Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,466,996	T→C	pseudogene (1605/2513 nt)	ydbA →	pseudogene, autotransporter homolog, interrupted by IS2 and IS30

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,466,996	0	T	C	100.0%	248.8 / NA	69	pseudogene (1605/2513 nt)	ydbA	pseudogene, autotransporter homolog, interrupted by IS2 and IS30
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (33/36);  total (33/36)

CGGCGACCAGGCCATCGTCAATAACGAAGGCGAGAGCACTATCACCAATGGCGGCACCGGCACTCAGATCAACGGTAACGACGCCACCGCGAATAACAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGTACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGCGCATGGTGTTGAGAACATTGGTGACAACGGCACGGTTAACAACAAAGGAGATATTGTTGTTTC  >  NC_000913/1466861‑1467124                                                                                                                                        |                                                                                                                                 cGGCGACCAGGCCATCGTCAATAACGAAGGCGAGAGCACTATCACCAATGGCGGCACCGGCACTCAGATCAACGGTAACGACGCCACCGCGAATAACAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGCAcc                                                                                                                               >  1:501391/1‑139 (MQ=255)          ggCCATCGTCAATAACGAAGGCGAGAGCACTATCACCAATGGCGGCACCGGCACTCAGATCAACGGTAACGACGCCACCGCGAATAACAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATcgcg                                                                                                                      >  2:795745/1‑139 (MQ=255)           gCCATCGTCAATAACGAAGGCGAGAGCACTATCACCAATGGCGGCACCGGCACTCAGATCAACGGTAACGACGCCACCGCGAATAACAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCgg                                                                                                                     <  1:243872/139‑1 (MQ=255)            ccATCGTCAATAACGAAGGCGAGAGCACTATCACCAATGGCGGCACCGGCACTCAGATCAACGGTAACGACGCCACCGCGAATAACAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCggg                                                                                                                    >  2:592879/1‑139 (MQ=255)                  tCAATAACGAAGGCGAGAGCACTATCACCAATGGCGGCACCGGCACTCAGATCAACGGTAACGACGCCACCGCGAATAACAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAatat                                                                                                              <  2:1011669/139‑1 (MQ=255)                         cGAAGGCGAGAGCACTATCACCAATGGCGGCACCGGCACTCAGATCAACGGTAACGACGCCACCGCGAATAACAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGc                                                                                                                   <  2:828580/127‑1 (MQ=255)                         cGAAGGCGAGAGCACTATCACCAATGGCGGCACCGGCACTCAGATCAACGGTAACGACGCCACCGCGAATAACAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGc                                                                                                                   >  1:828580/1‑127 (MQ=255)                             ggCGAGAGCACTATCACCAATGGCGGCACCGGCACTCAGATCAACGGTAACGACGCCACCGCGAATAACAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTaa                                                                                                   <  2:258076/139‑1 (MQ=255)                             ggCGAGAGCACTATCACCAATGGCGGCACCGGCACTCAGATCAACGGTAACGACGCCACCGCGAATAACAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTaa                                                                                                   >  1:1287568/1‑139 (MQ=255)                                 agagCACTATCACCAATGGCGGCACCGGCACTCAGATCAACGGTAACGACGCCACCGCGAATAACAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCa                                                                                                         <  2:699013/129‑1 (MQ=255)                                 agagCACTATCACCAATGGCGGCACCGGCACTCAGATCAACGGTAACGACGCCACCGCGAATAACAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCa                                                                                                         >  1:699013/1‑129 (MQ=255)                                   agCACTATCACCAATGGCGGCACCGGCACTCAGATCAACGGTAACGACGCCACCGCGAATAACAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTgg                                                                                             >  1:584257/1‑139 (MQ=255)                                     cACTATCACCAATGGCGGCACCGGCACTCAGATCAACGGTAACGACGCCACCGCGAATAACAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGAt                                                                                           >  1:926334/1‑139 (MQ=255)                                        tATCACCAATGGCGGCACCGGCACTCAGATCAACGGTAACGACGCCACCGCGAATAACAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGt                                                                                        >  2:1253692/1‑139 (MQ=255)                                               aaTGGCGGCACCGGCACTCAGATCAACGGTAACGACGCCACCGCGAATAACAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCgg                                                                                                                     >  1:160539/1‑103 (MQ=255)                                               aaTGGCGGCACCGGCACTCAGATCAACGGTAACGACGCCACCGCGAATAACAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCgg                                                                                                                     <  2:160539/103‑1 (MQ=255)                                               aaTGGCGGCACCGGCACTCAGATCAACGGTAACGACGCCACCGCGAATAACAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGa                                                                                 <  2:293467/139‑1 (MQ=255)                                                aTGGCGGCACCGGCACTCAGATCAACGGTAACGACGCCACCGCGAATAACAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGAc                                                                                >  2:636506/1‑139 (MQ=255)                                                  ggcggcACCGGCACTCAGATCAACGGTAACGACGCCACCGCGAATAACAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCgg                                                                                                           >  2:77418/1‑110 (MQ=255)                                                  ggcggcACCGGCACTCAGATCAACGGTAACGACGCCACCGCGAATAACAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCgg                                                                                                           <  1:77418/110‑1 (MQ=255)                                                  