Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	CP009273	1,466,255	C→A	pseudogene (1482/3497 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
*	CP009273	1,466,255	0	C	A	100.0%	150.8 / NA	45	pseudogene (1482/3497 nt)	ydbA	pseudogene, autotransporter homolog; interrupted by IS2 and IS30
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base A (30/15);  total (30/15)

GCAAATAACGAAGGAACCTGGAACCTCGGAAGTAGTAGTGAGGGTAACAACACCGGGATGCTGGAAGTTAATAATAATTCAGCTTTCAATAACCGCGGCGAGTTTATTCTTGATAACGACAAGAATGCTGTGCACATCAACCAGTCCGGTACGCTTTATAATACCGGTCACATGAACATCAGTAATTCTTCCCACAACGGAGCCGTTAATATGTGGGGCGGAAATGGTCGTTTTATCAATGACGGAACGATTGATGTTTCTGCGAAGTCACTGGTAGTCAGCGC  >  CP009273/1466114‑1466397                                                                                                                                              |                                                                                                                                               gCAAATAACGAAGGAACCTGGAACCTCGGAAGTAGTAGTGAGGGTAACAACACCGGGATGCTGGAAGTTAATAATAATTCAGCTTTCAATAACCGCGGCGAGTTTATTCTTGATAACGACAAGAATGCTGTGCACATCAACAAGTCCgg                                                                                                                                         >  1:666479/1‑149 (MQ=255)   aaaTAACGAAGGAACCTGGAACCTCGGAAGTAGTAGTGAGGGTAACAACACCGGGATGCTGGAAGTTAATAATAATTCAGCTTTCAATAACCGCGGCGAGTTTATTCTTGATAACGACAAGAATGCTGTGCACATCAACAAATCCGGTa                                                                                                                                       >  2:378004/1‑149 (MQ=255)       aaCGAAGGAACCTGGAACCTCGGAAGTAGTAGTGAGGGTAACAACACCGGGATGCTGGAAGTTAATAATAATTCAGCTTTCAATAACCGCGGCGAGTTTATTCTTGATAACGACAAGAATGCTGTGCACATCAACAAGTCCGGTACGCt                                                                                                                                   <  1:873815/149‑1 (MQ=255)          gaagaaACCTGGAACCTCGGAAGTAGTAGTGAGGGTAACAACACCGGGATGCTGGAAGTTAATAATAATTCAGCTTTCAATAACCGCGGCGAGTTTATTCTTGATAACGACAAGAATGCTGTGCACATCAACAAGACCGGTAGGCTTta                                                                                                                                >  2:930120/1‑149 (MQ=255)          gAAGGAACCGGGAACCCCGGAAGTAGTAGGTAGGGTAACAACACCGGGATGCTGGAAGTTAATAATAATTCAGCTTTCAATAACCGCGGCGAGTTTATTCTTGATAACGACAAGAATGCTGTGCACATCAACAAGTCCGGTACGCTTta                                                                                                                                <  2:264036/149‑1 (MQ=255)                   tggaacctCGGAAGTAGTAGTGAGGGTAACAACACCGGGATGCTGGAAGTTAATAATAATTCAGCTTTCAATAACCGCGGCGAGTTTATTCTTGATAACGACAAGAATGCTGTGCACATCAACAAGTCCGGTACGCTTTATAATACCgg                                                                                                                       >  1:337080/1‑149 (MQ=255)                      aacctCGGAAGTAGTTGTGAGGGTAACAACACCGGGATGCTGGAAGTTAATAATAATTCAGCTTGCAATAACCGCGGCGAGTTTATTCTTGATAACGACAAGACTGCTGTGCACATCAACAAGACCGGTACGCTTTATAATACCGGTca                                                                                                                    >  2:633884/1‑149 (MQ=255)                            ggAAGTAGTAGTGAGGGTAACAACACCGGGATGCTGGAAGTTAATAATAAGTCAGCTTTCAATAACCGCGGCGAGTTTATTCTTGATAACGACAAGAATGCTGTGCACATCAACAAGTCCGGTACGCTTTATAATACCGGTCACATGaa                                                                                                              <  2:143475/149‑1 (MQ=255)                                   gtagtGAGGGTAACAACACCGGGATGCTGGAAGTTAATAATAATTCAGCTTTCAATAACCGCGGCGAGTTTATTCTTGATAACGACAAGAATGCTGTGCACATCAACAAGTCCGGTACGCTTTATAATACCGGTCACATGAACATCAGt                                                                                                       >  1:123521/1‑149 (MQ=255)                                      