Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,594,256	(C)8→9	pseudogene (3831/5422 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	1,594,248	1	.	C	100.0%	176.4 / NA	50	pseudogene (3839/5422 nt)	yneO	AIDA‑I family autotransporter YneO
Reads supporting (aligned to +/- strand):  ref base . (0/0);  new base C (29/21);  total (29/21)

AGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTT‑‑CCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCACCGCTACCGCTGATACTGTGCGTCATCGCCCAGCTACGCTCAG  >  NC_000913/1594133‑1594377                                                                                                                     |                                                                                                                                   aGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCCCCCCCCCCACGATATCcgtcgt                                                                                                             >  1:344037/1‑140 (MQ=255) aGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTC‑CCCCCCCCACGATATCcgtcg                                                                                                              >  2:755637/1‑138 (MQ=255) aGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTC‑CCCCCCCCACGATATCcgtcg                                                                                                              <  1:755637/138‑1 (MQ=255) aGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTC‑CCCCCCCCACGATATCCGTCGTa                                                                                                            >  2:895062/1‑140 (MQ=255) aGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTC‑CCCCCCCCACGATATCCGTCGTa                                                                                                            >  2:134515/1‑140 (MQ=255) aGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTC‑CCCCCCCCACGATATCCGTCGTa                                                                                                            <  2:127603/140‑1 (MQ=255)        aCGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTC‑CCCCCCCCACGATATCCGTCGTACCCTGAt                                                                                                     >  2:185607/1‑140 (MQ=255)            tCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTC‑CCCCCCCCACGATATCCGTCGTACCCTGATAcgc                                                                                                 <  1:357673/140‑1 (MQ=255)             cATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTC‑CCCCCCCCACGATATCCGTCGTACCCTGATAcgcc                                                                                                >  1:741092/1‑140 (MQ=255)                   aCCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTC‑CCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGaa                                                                                          <  2:217259/140‑1 (MQ=255)                        cAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTC‑CCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGAATCgtt                                                                                     >  1:681778/1‑140 (MQ=255)                        cAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTC‑CCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGAATCgtt                                                                                     >  2:568766/1‑140 (MQ=255)                        cAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTC‑CCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGAATCgtt                                                                                     >  2:202199/1‑140 (MQ=255)                           tggtgACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTC‑CCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGAATCgttgtt                                                                                  <  2:489074/140‑1 (MQ=255)                             gtgACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTC‑CCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTaa                                                                                <  2:741092/140‑1 (MQ=255)                             gtgACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTC‑CCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTaa                                                                                >  1:695387/1‑140 (MQ=255)                                     tCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTC‑CCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAgg                                                                        >  1:738875/1‑140 (MQ=255)                                      cccGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTCCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTC‑CCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGa                                                                       <  2:681778/140‑1 (MQ=255)                                              cacaCCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTC‑CCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTa                                                               >  2:236784/1‑140 (MQ=255)                                                 cccGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTC‑CCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTAccc                                                            <  2:546187/139‑1 (MQ=255)                                                           tGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTC‑CCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTca                                                  >  2:746918/1‑140 (MQ=255)                                                               tatTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTC‑CCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTGCCCAGTTTTGTCACATc                                              <  2:738875/140‑1 (MQ=255)                                                               tatTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTC‑CCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATc                                              >  1:799333/1‑140 (MQ=255)                                                                atTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTC‑CCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCa                                             >  2:946957/1‑140 (MQ=255)                                                                  tAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTC‑CCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCacc                                           >  2:560832/1‑140 (MQ=255)                                                                    aTGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTC‑CCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCaccgc                                         >  1:419463/1‑140 (MQ=255)                                                                     tgtgTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTC‑CCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCaccgct                                        <  1:746918/140‑1 (MQ=255)                                                                      gtgtTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCCCCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCaccgct                                        <  2:344037/140‑1 (MQ=255)                                                                        gtTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTC‑CCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCaccg                                          >  2:187549/1‑135 (MQ=255)                                                                        gtTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTC‑CCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCaccg                                          <  1:187549/135‑1 (MQ=255)                                                                            aCTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCCCCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCaccgctaccgct                                  >  2:795793/1‑140 (MQ=255)                                                                            aCTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTC‑CCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCACCGCTACCGCTg                                 >  1:612020/1‑140 (MQ=255)                                                                              ttGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTC‑CCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCACCGCTACCGCTGAt                               >  1:624542/1‑140 (MQ=255)                                                                               tGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTC‑CCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCACCGCTACCGCTGATa                              <  2:419463/140‑1 (MQ=255)                                                                               tGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTC‑CCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCACCGCTACCGCTGATa                              <  1:946957/140‑1 (MQ=255)                                                                                 ccATATTAATGGCAGAGTCGGAACCGAAAGCAATTTC‑CCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCACCGCTACCGCTGATACt                            >  1:807471/1‑140 (MQ=255)                                                                                         aTGGCAGAGTCGGAACCGAAAGCAATTTC‑CCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCACCGCTACCGCTGATACTGTGCGTCa                    <  2:695387/140‑1 (MQ=255)                                                                                           ggCAGAGTCGGAACCGAAAGCAATTTC‑CCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCACCGCTACCGCTGATACTGTGCGTCATc                  >  2:760874/1‑140 (MQ=255)                                                                                              agagTCGGAACCGAAAGCAATTTC‑CCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCACCGCTACCGCTGATACTGTGCGTCATCGcc               <  1:134515/140‑1 (MQ=255)                                                                                                agTCGGAACCGAAAGCAATTTC‑CCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCACCGCTACCGCTGATACTGTGCGTCATCGCCCa             >  2:693422/1‑140 (MQ=255)                                                                                                agTCGGAACCGAAAGCAATTTC‑CCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCACCGCTACCGCTGATACTGTGCGTCATCGCCCa             >  1:783594/1‑140 (MQ=255)                                                                                                agTCGGAACCGAAAGCAATTTC‑CCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCACCGCTACCGCTGATACTGTGCGTCATCGCCCa             >  2:927899/1‑140 (MQ=255)                                                                                                agTCGGAACCGAAAGCAATTTC‑CCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCACCGCTACCGCTGATACTGTGCGTCATCGCCCa             >  2:884824/1‑140 (MQ=255)                                                                                                 gTCGGAACCGAAAGCAATTTC‑CCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCACCGCTACCGCTGATACTGTGCGTCATCGCCCAg            >  2:46044/1‑140 (MQ=255)                                                                                                   cGGAACCGAAAGCAATTTC‑CCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCACCGCTACCGCTGATACTGTGCGTCATCGCCCAGCt          <  1:693422/140‑1 (MQ=255)                                                                                                      aaCCGAAAGCAATTTC‑CCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCACCGCTACCGCTGATACTGTGCGTCATCGCCCAGCTACg       <  2:783594/140‑1 (MQ=255)                                                                                                      aaCCGAAAGCAATTTC‑CCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCACCGCTACCGCTGATACTGTGCGTCATCGCCCAGCTACg       <  1:799695/140‑1 (MQ=255)                                                                                                      aaCCGAAAGCAATTTC‑CCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCACCGCTACCGCTGATACTGTGCGTCATCGCCCAGCTACg       <  1:895062/140‑1 (MQ=255)                                                                                                         cGAAAGCAATTTC‑CCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCACCGCTACCGCTGATACTGTGCGTCATCGCCCAGCTACGCTc    <  1:185607/140‑1 (MQ=255)                                                                                                         cGAAAGCAATTTC‑CCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCACCGCTACCGCTGATACTGTGCGTCATCGCCCAGCTACGCTc    <  2:799333/140‑1 (MQ=255)                                                                                                          gAAAGCAATTTCCCCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCACCGCTACCGCTGATACTGTGCGTCATCGCCCAGCTACGCTc    <  1:795793/140‑1 (MQ=255)                                                                                                           aaaGCAATTTC‑CCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCACCGCTACCGCTGATACTGTGCGTCATCGCCCAGCTACGCTCAg  >  2:97606/1‑140 (MQ=255)                                                                                                                     |                                                                                                                                   AGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTT‑‑CCCCCCCCACGATATCCGTCGTACCCTGATACGCCGCGGAATCGTTGTTAAGAGTCAGGATCCCGGTACCCAGTTTTGTCACATCACCGCTACCGCTGATACTGTGCGTCATCGCCCAGCTACGCTCAG  >  NC_000913/1594133‑1594377

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