Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,597,313	(C)7→8	pseudogene (774/5422 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	1,597,306	1	.	C	100.0%	145.2 / NA	41	pseudogene (781/5422 nt)	yneO	AIDA‑I family autotransporter YneO
Reads supporting (aligned to +/- strand):  ref base . (0/0);  new base C (26/15);  total (26/15)

AATATTGACTGTGCCATTACCGAAATATCCATTATAGAGTCTGCGTACCGTGATGACAGAGTCTTGATCCTGCACATTCAGGGTTCCGATACCGGTGGCATTGCCACCGATAATCGTATTTTCAGCCGTAACCAA‑CCCCCCCTCGCGAATAGTCGCCTCCCCAGTTCCTTGATTACCAATTTGAAATTCAATTGAGGAATCATTATTTTTTATTAGCCACTCGCCACCCTTTTCAACGACAACCTGGCCATTACTGCCCGCCTGATA  >  NC_000913/1597172‑1597438                                                                                                                                        |                                                                                                                                     aaTATTGACTGTGCCATTACCGAAATATCCATTATAGAGTCTGCGTACCGTGATGACAGAGTCTTGATCCTGCACATTCAGGGTTCCGATACCGGTGGCATTGCCACCGATAATCGTATTTTCAGCCGTAACCAA‑ccccc                                                                                                                                 <  1:385270/140‑1 (MQ=255) aaTATTGACTGTGCCATTACCGAAATATCCATTATAGAGTCTGCGTACCGTGATGACAGAGTCTTGATCCTGCACATTCAGGGTTCCGATACCGGTGGCATTGCCACCGATAATCGTATTTTCAGCCGTAACCAA‑ccccc                                                                                                                                 <  2:116626/140‑1 (MQ=255)   tatTGACTGTGCCATTACCGAAATATCCATTATAGAGTCTGCGTACCGTGATGACAGAGTCTTGATCCTGCACATTCAGGGTTCCGATACCGGTGGCATTGCCACCGATAATCGTATTTTCAGCCGTAACCAA‑ccccccc                                                                                                                               <  1:314796/140‑1 (MQ=255)   tatTGACTGTGCCATTACCGAAATATCCATTATAGAGTCTGCGTACCGTGATGACAGAGTCTTGATCCTGCACATTCAGGGTTCCGATACCGGTGGCATTGCCACCGATAATCGTATTTTCAGCCGTAACCAA‑ccccccc                                                                                                                               <  1:514594/140‑1 (MQ=255)      tGACTGTGCCATTACCGAAATATCCATTATAGAGTCTGCGTACCGTGATGACAGAGTCTTGATCCTGCACATTCAGGGTTCCGATACCGGTGGCATTGCCACCGATAATCGTATTTTCAGCCGTAACCAA‑cccccccctc                                                                                                                            >  2:352918/1‑137 (MQ=255)            tgCCATTACCGAAATATCCATTATAGAGTCTGCGTACCGTGATGACAGAGTCTTGATCCTGCACATTCAGGGTTCCGATACCGGTGGCATTGCCACCGATAATCGTATTTTCAGCCGTAACCAACCCCCCCCTCGCGAAt                                                                                                                       >  2:104102/1‑140 (MQ=255)                    ccGAAATATCCATTATAGAGTCTGCGTACCGTGATGACAGAGTCTTGATCCTGCACATTCAGGGTTCCGATACCGGTGGCATTGCCACCGATAATCGTATTTTCAGCCGTAACCAACCCCCCCCTCGCGAATAGTCGCCt                                                                                                               >  2:562488/1‑140 (MQ=255)                       aaaTATCCATTATAGAGTCTGCGTACCGTGATGACAGAGTCTTGATCCTGCACATTCAGGGTTCCGATACCGGTGGCATTGCCACCGATAATCGTATTTTCAGCCGTAACCAACCCCCCCCTCGCGAATAGTCGCCTccc                                                                                                            <  2:789329/140‑1 (MQ=255)                        aaTATCCATTATAGAGTCTGCGTACCGTGATGACAGAGTCTTGATCCTGCACATTCAGGGTTCCGATACCGGTGGCATTGCCACCGATAATCGTATTTTCAGCCGTAACCAACCCCCCCCTCGCGAATAGTCGCCTcccc                                                                                                           <  2:549173/140‑1 (MQ=255)                         atatCCATTATAGAGTCTGCGTACCGTGATGACAGAGTCTTGATCCTGCACATTCAGGGTTCCGATACCGGTGGCATTGCCACCGATAATCGTATTTTCAGCCGTAACCAACCCCCCCCTCGCGaa                                                                                                                        >  1:109613/1‑126 (MQ=255)                         atatCCATTATAGAGTCTGCGTACCGTGATGACAGAGTCTTGATCCTGCACATTCAGGGTTCCGATACCGGTGGCATTGCCACCGATAATCGTATTTTCAGCCGTAACCAACCCCCCCCTCGCGaa                                                                                                                        <  2:109613/126‑1 (MQ=255)                           atCCATTATAGAGTCTGCGTACCGTGATGACAGAGTCTTGATCCTGCACATTCAGGGTTCCGATACCGGTGGCATTGCCACCGATAATCGTATTTTCAGCCGTAACCAACCCCCCCCTCGCGAATAGTCGCCTCCCCAGt                                                                                                        <  1:104102/140‑1 (MQ=255)                                        tCTGCGTACCGTGATGACAGAGTCTTGATCCTGCACATTCAGGGTTCCGATACCGGTGGCATTGCCACCGATAATCGTATTTTCAGCCGTAACCAACCCCCCCCTCGCGAATAGTCGCCTCCCCAGTTCCTTGATTACCa                                                                                           >  2:840754/1‑140 (MQ=255)                                        tCTGCGTACCGTGATGACAGAGTCTTGATCCTGCACATTCAGGGTTCCGATACCGGTGGCATTGCCACCGATAATCGTATTTTCAGCCGTAACCAACCCCCCCCTCGCGAATAGTCGCCTCCCCAGTTCCTTGATTACCa                                                                                           >  1:599548/1‑140 (MQ=255)                                        tCTGCGTACCGTGATGACAGAGTCTTGATCCTGCACATTCAGGGTTCCGATACCGGTGGCATTGCCACCGATAATCGTATTTTCAGCCGTAACCAACCCCCCCCTCGCGAATAGTCGCCTCCCCAGTTCCTTGATTACCa                                                                                           >  1:627284/1‑140 (MQ=255)                                        tCTGCGTACCGTGATGACAGAGTCTTGATCCTGCACATTCAGGGTTCCGATACCGGTGGCATTGCCACCGATAATCGTATTTTCAGCCGTAACCAACCCCCCCCTCGCGAATAGTCGCCTCCCCAGTTCCTTGATTACCa                                                                                           >  2:266863/1‑140 (MQ=255)                                        tCTGCGTACCGTGATGACAGAGTCTTGATCCTGCACATTCAGGGTTCCGATACCGGTGGCATTGCCACCGATAATCGTATTTTCAGCCGTAACCAACCCCCCCCTCGCGAATAGTCGCCTCCCCAGTTCCTTGATTACCa                                                                                           >  2:211004/1‑140 (MQ=255)                                          tGCGTACCGTGATGACAGAGTCTTGATCCTGCACATTCAGGGTTCCGATACCGGTGGCATTGCCACCGATAATCGTATTTTCAGCCGTAACCAACCCCCCCCTCGCGAATAGTCGCCTCCCCAGTTCCTTGATTACCAAt                                                                                         >  1:854573/1‑140 (MQ=255)                                          tGCGTACCGTGATGACAGAGTCTTGATCCTGCACATTCAGGGTTCCGATACCGGTGGCATTGCCACCGATAATCGTATTTTCAGCCGTAACCAACCCCCCCCTCGCGAATAGTCGCCTCCCCAGTTCCTTGATTACCAAt                                                                                         >  2:523884/1‑140 (MQ=255)                                           gCGTACCGTGATGACAGAGTCTTGATCCTGCACATTCAGGGTTCCGATACCGGTGGCATTGCCACCGATAATCGTATTTTCAGCCGTAACCAACCCCCCCCTCGCGAATAGTCGCCTCCCCAGTTCCTTGATTACCAAtt                                                                                        <  2:123469/140‑1 (MQ=255)                                                ccGTGATGACAGAGTCTTGATCCTGCACATTCAGGGTTCCGATACCGGTGGCATTGCCACCGATAATCGTATTTTCATCCGTAACCAACCCCCCCCACGCGAATAGTCGCCTCCCCAGTTCCTTGATTACCAATTTGaaa                                                                                   <  2:767504/140‑1 (MQ=255)                                                ccGTGATGACAGAGTCTTGATCCTGCACATTCAGGGTTCCGATACCGGTGGCATTGCCACCGATAATCGTATTTTCAGCCGTAACCAACCCCCCCCTCGCGAATAGTCGCCTCCCCAGTTCCTTGATTACCAATTTGaaa                                                                                   <  1:352918/140‑1 (MQ=255)                                                          