gtGAGGGTAACAACACCGGGATGCTGGAAGTTAATAATAATTCAGCTTTCAATAACCGCGGCGAGTTTATTCTTGATAACGACAAGAATGCTGTGCACATCAACAAGTCCGGTACGCTTTATAATACCGGTCACATGAACATCAGTAAt                                                                                                    <  2:633921/149‑1 (MQ=255)                                           ggTAGCAACGCCGGGAGGGTGGTAGTTGATAATAATTCAGCTTTCAATAGCCGCGGCGAGTTTATTCTTGATATCGACCAGAATGCTGTGCACATCAACAAGTCCGGTACGCTTTATCATACCGGTCACATGAACATCAGTAAttcttc                                                                                               <  2:225112/149‑1 (MQ=255)                                                 aacaCCGGGATGCTGGAAGTTAATAATAATTCAGCTTTCAATAACCGCGGCGAGTTTATTCTTGATAACGACAAGAATGCTGTGCACATCAACAAGTCCGGTACGCTTTATAATACCGGTCACATGAACATCAGTAATTCTTCCCCCaa                                                                                         >  1:475864/1‑149 (MQ=255)                                                  acacCGGGATGCTGGAAGTTAATAATAATTCAACAGTCAATAACCGCGGCGAGTTTATTCTTGATAACGACAAGAATGCTGTGCACATCAACAAGTCCGGTACGCTTTATAATACCGGTCACATGAACATCAGTAATTCTTCCCACAAc                                                                                        >  2:961821/1‑149 (MQ=255)                                                      cGGGATGCTGGAAGTTAATAATAATTCAGCTTTCAATAACCGCGGCGAGTTTATTCTTGATAACGACAAGAATGCTGTGCACATCAACAAGTCCGGTACGCTTTATAATACCGGTCACATGAACATCAGTAATTCTTCCCACAACGGat                                                                                    >  1:800185/1‑148 (MQ=255)                                                      cGGGATGCTGGAAGTTAATAATAATTCAGCTTTCAATAACCGCGGCGAGTTTATTCTTGATAACGACAAGAATGCTGTGCACATCAACAAGTCCGGTACGCTTTATAATACCGGTCACATGAACATCAGTAATTCTTCCCACAACGGAg                                                                                    >  2:276115/1‑149 (MQ=255)                                                      cGGGATGCTGGAAGTTAATAATAATTCAGCTTTCAATAACCGCGGCGAGTTTATTCTTGATAACGACAAGAATGCTGTGCACATCAACAAGTCCGGTACGCTTTATAATACCGGTCACATGAACATCAGTAATTCTTCCCACAACGGAg                                                                                    >  1:795909/1‑149 (MQ=255)                                                       gggATGCTGGAAGTTAATAATAATTCAGCTTTCAATAACCGCGGCGAGTTTATTCTTGATAACGACAAGAATGCTGTGCACATCAACAAGTCCGGTACGCTTTATAATACCGGTCACATGAACATCAGTAATTCTTCCCACAACGGAGc                                                                                   >  1:452708/1‑149 (MQ=255)                                                             cTGGAAGTTAATAATAATTCAGCTTTCAATAACCGCGGCGAGTTTATTCTTGATAACGAGAAGAATGCTGTGCACATCAACAAGTCCGGTACGCTTTATAATACCGGTCACATGAACATCAGTAATTCTTCCCACAACGGAGcccgtaa                                                                             >  2:740181/1‑144 (MQ=255)                                                             cTGGAAGTTAATAATAATTCAGCTTTCAATAACCGCGGCGAGTTTATCCTTTATAACGACAAGAATGCTGTGCACATCAACAAGTCCGGTACGCTTTATAATACCGGTCACATGAACATCAGTAATTCTTCCCACAACGGAGCCGTTaa                                                                             <  1:774100/149‑1 (MQ=255)                                                               ggAAGTTAATAATAATTCAGCTTTCAATAACCGCGGCGAGTTTATTCTTGATAACGACAAGAATGCTGTGCACATCAACAAGTCCGGTACGCTTTATAATACCGGTCACATGAACATCAGTAATTCTTCCCACCACGGAGCCGTTAata                                                                           >  1:589250/1‑149 (MQ=255)                                                                     taataataaTTCAGCTTTCAATAACCGCGGCGAGTTTATTCTTGATAACGACAAGAATGCTGTGCACATCAACAAGTCCGGTACGCTTTATAATACCGGTCACATGAACATCAGTAATTCTTCCCACAACGGAGCCGTTAATATATggg                                                                     >  1:679024/1‑149 (MQ=255)                                                                       ataataatTCAGCTTTCAATAACCGCGGCGAGTTTATTCTTGATAACGACAAGAATGTTGTGCACATCAACAAGTCCGGTACGCTTTATAATACCGGTCACATGAACATCAGTAATTCTTCCCACAACGGAGCCGTTAATATGTGGGGc                                                                   >  1:444126/1‑149 (MQ=255)                                                                       ataataatTCAGCTTTCAATAACCGCGGCGAGTTTATTCTTGATAACGACAAGAATGCTGTGCACATCAACACGTCCGGTACGCTTTATAATACCGGTCACATGCACGCCAGTAATCCTTCCCCCAACGGAGCCGTTAATATGTGGGGc                                                                   >  2:812476/1‑149 (MQ=255)                                                                           taatTCAGCTTTCAATAACCGCGGCGAGTTTATTCTTGATAACGACAAGAATGCTGTGCACATCAACAAGTCCGGTACGCTTTATAATACCGGTCACATGAACATCAGTAATTCTTCCCACAACGGAGCCGTTAATATGTGGGGCGGaa                                                               >  1:485379/1‑149 (MQ=255)                                                                                   cTTTCAATAACCGCGGCGAGTTTATTCTTGATAACGACAAGAATGCTGTGCACATCAACAAGTCCGGTACGCTTTATAATACCGGTCACATGAACATCAGTAATTCTTCCCACAACGGAGCCGTTAATATGTGGGGCGGAAATGGTCGt                                                       <  2:123521/149‑1 (MQ=255)                                                                                    tttCAATAACCGCGGCGAGTTTATTCTTGATAACGACAAGAATGCTGTGCACATCAACAAGTCCGGTACGCTTTATAATACCGGTCACATGAACATCAGTAATTCTTCCCACAACGGAGCCGTTAATATGTGGGGCGGAAACGGTCGtt                                                      >  2:874927/1‑149 (MQ=255)                                                                                        aaTAACCGCGGCGAGTTTATTCTTGATAACGACAAGAATGCTGTGCACATCCACAAGTCCGGTACGCTTTATAATACCGGTCACATGAACATCAGTAATTCTTCCCCCAACGGAGCCGTGAATATGTGGGGCGTAAATGGTAGTTTTAt                                                  >  1:109191/1‑149 (MQ=255)                                                                                          tAACCGCGGCGAGTTTATTCTTGATAACTACAAGAATGCTGTGCACATCAACAAGTCCGGTACGCTTTATAATACCGGTCACATGAACATCAGTAATTCTTCCCACAACGGAGCCGTTAATATGTGGGGCGGAAATGGTCGTTTTATCa                                                <  1:544921/149‑1 (MQ=255)                                                                                                cggcgAGTTTATTCTTGATAACGACAAGAATGCTGTGCACATCAACACGTCCGGTACGCTTTATAATACCGGTCACATGAACATCAGTAATTCTTCCCACAACGGGGCCGTTACTGTGTGGGGGGGTGATGGTGGTTTTATCaaggcag                                          >  2:12569/1‑144 (MQ=255)                                                                                                cggcgAGTTTATTCTTGATAACGACAAGAATGCTGTGCACATCAACAAGTCCGGTACGCTTTATAATACCGGTCACATGAACATCAGTAATTCTTCCCACAACGGAGCCGTTAATATGTGGGGCGGAAATGGTCGTTTTATCAATGACg                                          <  2:337080/149‑1 (MQ=255)                                                                                                cggcgAGTTTATTCTTGATAACGACAAGAATGCTGTGCACATCAACAAGTCCGGTACGCTTTATAATACCGGTCACATGAACATCAGTAATTCTTCCCACAACGGAGCCGTTAATATGTGGGGCGGAAATGGTCGTTTTATCAATGACg                                          <  2:413466/149‑1 (MQ=255)                                                                                                   cgAGTTTATTCTTGATAACGACAAGAATGCTGTGCACATCAACAAGTCCGGTACGCTTTATAATACCGGTCACATGAACATCAGTAATTCTTCCCACAACGGAGCCGTTAATATGCTCGTCGTAAATGGTCGTTTTATCAATGACGGaa                                       <  1:493247/149‑1 (MQ=255)                                                                                                       tttATTCTTGATAACGACAAGAATGCTGTGCACATCAACAAGTCCGGTACGCTTTATAATACCGGTCACATGAACATCAGTAATTCTTCCCACAACGGAGCCGTTAATATGTGGGGCGGAAATGGTCGTTTTATCAATGACGGAACGAt                                   <  1:359704/149‑1 (MQ=255)                                                                                                        ttATTCTTGATAGCGACAAGAATGCTGTGCACATCAACAAGTCCGGTACGCTCTTTAATACCGGTCACATGAACATCAGTAATTCTTCCCACAACGGAGCCGTTAATATGTGGGGCGGAAATGGTCGTTTTATCAATGACGGAACGAtt                                  <  2:555595/149‑1 (MQ=255)                                                                                                          