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%	171.1 / NA	49	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 (24/25);  total (24/25)

CATCGTCAATAACGAAGGCGAGAGCACTATCACCAATGGCGGCACCGGCACTCAGATCAACGGTAACGACGCCACCGCGAATAACAGTGGAAAAA‑CCACTGTTGATGGAAAAGATTCCACGGGTACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGCGCATGGTGTTGAGAACATTGGTGACAACGGCACGGTTAACAACAAAGGAGATATTGTTGTT  >  NC_000913/1466873‑1467122                                                                                                                             |                                                                                                                               cATAGTCAAGAACGAAGGCGAGTGCACAATCACCAATGGCGGAACGGGCACTCAGATCAACGGTAACGGCACCACCGCGATTAACAGTGGAAAAA‑CCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCggga                                                                                                                 <  2:1338837/139‑2 (MQ=255)  aTCGTCAATAACGAAGGCGAGAGCACCATCACCAACGGCGGCACCGGCACCCAGATCAACGGTGACGACGCCACCGCAAATAACAACGGAAAAA‑CCACTGTTGACGGAAAAGATTCCACCGGAACGGAAATCGCgggaa                                                                                                                >  2:64878/1‑137 (MQ=11)   tCGTCAATAACGAAGGCGAGAGCACTATCACCAATGGCGGCACCGGCACTCAGATCAACGGTAACGACGCCACCGCGAATAACAGTGGAAAAA‑CCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCaa                                                                                                               <  2:1315017/139‑1 (MQ=255)         aTAACGAAGGCGAGAGCACTATCACCAATGGCGGCACCGGCACTCAGATCAACGGTAACGACGCCACCGCGAATAACAGTGGAAAAA‑CCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCgg                                                                                                         >  2:780817/1‑139 (MQ=255)         aTAACGAAGGCGAGAGCACTATCACCAATGGCGGCACCGGCACTCAGATCAACGGTAACGACGCCACCGCGAATAACAGTGGAAAAA‑CCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCgg                                                                                                         <  1:780817/139‑1 (MQ=255)          tAACGAAGGCGAGAGCACTATCACCAATGGCGGCACCGGCACTCAGATCAACGGTAACGCCGCCACCGCGAATAACAGTGGAAAAACCCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCgg                                                                                                         <  2:814411/139‑1 (MQ=255)                                    aTGGCGGCACCGGCACTCAGATCAACGGTAACGACGCCACCGCGAATAACAGTGGAAAAA‑CCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGa                                                                               >  1:1047300/1‑138 (MQ=255)                                    aTGGCGGCACCGGCACTCAGATCAACGGTAACGACGCCACCGCGAATAACAGTGGAAAAA‑CCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGa                                                                               <  2:1047300/138‑1 (MQ=255)                                        cggcaccggcacTCAGATCAACGGTAACGACGCCACCGCGAATAACAGTGGAAAAA‑CCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCg                                                                                                          <  2:1283425/107‑1 (MQ=255)                                        cggcaccggcacTCAGATCAACGGTAACGACGCCACCGCGAATAACAGTGGAAAAA‑CCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCg                                                                                                          >  1:1283425/1‑107 (MQ=255)                                        cggcaccggcacTCAGATCAACGGTAACGACGCCACCGCGAATAACAGTGGAAAAA‑CCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGtt                                                                          >  1:1192407/1‑139 (MQ=255)                                        cggcaccggcacTCAGATCAACGGTAACGACGCCACCGCGAATAACAGTGGAAAAA‑CCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGtt                                                                          >  2:1239037/1‑139 (MQ=255)                                          gcaccggcacTCAGATCAACGGTAACGACGCCACCGCGAATAACAGTGGAAAAA‑CCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTAc                                                                        >  1:130008/1‑139 (MQ=255)                                            accggcacTCAGATCAACGGTAACGACGCCACCGCGAATAACAGTGGAAAAA‑CCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGc                                                                                                                 <  2:1255783/96‑1 (MQ=255)                                            accggcacTCAGATCAACGGTAACGACGCCACCGCGAATAACAGTGGAAAAA‑CCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGc                                                                                                                 >  1:1255783/1‑96 (MQ=255)                                                gcacTCAGATCAACGGTAACGACGCCACCGCGAATAACAGTGGAAAAA‑CCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCgg                                                                  >  1:895009/1‑139 (MQ=255)                                                 cacTCAGATCAACGGTAACGACGCCACCGCGAATAACAGTGGAAAAA‑CCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGt                                                                 <  2:346690/139‑1 (MQ=255)                                                 cacTCAGATCAACGGTAACGACGCCACCGCGAATAACAGTGGAAAAA‑CCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGt                                                                 <  2:895009/139‑1 (MQ=255)                                                      aGATCAACGGTAACGACGCCACCGCGAATAACAGTGGAAAAA‑CCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGCGCa                                                            <  2:130008/139‑1 (MQ=255)                                                      aGATCAACGGTAACGACGCCACCGCGAATAACAGTGGAAAAA‑CCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGCGCa                                                            <  1:1239037/139‑1 (MQ=255)                                                      aGATCAACGGTAACGACGCCACCGCGAATAACAGTGGAAAAA‑CCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGCGCa                                                            <  2:1192407/139‑1 (MQ=255)                                                      aGATCAACGGTAACGACGCCACCGCGAATAACAGTGGAAAAA‑CCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGCGCa                                                            <  2:35035/139‑1 (MQ=255)                                                        aTCAACGGTAACGACGCCACCGCGAATAACAGTGGAAAAA‑CCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGCGCATg                                                          <  2:469054/139‑1 (MQ=255)                                                                  acgacgCCACCGCGAATAACAGTGGAAAAA‑CCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGCGCATGGTGTTGAGaa                                                >  2:644417/1‑139 (MQ=255)                                                                       