agagTCTTGATCCTGCACATTCAGGGTTCCGATGCCGGTGGCATTGCCACCGATAATCGTATTTTCAGCCGTAACCAACCCCCCCCTCGCGAATAGTCTCCTCCCCAGTTCCTTGATTACCAATTTGAAATTCAATTGAg                                                                         <  1:211004/140‑1 (MQ=255)                                                          agagTCTTGATCCTGCACATTCAGGGTTCCGATACCGGTGGCATTGCCACCGATAATCGTATTTTCAGCCGTAACCAACCCCCCCCTCGCGAATAGTCGCCTCCCCAGTTCCTTGATTACCAATTTGAAATTCAATTGAg                                                                         <  1:840754/140‑1 (MQ=255)                                                             gTCTTGATCCTGCACATTCAGGGTTCCGATACCGGTGGCATTGCCACCGATAATCGTATTTTCAGCCGTAACCAACCCCCCCCTCGCGAATAGTCGCCTCCCCAGTTCCTTGATTACCAATTTGAAATTCAATTGAGGaa                                                                      >  1:98659/1‑140 (MQ=255)                                                              tCTTGATCCTGCACATTCAGGGTTCCGATACCGGTGGCATTGCCACCGATAATCGTATTTTCAGCCGTAACCAACCCCCCCCTCGCGAATAGTCGCCTCCCCAGTTCCTTGATTACCAATTTGAAATTCAATTGAGGAAt                                                                     <  2:98659/140‑1 (MQ=255)                                                                ttGATCCTGCACATTCAGGGTTCCGATACCGGTGGCATTGCCACCGATAATCGTATTTTCAGCCGTAACCAACCCCCCCCTCGCGAATAGTCGCCTCCCCAGTTCCTTGATTACCAATTTGAAATTCAATTGAGGAATCa                                                                   >  1:489028/1‑140 (MQ=255)                                                                ttGATCCTGCACATTCAGGGTTCCGATACCGGTGGCATTGCCACCGATAATCGTATTTTCAGCCGTAACCAACCCCCCCCTCGCGAATAGTCGCCTCCCCAGTTCCTTGATTACCAATTTGAAATTCAATTGAGGAATCa                                                                   <  1:523884/140‑1 (MQ=255)                                                                        gCACATTCAGGGTTCCGATACCGGTGGCATTGCCACCGATAATCGTATTTTCAGCCGTAACCAACCCCCCCCTCGCGAATAGTCGCCTCCCCAGTTCCTTGATTACCAATTTGAAATTCAAtt                                                                            <  2:840291/123‑1 (MQ=255)                                                                        gCACATTCAGGGTTCCGATACCGGTGGCATTGCCACCGATAATCGTATTTTCAGCCGTAACCAACCCCCCCCTCGCGAATAGTCGCCTCCCCAGTTCCTTGATTACCAATTTGAAATTCAAtt                                                                            >  1:840291/1‑123 (MQ=255)                                                                        gCACATTCAGGGTTCCGATACCGGTGGCATTGCCACCGATAATCGTATTTTCAGCCGTAACCAACCCCCCCCTCGCGAATAGTCGCCTCCCCAGTTCCTTGATTACCAATTTGAAATTCAATTGAGGAATCATTAttttt                                                           >  2:593632/1‑140 (MQ=255)                                                                          acaTTCAGGGTTCCGATACCGGTGGCATTGCCACCGATAATCGTATTTTCAGCCGTAACCAACCCCCCCCTCGCGAATAGTCGCCTCCCCAGTTCCTTGATTACCAATTTGAAATTCAATTGAGGAATCATTATTTTtta                                                         >  2:223925/1‑140 (MQ=255)                                                                              tCAGGGTTCCGATACCGGTGGCATTGCCACCGATAATCGTATTTTCAGCCGTAACCAACCCCCCCCTCGCGAATAGTCGCCTCCCCGGTTCCTTGATTTCCAATTTGAAATTCAATTGAGGAATCATTATTTTTTATTAg                                                     >  2:750006/1‑140 (MQ=255)                                                                              tCAGGGTTCCGATACCGGTGGCATTGCCACCGATAATCGTATTTTCAGCCGTAACCAACCCCCCCCTCGCGAATAGTCGCCTCCCCAGTTCCTTGATTACCAATTTGAAATTCAATTGAGGAATCATTATTTTTTATTAg                                                     >  2:520061/1‑140 (MQ=255)                                                                              tCAGGGTTCCGATACCGGTGGCATTGCCACCGATAATCGTATTTTCAGCCGTAACCAACCCCCCCCTCGCGAATAGTCGCCTCCCCAGTTCCTTGATTACCAATTTGAAATTCAATTGAGGAATCATTATTTTTTATTAg                                                     >  2:89376/1‑140 (MQ=255)                                                                              