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%	251.0 / NA	70	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 (34/36);  total (34/36)

CAGGCCATCGTCAATAACGAAGGCGAGAGCACTATCACCAATGGCGGCACCGGCACTCAGATCAACGGTAACGACGCCACCGCGAATAACAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGTACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGCGCATGGTGTTGAGAACATTGGTGACAACGGCACGGTTAACAACAAAGGAGATATTGTTGTTTCCGATA  >  NC_000913/1466868‑1467129                                                                                                                                 |                                                                                                                                      cAGGCCATCGTCAATAACGAAGGCGAGAGCACTATCACCAATGGCGGCACCGGCACTCAGATCAACGGTAACGACGCCACCGCGAATAACAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATcg                                                                                                                             <  2:135115/139‑1 (MQ=255)                  cGAAGGCGAGAGCACTATCACCAATGGCGGCACCGGCACTCAGATCAACGGTAACGACGCCACCGCGAATAACAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGAGCAat                                                                                                                     <  1:1052562/130‑1 (MQ=255)                  cGAAGGCGAGAGCACTATCACCAATGGCGGCACCGGCACTCAGATCAACGGTAACGACGCCACCGCGAATAACAGTGGAAAAAACACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAat                                                                                                                     >  2:1052562/1‑130 (MQ=255)                        cGAGAGCACTATCACCAATGGCGGCACCGGCACTCAGATCAACGGTAACGACGCCACCGCGAATAACAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAAt                                                                                                      <  1:328711/139‑1 (MQ=255)                             gCACTATCACCAATGGCGGCACCGGCACTCAGATCAACGGTAACGACGCCACCGCGAATAACAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGa                                                                                                 >  1:690984/1‑139 (MQ=255)                                 tATCACCAATGGCGGCACCGGCACTCAGATCAACGGTAACGACGCCACCGCGAATAACAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCggg                                                                                                                         <  2:434629/111‑1 (MQ=255)                                 tATCACCAATGGCGGCACCGGCACTCAGATCAACGGTAACGACGCCACCGCGAATAACAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCggg                                                                                                                         >  1:434629/1‑111 (MQ=255)                                      ccAATGGCGGCACCGGCACTCAGATCAACGGTAACGACGCCACCGCGAATAACAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATcg                                                                                                                             >  1:584831/1‑102 (MQ=255)                                      ccAATGGCGGCACCGGCACTCAGATCAACGGTAACGACGCCACCGCGAATAACAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATcg                                                                                                                             <  2:584831/102‑1 (MQ=255)                                        aaTGGCGGCACCGGCACTCAGATCAACGGTAACGACGCCACCGCGAATAACAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGa                                                                                      >  2:1446679/1‑139 (MQ=255)                                         aTGGCGGCACCGGCACTCAGATCAACGGTAACGACGCCACCGCGAATAACAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCgg                                                                                                                >  2:530603/1‑112 (MQ=255)                                         aTGGCGGCACCGGCACTCAGATCAACGGTAACGACGCCACCGCGAATAACAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCgg                                                                                                                <  1:530603/112‑1 (MQ=255)                                             cggcaccggcacTCAGATCAACGGTAACGACGCCACCGCGAATAACAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCgg                                                                                                                >  1:1039178/1‑108 (MQ=255)                                             cggcaccggcacTCAGATCAACGGTAACGACGCCACCGCGAATAACAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCgg                                                                                                                <  2:1039178/108‑1 (MQ=255)                                             cggcaccggcacTCAGATCAACGGTAACGACGCCACCGCGAATAACAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGC‑GGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTa                                                                                >  1:1503750/1‑139 (MQ=255)                                               gcaccggcacTCAGATCAACGGTAACGACGCCACCGCGAATAACAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTAc                                                                               <  1:125390/139‑1 (MQ=255)                                                     gcacTCAGATCAACGGTAACGACGCCACCGCGAATAACAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCgg                                                                         >  1:1193980/1‑139 (MQ=255)                                                           aGATCAACGGTAACGACGCCACCGCGAATAACAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGCGCa                                                                   <  2:356353/139‑1 (MQ=255)                                                           aGATCAACGGTAACGACGCCACCGCGAATAACAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGCGCa                                                                   <  2:988019/139‑1 (MQ=255)                                                             aTCAACGGTAACGACGCCACCGCGAATAACAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGCGCATg                                                                 >  2:855880/1‑139 (MQ=255)                                                                aaCGGTAACGACGCCACCGCGAATAACAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCgg                                                                                                                          >  1:165406/1‑79 (MQ=255)                                                                aaCGGTAACGACGCCACCGCGAATAACAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCgg                                                                                                                          <  2:165406/79‑1 (MQ=255)                                                                aaCGGTAACGACGCCACCGCGAATAACAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGCGCATGgtg                                                              >  1:799741/1‑139 (MQ=255)                                                                     tAACGACGCCACCGCGAATAACAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAatgccgat                                                                                                               <  2:756442/85‑7 (MQ=255)                                                                     tAACGACGCCACCGCGAATAACAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAatgccgat                                                                                                               >  1:756442/1‑79 (MQ=255)                                                                     tAACGACGCCACCGCGAATAACAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCg                                                                          >  2:1322870/1‑122 (MQ=255)                                                                     tAACGACGCCACCGCGAATAACAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCg                                                                          <  1:1322870/122‑1 (MQ=255)                                                                     tAACGACGCCACCGCGAATAACAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGCGCa                                                                   >  2:1325433/1‑129 (MQ=255)                                                                     tAACGACGCCACCGCGAATAACAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGCGCa                                                                   <  1:1325433/129‑1 (MQ=255)                                                                      aaCGACGCCACCGCGAATAACAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGCGCATGGTGTTgaga                                                        <  1:855880/139‑1 (MQ=255)                                                                       acgacgCCACCGCGAATAACAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATcgcg                                                                                                                           >  2:133588/1‑71 (MQ=255)                                                                       acgacgCCACCGCGAATAACAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATcgcg                                                                                                                           <  1:133588/71‑1 (MQ=255)                                                                            gCCACCGCGAATAACAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATgg                                                                                              >  2:1227450/1‑95 (MQ=255)                                                                            gCCACCGCGAATAACAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATgg                                                                                              <  1:1227450/95‑1 (MQ=255)                                                                            gCCACCGCGAATAACAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGCGCATGGTGTTGAGAACATTg                                                  >  2:824113/1‑139 (MQ=255)                                                                             ccACCGCGAATAACAGAGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCgg                                                                                                                <  1:1379436/76‑1 (MQ=255)                                                                             ccACCGCGAATAACAGAGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCgg                                                                                                                >  2:1379436/1‑76 (MQ=255)                                                                                 cgcgAATAACAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCt                                                                                                    >  1:428943/1‑84 (MQ=255)                                                                                 cgcgAATAACAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCt                                                                                                    <  2:428943/84‑1 (MQ=255)                                                                                   cgAATAACAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGCGCATGGTGTTGAGAACATTGGTGACaa                                           >  2:124906/1‑139 (MQ=255)                                                                                     aaTAACAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGCGCATGGTGTTGAGAACATTGGTGACAACg                                         <  2:799741/139‑1 (MQ=255)                                                                                      aTAACAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGCGCATGGTGTTGAGAACATTGGTGACAACgg                                        <  1:124906/139‑1 (MQ=255)                                                                                        aaCAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGCGCATGGTGTTGAGAACATTGGTGACAACGGCa                                      <  2:1193980/139‑1 (MQ=255)                                                                                        aaCAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGCGCATGGTGTTGAGAACATTGGTGACAACGGCa                                      <  1:500535/139‑1 (MQ=255)                                                                                        aaCAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGCGCATGGTGTTGAGAACATTGGTGACAACGGCa                                      <  2:690984/139‑1 (MQ=255)                                                                                             tGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCgg                                                                                                                <  2:181399/60‑1 (MQ=255)                                                                                             tGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCgg                                                                                                                >  1:181399/1‑60 (MQ=255)                                                                                             tGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTg                                                                                                           <  2:1208913/65‑1 (MQ=255)                                                                                             tGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTg                                                                                                           >  1:1208913/1‑65 (MQ=255)                                                                                               gAAAAACCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCgg                                                                         <  1:1645138/97‑1 (MQ=255)                                                                                               gAAAAACCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCgg                                                                         >  2:1645138/1‑97 (MQ=255)                                                                                               gAAAAACCACTGTTGATGGAAAAGATTCAACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGCGCATGGTGTTGAGAACATTGGTGACAACGGCACGGTTaa                               >  1:1047692/1‑139 (MQ=255)                                                                                                    aCCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGCGCATGGTGTTGAGAACATTGGTGACAACGGCACGGTTAacaaca                          >  1:267386/1‑139 (MQ=255)                                                                                                     ccACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCg                                                                          <  2:1435382/90‑1 (MQ=255)                                                                                                     ccACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCg                                                                          >  1:1435382/1‑90 (MQ=255)                                                                                                     ccACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGCGCATGGTGTTGAGAACATTGGTGACAACGGCACGGTTAAcaacaa                         <  1:1446679/139‑1 (MQ=255)                                                                                                           ttGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCt                                                                                                    <  1:130049/58‑1 (MQ=255)                                                                                                           ttGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCt                                                                                                    >  2:130049/1‑58 (MQ=255)                                                                                                                  aaaaGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGCGCATGGTGTTGAGAACGTTGGTGACAACGGCACGGTTAACAACAAAGGAGATAttgtt            <  2:1047692/139‑1 (MQ=255)                                                                                                                   aaaGATTCCACGGGCACCAAAATCGCGGGCAATATCGGGATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGCGCATGGTGTTGAGAACATTGGTGACAACGGCACGGTTAACAACAAAGGAGATAttgttg           >  2:747889/1‑139 (MQ=255)                                                                                                                     aGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTgcgc                                                                    <  1:887933/80‑1 (MQ=255)                                                                                                                     aGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTgcgc                                                                    >  2:887933/1‑80 (MQ=255)                                                                                                                       aTTCCACGGGCACCAAAATCGCGGGCAATATCGGGATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGCGCATGGTGTTGAGAACATTGGTGACAACGGCACGGTTAACAACAAAGGAGATATTGTTGTTTc       <  1:747889/139‑1 (MQ=255)                                                                                                                       aTTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTaa                                                                                                        <  1:94026/42‑1 (MQ=255)                                                                                                                       aTTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTaa                                                                                                        >  2:94026/1‑42 (MQ=255)                                                                                                                           cACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGCGCATGGTGTTGAGAACATTGGTGACAACGGCACGGTTAACAACAAAGGAGATATTGTTGTTTc       <  2:359771/135‑1 (MQ=255)                                                                                                                           cACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGCGCATGGTGTTGAGAACATTGGTGACAACGGCACGGTTAACAACAAAGGAGATATTGTTGTTTc       >  1:359771/1‑135 (MQ=255)                                                                                                                            aCGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGCGCATGGTGTTGAGAACATTGGTGACAACGGCACGGTTAACAACAAAGGAGATATTGTTGTTTCCGATa  >  1:328390/1‑139 (MQ=255)                                                                                                                             cGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGCGCATGGTGTTgaga                                                        >  1:1351599/1‑84 (MQ=255)                                                                                                                             cGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGCGCATGGTGTTgaga                                                        <  2:1351599/84‑1 (MQ=255)                                                                                                                                 |                                                                                                                                      CAGGCCATCGTCAATAACGAAGGCGAGAGCACTATCACCAATGGCGGCACCGGCACTCAGATCAACGGTAACGACGCCACCGCGAATAACAGTGGAAAAACCACTGTTGATGGAAAAGATTCCACGGGTACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGCGCATGGTGTTGAGAACATTGGTGACAACGGCACGGTTAACAACAAAGGAGATATTGTTGTTTCCGATA  >  NC_000913/1466868‑1467129

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