:970697/96‑1 (MQ=255)                                                                                                                             tCGAGATGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTCAGAAACGACAGGATTTAATTTCCGCACATACACAAATTTCAACGCTGCATgg         >  2:99224/1‑139 (MQ=255)                                                                                                                                  aTGCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTCAGAAACGACAGGATTTAATTTCCGCACATACACAGATTTCAACGCTGCATGGTGTgg    >  1:165811/1‑139 (MQ=255)                                                                                                                                    gCAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTCAGAAACGACAGGATTTAATTTCCGCACATACACAAATTTCAACGCTGCATGGTGTGGag  <  1:1346874/139‑1 (MQ=255)                                                                                                                                     cAGTCCGCATTTTCGCCGCGAGGGTTATTGGCAAAatat                                                                                                     <  2:563165/39‑1 (MQ=255)                                                                                                                                        |                                                                                                                                       CTCTTTTCTCCTGTCTACTCAAAACATGAAGATGGCAGGTTTCTTGATAGCAACAGCACTATCCTCAATGTTGCTGTCTCACGCGCTAAAGATAGTTTTCTGGTATTTGGCGATATGGACCTTATCGAGATGCAGCCCGCATTTTCGCCGCGAGGGTTATTGGCAAAATATCTCTTTTCTTCAGATAATAATGCGTTGCAATTTGAGTTTCAGAAACGACAGGATTTAATTTCCGCACATACACAAATTTCAACGCTGCATGGTGTGGAG  >  NC_000913/4535306‑4535575

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