gCCACCGCGAATAACAGTGGAAAAA‑CCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGa                                                                               >  1:451323/1‑103 (MQ=255)                                                                       gCCACCGCGAATAACAGTGGAAAAA‑CCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGa                                                                               <  2:451323/103‑1 (MQ=255)                                                                          aCCGCGAATAACAGTGGAAAAA‑CCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGCGCa                                                            <  2:1322239/119‑1 (MQ=255)                                                                          aCCGCGAATAACAGTGGAAAAA‑CCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGCGCa                                                            >  1:1035268/1‑119 (MQ=255)                                                                          aCCGCGAATAACAGTGGAAAAA‑CCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGCGCa                                                            <  2:1035268/119‑1 (MQ=255)                                                                          aCCGCGAATAACAGTGGAAAAA‑CCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGCGCa                                                            >  1:1322239/1‑119 (MQ=255)                                                                                        tGGAAAAA‑CCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGCGCATGGTGTTga                                                   >  2:524888/1‑114 (MQ=255)                                                                                        tGGAAAAA‑CCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGCGCATGGTGTTga                                                   <  1:524888/114‑1 (MQ=255)                                                                                          gAAAAA‑CCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGCGCATGGTGTTGAGAACAt                                             <  1:771555/118‑1 (MQ=255)                                                                                          gAAAAA‑CCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGCGCATGGTGTTGAGAACAGTGGTGACAACGGCAAGGTTaa                        >  1:1056643/1‑139 (MQ=255)                                                                                          gAAAAA‑CCACTGTTGATAGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGAATGGTAGCCTGACTGTTACAGGCGGTGCGCATGGTGTTGAGAACAt                                             >  2:771555/1‑118 (MQ=255)                                                                                              aa‑CCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGCGCATGGTGTTGAGAACATTGGTGACAACGGCACGGTTaacaac                    <  2:1059129/139‑1 (MQ=255)                                                                                               a‑CCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGt                                                                 <  2:415158/93‑1 (MQ=255)                                                                                               a‑CCACTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGt                                                                 >  1:415158/1‑93 (MQ=255)                                                                                                   aCTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGCGCATGGTGTTGAGAACATTGGTGACAACGGCACGGTTAACAACAAAg                >  2:1288244/1‑139 (MQ=255)                                                                                                   aCTGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGCGCATGGTGTTGAGAACATTGGTGACAACGGCACGGTTAACAACAAAg                >  2:661665/1‑139 (MQ=255)                                                                                                     tGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGCGCa                                                            >  1:1031408/1‑93 (MQ=255)                                                                                                     tGTTGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGCGCa                                                            <  2:1031408/93‑1 (MQ=255)                                                                                                       ttGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATc                                                                                                           <  1:762258/44‑1 (MQ=255)                                                                                                       ttGATGGAAAAGATTCCACGGGCACCAAAATCGCGGGCAATATc                                                                                                           >  2:762258/1‑44 (MQ=255)                                                                                                               aaaGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGCGCATGGTGTTGAGAACATTGGTGACAACGGCACGGTTAACAACAAAGGAGATAttgttg    >  1:1174637/1‑139 (MQ=255)                                                                                                                 aGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATgg                                                                                       <  2:1208913/54‑1 (MQ=255)                                                                                                                 aGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATgg                                                                                       >  1:1208913/1‑54 (MQ=255)                                                                                                                 aGATTCCACGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGCGCATGGTGTTGAGAACATTGGTGACAACGGCACGGTTAACAACAAAGGAGATATTgttgtt  >  2:997097/1‑139 (MQ=255)                                                                                                                        aCGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTAc                                                                        <  2:282013/62‑1 (MQ=255)                                                                                                                        aCGGGCACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTAc                                                                        >  1:282013/1‑62 (MQ=255)                                                                                                                             |                                                                                                                               CATCGTCAATAACGAAGGCGAGAGCACTATCACCAATGGCGGCACCGGCACTCAGATCAACGGTAACGACGCCACCGCGAATAACAGTGGAAAAA‑CCACTGTTGATGGAAAAGATTCCACGGGTACCAAAATCGCGGGCAATATCGGCATTGTAAATCTGGATGGTAGCCTGACTGTTACAGGCGGTGCGCATGGTGTTGAGAACATTGGTGACAACGGCACGGTTAACAACAAAGGAGATATTGTTGTT  >  NC_000913/1466873‑1467122

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