aTTTTTGACAACGACAAGAATGCTGTGCACATCAACAAGTCCGGTACGCTTTATAATACAGGTCACATGAAGATCAGTAATTCTTCCCACAACGGAGCCGTTAATATGTGGGGCGGAAATGGTCGTTTTATCAATGACGGAACTATTGa                                <  2:932982/149‑1 (MQ=255)                                                                                                           ttCTTGATAACGACAAGAATGCTGTGCACATCAACAAGTCCGGTACGCTTTATAATACCGGTCACATGAACATCAGTAATTCTTCCCACAACGGAGCCGTTAATATGTGGGGCGGAAATGGTCGTTTTATCAATGACGGAACGATTGAt                               >  1:781945/1‑149 (MQ=255)                                                                                                            tCTTGATAACGACAAGAATGCTGTTCACATCAACAAGTACGTTACGCTTTATAATAACGGTCACATGAACATCAGTAATTCTTCCCACAACGGAGCCGTTAATAGGTGAGGCGGAAATGGACGTTTTATCAATGAAGGAACGTTTGATg                              >  2:367630/1‑149 (MQ=255)                                                                                                               tGATAACGACAAGAATGCTGTGCACATCAACAAGTCCGGTACGCTTTATAATACCGGTCACATGAACATCAGTAATTCTTCCCACAACGGAGCCGTTAATATGTGGGGCGGAAATGGTCGTTTTATCAATGACTGAACGATTCGTGttt                           >  1:100588/1‑149 (MQ=255)                                                                                                                 aTAACGACAAGAATGCTGTGCACATCAACAAGTCCGGTACGCTTTATAATACCGGTCACATGAACATCAGTAATTCTTCCCACAACGGAGCCGTTAATATGTGGGGCGGAAATGGTCGTCTTATCAATGACGGAACGATTGATGTTTCt                         >  2:627107/1‑149 (MQ=255)                                                                                                                      gACAAGAATGCTGTGCACATCAACAAGTCCGGTACGCTTTATAATACCGGTCACATGAACATCAGTAATTCTTCCCACAACGGAGCCGTTAATATGTGGGGCGGAAATGGTCGTTTTATCAATGACGGAACGGTTGATGTGTCTGCGaa                    >  1:251183/1‑149 (MQ=255)                                                                                                                            aaTGCTGTGCACATCAACAAGTCCGGTACGCTTTATAATACCGGTCACATGAAAATCAGTAATTCTTCCCACAACGGAGCCGTTAATATGTGGGGCGGAAATGGTCGTTTTATCAATGACGGAACGATTGATGTTTCTGCGAAGTCACt              <  1:177963/149‑1 (MQ=255)                                                                                                                               gCTGTGCACATCAACAAGTCCGGTACGCTTTATAATACCGGTCACATGAACATCAGTAATTCTTCCCACAACGGAGCCGTTAATATGTGGGGCGGAAATGGTCGTTTTATCAATGACGGAACGATTGAGGTTTCTGCGAAGTCACTGGt           >  2:772903/1‑149 (MQ=255)                                                                                                                                 tgtgCACATCAACAAGTCCGGTACGCTTTATAATACCGGTCACATGAACATCAGTAATTCTTCCCACAACGGAGCCGTTAATATGTGGGGCGGAAATGGTCGTTTTATCAATGACGGAACGATTGATGTTTCTGCGAAGTCCCTGGtgg         >  2:95440/1‑147 (MQ=255)                                                                                                                                   tgCACATCAACAAGTCCGGTACGCTTTATAATACCGGTCACATGAACATCAGTAATTCTTCCCACAACGGAGCCGTTAATATGTGGGGCGGAAATGGTCGTTTTATCAATGACGGAACGATTGATGTTTCTGCGAAGTCACTGGTAGTc       >  1:798953/1‑149 (MQ=255)                                                                                                                                        aTCAACAAGTCCGGTACGCTTTATAATACCGGTCACATGAACATCAGTAATTCTTCCCACAACGGAGCCGGTAATATGTGGGGCGGAAATGGTCGTTTTATCAATGACGGAACGATTGATGTTTCTGCGAAGTCACTGGTAGTCAgcgc  >  2:439004/1‑149 (MQ=255)                                                                                                                                              |                                                                                                                                               GCAAATAACGAAGGAACCTGGAACCTCGGAAGTAGTAGTGAGGGTAACAACACCGGGATGCTGGAAGTTAATAATAATTCAGCTTTCAATAACCGCGGCGAGTTTATTCTTGATAACGACAAGAATGCTGTGCACATCAACCAGTCCGGTACGCTTTATAATACCGGTCACATGAACATCAGTAATTCTTCCCACAACGGAGCCGTTAATATGTGGGGCGGAAATGGTCGTTTTATCAATGACGGAACGATTGATGTTTCTGCGAAGTCACTGGTAGTCAGCGC  >  CP009273/1466114‑1466397

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