tCAGGGTTCCGATACCGGTGGCATTGCCACCGATAATCGTATTTTCAGCCGTAACCAACCCCCCCCTCGCGAATAGTCGCCTCCCCAGTTCCTTGATTACCAATTTGAAATTCAATTGAGGAATCATTATTTTTTATTAg                                                     >  1:633906/1‑140 (MQ=255)                                                                                      ccGATACCGGTGGCATTGCCACCGATAATCGTATTTTCAGCCGTAACCAACCCCCCCCTCGCGAATAGTCGCCTCCCCAGTTCCTTGATTACCAATTTGAAATTCAATTGAGGAATCATTATTTTTTATTAGCCACTCGc                                             >  2:47933/1‑140 (MQ=255)                                                                                          tACCGGTGGCATTGCCACCGATAATCGTATTTTCAGCCGTAACCAACCCCCCCCTCGCGAATAGTCGCCTCCCCAGTTCCTTGATTACCAATTTGAAATTCAATTGAGGAATCATTATTTTTTATTAGCCACTCGCCAcc                                         >  2:724008/1‑140 (MQ=255)                                                                                                      tGCCACCGATAATCGTATTTTCAGCCGTAACCAACCCCCCCCTCGCGAATAGTCGCCTCCCCAGTTCCTTGATTACCAATTTGAAATTCAATTGAGGAATCATTATTTTTTATTAGCCACTCGCCACCCTTTTCAACGAc                             <  1:8938/140‑1 (MQ=255)                                                                                                          aCCGATAATCGTATTTTCAGCCGTAACCAACCCCCCCCTCGCGAATAGTCGCCTCCCCAGTTCCTTGATTACCAATTTGAAATTCAATTGAGGAATCATTATTTTTTATTAGCCACTCGCCACCCTTTTCAACGACAAcc                         >  1:567073/1‑140 (MQ=255)                                                                                                            cGATAATCGTATTTTCAGCCGTAACCAACCCCCCCCTCGCGAATAGTCGCCTCCCCAGTTCCTTGATTACCAATTTGAAATTCAATTGAGGAATCATTATTTTTTATTAGCCACTCGCCACCCTTTTCAACGACAACCTg                       >  2:776415/1‑140 (MQ=255)                                                                                                            cGATAATCGTATTTTCAGCCGTAACCAACCCCCCCCTCGCGAATAGTCGCCTCCCCAGTTCCTTGATTACCAATTTGAAATTCAATTGAGGAATCATTATTTTTTATTAGCCACTCGCCACCCTTTTCAACGACAACCTg                       >  2:798130/1‑140 (MQ=255)                                                                                                             gATAATCGTATTTTCAGCCGTAACCAACCCCCCCCTCGCGAATAGTCGCCTCCCCAGTTCCTTGATTACCAATTTGAAATTCAATTGAGGAATCATTATTTTTTATTAGCCACTCGCCACCCTTTTCAACGACAACCTgg                      <  1:29334/140‑1 (MQ=255)                                                                                                                       ttttCAGCCGTAACCAACCCCCCCCTCGCGAATAGTCGCCTCCCCAGTTCCTTGATTACCAATTTGAAATTCAATTGAGGAATCATTATTTTTTATTAGCCACTCGCCACCCTTTTCAACGACAACCTGGCCATTACTGc            >  1:519452/1‑140 (MQ=255)                                                                                                                               cGTAACCAACCCCCCCCTCGCGAATAGTCGCCTCCCCAGTTCCTTGATTACCAATTTGAAATTCAATTGAGGAATCATTATTTTTTATTAGCCACTCGCCACCCTTTTCAACGACAACCTGGCCATTACTGCCCGCCTGa    <  1:520061/140‑1 (MQ=255)                                                                                                                                 tAACCAACCCCCCCCTCGCGAATAGTCGCCTCCCCAGTTCCTTGATTACCAATTTGAAATTCAATTGAGGAATCATTATTTTTTATTAGCCACTCGCCACCCTTTTCAACGACAACCTGGCCATTACTGCCCGCCTGATa  >  2:760864/1‑140 (MQ=255)                                                                                                                                        |                                                                                                                                     AATATTGACTGTGCCATTACCGAAATATCCATTATAGAGTCTGCGTACCGTGATGACAGAGTCTTGATCCTGCACATTCAGGGTTCCGATACCGGTGGCATTGCCACCGATAATCGTATTTTCAGCCGTAACCAA‑CCCCCCCTCGCGAATAGTCGCCTCCCCAGTTCCTTGATTACCAATTTGAAATTCAATTGAGGAATCATTATTTTTTATTAGCCACTCGCCACCCTTTTCAACGACAACCTGGCCATTACTGCCCGCCTGATA  >  NC_000913/1597172‑1597438

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: ‑