Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,594,132	(C)8→9	pseudogene (3955/5422 nt)	yneO ←	AIDA‑I family autotransporter YneO

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,594,124	1	.	C	100.0%	184.7 / NA	51	pseudogene (3963/5422 nt)	yneO	AIDA‑I family autotransporter YneO
Reads supporting (aligned to +/- strand):  ref base . (0/0);  new base C (26/25);  total (26/25)

ACGTCATCAGGCCATTGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCG‑CCGATAGTGGTTTTAGCGACACGCAG‑TG‑‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCCCCCCCCAC  >  NC_000913/1593987‑1594258                                                                                                                                             |                                                                                                                                        aCGTCATCAGGCCATTGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCG‑CCGATAGTGGTTTTAGCGACACGCAG‑TG‑‑cc                                                                                                                                      <  2:824100/140‑1 (MQ=255)     catcaGGCCATTGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCG‑CCGATAGTGGTTTTAGCGACACGCAG‑TG‑‑cccccc                                                                                                                                  >  2:341119/1‑140 (MQ=255)          ggCCATTGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCTGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCG‑CCGATAGTGGTTTTAGCGACACGCAG‑TG‑‑cccccccccag                                                                                                                             <  1:644101/140‑4 (MQ=255)          ggCCATTGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCG‑CCGATAGTGGTTTTAGCGACACGCAG‑TG‑‑cccccccccag                                                                                                                             <  1:620784/140‑4 (MQ=255)             cATTGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCG‑CCGATAGTGGTTTTAGCGACACGCAG‑TG‑‑cc                                                                                                                                      >  2:821720/1‑128 (MQ=255)             cATTGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCG‑CCGATAGTGGTTTTAGCGACACGCAG‑TG‑‑cc                                                                                                                                      <  1:821720/128‑1 (MQ=255)              aTTGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCG‑CCGATAGTGGTTTTAGCGACACGCAG‑TGC‑CCCCCCCCAGGCAt                                                                                                                          >  2:885938/1‑140 (MQ=255)               ttGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCG‑CCGATAGTGGTTTTAGCGACACGCAG‑TGC‑CCCCCCCCAGGCATa                                                                                                                         >  1:214727/1‑140 (MQ=255)               ttGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCG‑CCGATAGTGGTTTTAGCGACACGCAG‑TGC‑CCCCCCCCAGGCATa                                                                                                                         >  2:102487/1‑140 (MQ=255)                         tataGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCG‑CCGATAGTGGTTTTAGCGACACGCAG‑TGC‑CCCCCCCCAGGCATAACGTTCatat                                                                                                               <  1:341119/140‑1 (MQ=255)                         tataGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCG‑CCGATAGTGGTTTTAGCGACACGCAG‑TGC‑CCCCCCCCAGGCATAACGTTCatat                                                                                                               >  1:62464/1‑140 (MQ=255)                         tataGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCG‑CCGATAGTGGTTTTAGCGACACGCAG‑TGC‑CCCCCCCCAGGCATAACGTTCat                                                                                                                 >  2:489308/1‑138 (MQ=255)                         tataGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCG‑CCGATAGTGGTTTTAGCGACACGCAG‑TGC‑CCCCCCCCAGGCATAACGTTCat                                                                                                                 <  1:489308/138‑1 (MQ=255)                            aGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCG‑CCGATAGTGGTTTTAGCGACACGCAG‑TGC‑CCCCCCCCAGGCATAACTTCCATTTCAc                                                                                                            >  1:339609/1‑140 (MQ=255)                              ttGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCG‑CCGGTAGTGGTTTTAGCGACACGCAG‑TGC‑CCCCCCCCAGGCATAACGTTCATATCACCt                                                                                                          >  2:42665/1‑140 (MQ=255)                               tGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCG‑CCGATAGTGGTTTTAGCGACACGCAG‑TGC‑CCCCCCCCAGGCATAACGTTCATATCACCTg                                                                                                         <  1:102487/140‑1 (MQ=255)                               tGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCG‑CCGATAGTGGTTTTAGCGACACGCAG‑TGC‑CCCCCCCCAGGCATAACGTTCATATCACCTg                                                                                                         <  2:908248/140‑1 (MQ=255)                                  cGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCG‑CCGATAGTGGTTTTAGCGACACGCAG‑TGC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAg                                                                                                      >  1:476269/1‑140 (MQ=255)                                   gTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCG‑CCGATAGTGGTTTTAGCGACACGCAG‑TGC‑CCCCCCCCAGGCATAACGTTCat                                                                                                                 <  1:266313/128‑1 (MQ=255)                                   gTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCG‑CCGATAGTGGTTTTAGCGACACGCAG‑TGC‑CCCCCCCCAGGCATAACGTTCat                                                                                                                 >  2:266313/1‑128 (MQ=255)                                               tACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCG‑CCGATAGTGGTTTTAGCGACACGCAG‑TGC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTcc                                                                                         <  2:62464/140‑1 (MQ=255)                                               tACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCG‑CCGATAGTGGTTTTAGCGACACGCAG‑TGC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTcc                                                                                         <  1:42665/140‑1 (MQ=255)                                                   ttCCCCGGTTTCCCCCCTTCGCTATTCATTTGAGCCGTGCCGCCATTCTCCAGGTTGCCG‑CCGATAGTGGTTTTAGCGACACGCAG‑TGC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGAc                                                                                     <  2:250225/140‑1 (MQ=255)                                                   ttCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCG‑CCGATAGTGGTTTTAGCGACACGCAG‑TGC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGAc                                                                                     >  1:250225/1‑140 (MQ=255)                                                    tCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCG‑CCGATAGTGGTTTTAGCGACACGCAG‑TGC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACa                                                                                    >  2:628831/1‑140 (MQ=255)                                                    tCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCG‑CCGATAGTGGTTTTAGCGACACGCAG‑TGC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACa                                                                                    >  1:874550/1‑140 (MQ=255)                                                    tCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCG‑CCGATAGTGGTTTTAGCGACACGCAG‑TGC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACa                                                                                    <  1:885938/140‑1 (MQ=255)                                                    tCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCG‑CCGATAGTGGTTTTAGCGACACGCAG‑TGC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACa                                                                                    >  1:624453/1‑140 (MQ=255)                                                       ccGGTTTCCCCCCTTCCCTATTTAATTGAACCCTGCCCCCATTCCCCCGGTTGCCGCCCGATAG‑GGTTTTAGGCACCCGCAGTTC‑‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATca                                                                                 <  2:339609/140‑1 (MQ=255)                                                         ggTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCG‑CCGATAGTGGTTTTAGCGACACGCAG‑TGC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACAt                                                                                   <  1:369346/136‑1 (MQ=255)                                                         ggTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCG‑CCGATAGTGGTTTTAGCGACACGCAG‑TGC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACAt                                                                                   >  2:369346/1‑136 (MQ=255)                                                            ttCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCG‑CCGATAGTGGTTTTAGCGACACGCAG‑TGC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCg                                                                            <  2:476269/140‑1 (MQ=255)                                                            tcccccccTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCG‑CCGATAGTGGTTTTAGCGACACGCAG‑TGC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCg                                                                            <  1:892486/138‑1 (MQ=255)                                                              ccccccTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCG‑CCGATAGTGGTTTTAGCGACACGCAG‑TGC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCt                                                                          <  1:661716/140‑1 (MQ=255)                                                                 cccTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCG‑CCGATAGTGGTTTTAGCGACACGCAG‑TGC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGtt                                                                       <  1:968973/140‑1 (MQ=255)                                                                   ctccGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCG‑CCGATAGTGGTTTTAGCGACACGCAG‑TGC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTAt                                                                     <  2:761728/137‑1 (MQ=255)                                                                     tCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCG‑CCGATAGTGGTTTTAGCGACACGCAG‑TGC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATg                                                                    >  2:349292/1‑139 (MQ=255)                                                                     tCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCG‑CCGATAGTGGTTTTAGCGACACGCAG‑TGC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATg                                                                    <  1:349292/139‑1 (MQ=255)                                                                           ttCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCG‑CCGATAGTGGTTTTAGCGACACGCAG‑TGC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTAt                                                                     >  2:28165/1‑132 (MQ=255)                                                                           ttCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCG‑CCGATAGTGGTTTTAGCGACACGCAG‑TGC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTAt                                                                     <  1:28165/132‑1 (MQ=255)                                                                                ttGAACCGTGCCGCCATTCTCCAGGTTGCCG‑CCGATAGTGGTTTTAGCGACACGCAG‑TGC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAAtgtg                                                        >  1:859245/1‑140 (MQ=255)                                                                                     ccGTGCCGCCATTCTCCAGGTTGCCG‑CCGATAGTGGTTTTAGCGACACGCAG‑TGC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGAc                                                   >  1:823307/1‑140 (MQ=255)                                                                                        tGCCGCCATTCTCCAGGTTGCCG‑CCGATAGTGGTTTTAGCGACACGCAG‑TGC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGa                                                                  >  1:568539/1‑122 (MQ=255)                                                                                        tGCCGCCATTCTCCAGGTTGCCG‑CCGATAGTGGTTTTAGCGACACGCAG‑TGC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGa                                                                  <  2:568539/122‑1 (MQ=255)                                                                                        tGCCGCCATTCTCCAGGTTGCCG‑CCGATAGTGGTTTTAGCGACACGCAG‑TGC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATAtt                                                              <  1:812020/126‑1 (MQ=255)                                                                                        tGCCGCCATTCTCCAGGTTGCCG‑CCGATAGTGGTTTTAGCGACACGCAG‑TGC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATAtt                                                              >  2:812020/1‑126 (MQ=255)                                                                                        tGCCGCCATTCTCCAGGTTGCCG‑CCGATAGTGGTTTTAGCGACACGCAG‑TGC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTg                                                <  2:859245/140‑1 (MQ=255)                                                                                        tGCCGCCATTCTCCAGGTTGCCG‑CCGATAGTGGTTTTAGCGACACGCAG‑TGC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTg                                                >  2:737666/1‑140 (MQ=255)                                                                                          ccgccATTCTCCAGGTTGCCG‑CCGATAGTGGTTTTAGCGACACGCAG‑TGC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGcc                                              <  2:439563/140‑1 (MQ=255)                                                                                            gccATTCTCCAGGTTGCCG‑CCGATAGTGGTTTTAGCGACACGCAG‑TGC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCat                                            <  2:214727/140‑1 (MQ=255)                                                                                                  ctcCAGGTTGCCG‑CCGATAGTGGTTTTAGCGACACGCAG‑TGC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAAt                                      >  2:959555/1‑140 (MQ=255)                                                                                                     cAGGTTGCCG‑CCGATAGTGGTTTTAGCGACACGCAG‑TGC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGc                                   >  1:131467/1‑140 (MQ=255)                                                                                                       ggTTGCCG‑CCGATAGTGGTTTTAGCGACACGCAG‑TGC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCag                                 <  1:31858/140‑1 (MQ=255)                                                                                                             cg‑ccgATAGTGGTTTTAGCGACACGCAG‑TGC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCat                                            <  2:685659/123‑1 (MQ=255)                                                                                                             cg‑ccgATAGTGGTTTTAGCGACACGCAG‑TGC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCat                                            >  1:685659/1‑123 (MQ=255)                                                                                                                                   cacGCAG‑TGCCCCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTccc         <  2:289974/138‑1 (MQ=255)                                                                                                                                   cacGCAG‑TGCCCCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTccc         >  1:289974/1‑138 (MQ=255)                                                                                                                                    acGCAG‑TGC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTccccccc     >  1:348103/1‑140 (MQ=255)                                                                                                                                       cAG‑TGC‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCCCCCCCCAc  <  2:874550/140‑1 (MQ=255)                                                                                                                                             |                                                                                                                                        ACGTCATCAGGCCATTGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCG‑CCGATAGTGGTTTTAGCGACACGCAG‑TG‑‑CCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCCCCCCCCAC  >  NC_000913/1593987‑1594258

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