ggcggcACCGGCACTCAGATCAACGGTAACGACGCCACCGCGAATAACAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTg                                                                              >  2:604507/1‑139 (MQ=255)                                                    cggcaccggcacTCAGATCAACGGTAACGACGCCACCGCGAATAACAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGtt                                                                            >  2:47791/1‑139 (MQ=255)                                                    cggcaccggcacTCAGATCAACGGTAACGACGCCACCGCGAATAACAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGtt                                                                            >  1:785627/1‑139 (MQ=255)                                                     ggcaccggcacTCAGATCAACGGTAACGACGCCACCGCGAATAACAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTa                                                                           <  2:658487/139‑1 (MQ=255)                                                      gcaccggcacTCAGATCAACGGTAACGACGCCACCGCGAATAACAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTAc                                                                          >  1:387939/1‑139 (MQ=255)                                                          cggcacTCAGATCAACGGTAACGACGCCACCGCGAATAACAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGc                                                                      <  1:636506/139‑1 (MQ=255)                                                          cggcacTCAGATCAACGGTAACGACGCCACCGCGAATAACAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGc                                                                      <  1:592879/139‑1 (MQ=255)                                                            gcacTCAGATCAACGGTAACGACGCCACCGCGAATAACAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCggg                                                                                                                    <  2:639510/91‑1 (MQ=255)                                                            gcacTCAGATCAACGGTAACGACGCCACCGCGAATAACAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCggg                                                                                                                    >  1:639510/1‑91 (MQ=255)                                                            gcacTCAGATCAACGGTAACGACGCCACCGCGAATAACAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCgg                                                                    >  1:1148276/1‑139 (MQ=255)                                                             cacTCAGATCAACGGTAACGACGCCACCGCGAATAACAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGt                                                                   <  2:785627/139‑1 (MQ=255)                                                                  aGATCAACGGTAACGACGCCACCGCGAATAACAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGCGCa                                                              <  2:1243101/139‑1 (MQ=255)                                                                  aGATCAACGGTAACGACGCCACCGCGAATAACAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGCGCa                                                              <  2:171137/139‑1 (MQ=255)                                                                  aGATCAACGGTAACGACGCCACCGCGAATAACAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGCGCa                                                              <  1:1253692/139‑1 (MQ=255)                                                                  aGATCAACGGTAACGACGCCACCGCGAATAACAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGCGCa                                                              <  1:47791/139‑1 (MQ=255)                                                                   gATCAACGGTAACGACGCCACCGCGAATAACAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGCGCAt                                                             <  1:1203342/139‑1 (MQ=255)                                                                       aaCGGTAACGACGCCCCCGCGAATAACAGTGGAAAAACCACTGCTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATACCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGCGCATGgtg                                                         >  2:542115/1‑139 (MQ=255)                                                                         cGGTAACGACGCCACCGCGAATAACAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGCGCATGGTGtt                                                       <  2:904947/139‑1 (MQ=255)                                                                             aaCGACGCCACCGCGAATAACAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGCGCATGGTGTTgaga                                                   <  2:387939/139‑1 (MQ=255)                                                                              acgacgCCACCGCGAATAACAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATcg                                                                                                                        <  1:249323/69‑1 (MQ=255)                                                                              acgacgCCACCGCGAATAACAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATcg                                                                                                                        >  2:249323/1‑69 (MQ=255)                                                                              acgacgCCACCGCGAATAACAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCggg                                                                                                                    >  2:1248048/1‑73 (MQ=255)                                                                              acgacgCCACCGCGAATAACAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCggg                                                                                                                    <  1:1248048/73‑1 (MQ=255)                                                                              acgacgCCACCGCGAATAACAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACt                                                                               <  1:354725/110‑1 (MQ=255)                                                                              acgacgCCACCGCGAATAACAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACt                                                                               >  2:354725/1‑110 (MQ=255)                                                                              acgacgCCACCGCGAATAACAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGCGCATGGTGTTGAGaa                                                  >  2:1215875/1‑139 (MQ=255)                                                                                            aaTAACAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTgc                                                                 <  2:925882/110‑1 (MQ=255)                                                                                            aaTAACAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTgc                                                                 >  1:925882/1‑110 (MQ=255)                                                                                               aaCAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGCGCATGGTGTTGAGAACATTGGTGACAACGGCa                                 <  2:646158/139‑1 (MQ=255)                                                                                               aaCAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGCGCATGGTGTTGAGAACATTGGTGACAACGGCa                                 <  2:501391/139‑1 (MQ=255)                                                                                                 cAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGCGCATGGTGTTGAGAACATTGGTGACAACGGCACg                               <  1:243288/139‑1 (MQ=255)                                                                                                    tGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGCGCATGGTGTTGAGAACATTGGTGACAACGGCACGGtt                            <  2:1148276/139‑1 (MQ=255)                                                                                                    tGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGCGCATGGTGTTGAGAACATTGGTGACAACGGCACGGtt                            <  2:279673/139‑1 (MQ=255)                                                                                                           aCCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATcg                                                                                                                        <  1:780517/40‑1 (MQ=255)                                                                                                           aCCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATcg                                                                                                                        >  2:780517/1‑40 (MQ=255)                                                                                                            ccACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGCGCATGGTGTTGAGAACATTGGTGACAACGGCACGGTTAAcaacaa                    <  1:486178/139‑1 (MQ=255)                                                                                                              aCTGTTGATGTAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGCGCa                                                              <  2:864807/95‑1 (MQ=255)                                                                                                              aCTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGCGCa                                                              >  1:864807/1‑95 (MQ=255)                                                                                                                tGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGCGCATGGTGTTGAGAACATTGGTGACAACGGCACGGTTAACAACAAAGga                >  2:257364/1‑139 (MQ=255)                                                                                                                tGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGCGCATGGTGTTGAGAACATTGGTGACAACGGCACGGTTAACAACAAAGga                >  1:1215686/1‑139 (MQ=255)                                                                                                                      tGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGCGCATGGTGTTGAGAACATTGGTGACAACGGCa                                 >  2:767133/1‑116 (MQ=255)                                                                                                                      tGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGCGCATGGTGTTGAGAACATTGGTGACAACGGCa                                 <  1:767133/116‑1 (MQ=255)                                                                                                                          aaaGATTCCACGGGCACCAAAATCGCGGGCAATATCTGCATTGTAAATCTGGATGGTAGCCTGCCTGTTACAGGCGGTGCGCATGGTCTTGAGAACATTGGTGACAACGGCACGGTTAACAACAAAGGAGATAttgttg      >  1:835762/1‑139 (MQ=255)                                                                                                                            aGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGCGCa                                                              <  1:408571/81‑1 (MQ=255)                                                                                                                            aGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGCGCa                                                              >  2:408571/1‑81 (MQ=255)                                                                                                                            aGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGCGCATGGTGTTGAGAACATTGGTGACAACGGCACGGTTAACAACAAAGGAGATATTgttgtt    >  2:42646/1‑139 (MQ=255)                                                                                                                              aTTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGCGCATGGTGTTGAGAACATTGGTGACAACGGCACGGTTAACAACAAAGGAGATATTGTTGTTTc  <  1:257364/139‑1 (MQ=255)                                                                                                                                   aCGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGCGCATGGTGTTGAGAACATTGGTGACAACGGCACGGTTAACAACAAAGGAGATATTGTTGTTTc  >  1:1252028/1‑134 (MQ=255)                                                                                                                                   aCGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGCGCATGGTGTTGAGAACATTGGTGACAACGGCACGGTTAACAACAAAGGAGATATTGTTGTTTc  <  2:1252028/134‑1 (MQ=255)                                                                                                                                        |                                                                                                                                 CGGCGACCAGGCCATCGTCAATAACGAAGGCGAGAGCACTATCACCAATGGCGGCACCGGCACTCAGATCAACGGTAACGACGCCACCGCGAATAACAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGTACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGCGCATGGTGTTGAGAACATTGGTGACAACGGCACGGTTAACAACAAAGGAGATATTGTTGTTTC  >  NC_000913/1466861‑1467124

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: ‑