Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,129,594	G→A	pseudogene (550/1101 nt)	yghO ←	pseudogene, IS‑interrupted

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,129,594	0	G	A	100.0%	191.9 / NA	55	pseudogene (550/1101 nt)	yghO	pseudogene, IS‑interrupted
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (27/28);  total (27/28)

GGTCGCGAATTCATGTTCGGTAAACGGCACAAATCCCCAGTTGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGGTCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCGCTGCATCCACCACGCCAGTAAATCAATGCCTTTGTGATAACCCAGTTGTTCAATATGCGCGGCATACCACGGTTTGCCGTGTGG  >  NC_000913/3129460‑3129729                                                                                                                                       |                                                                                                                                        ggTCGCGAATTCATGTTCGGTAAACGGCACAAATCCCCAGTTGTGCTGCCAGCCAGAGTTGAAAATCTCACACAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGGTCACCTTTTTGCACAcc                                                                                                                                     <  2:389128/139‑1 (MQ=255)      cgAATTCATGTTCGGTAAACGGCACAAATCCCCAGTTGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGGTCACCTTTTTGCACACCTGATc                                                                                                                                >  2:371859/1‑139 (MQ=255)         aTTCATGTTCGGTAAACGGCACAAATCCCCAGTTGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGGTCACCTTTTTGCACACCTGATCCAt                                                                                                                             <  2:318491/139‑1 (MQ=255)             aTGTTCGGTAAACGGCACAAATCCCCAGTTGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGGTCACCTTTTTGCACAcc                                                                                                                                     >  1:863650/1‑127 (MQ=255)             aTGTTCGGTAAACGGCACAAATCCCCAGTTGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGGTCACCTTTTTGCACAcc                                                                                                                                     <  2:863650/127‑1 (MQ=255)                   ggTAAACGGCACAAATCCCCAGTTGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGGTCACCTTTTTGCACACCTGATCCATCAGttttttt                                                                                                                   >  1:263000/1‑139 (MQ=255)                        aCGGCACAAATCCCCAGTTGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGGTCACCTTTTTGCACACCTGATCCATCAGTTTTTTTAgcgc                                                                                                              <  1:910075/139‑1 (MQ=255)                         cGGCACAAATCCCCAGTTGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGGTCACCTTTTTGCACACCTGATCCATCAGTTTTTTTAGCGcc                                                                                                             >  2:387012/1‑139 (MQ=255)                          ggCACAAATCCCCAGTTGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGGTCACCTTTTTGCACACCTGATCCATCAGTTTTTTTAGCGCCg                                                                                                            <  2:1128801/139‑1 (MQ=255)                            cacaAATCCCCAGTTGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGGTCACCTTTTTGCACACCTGATCCATCAGTTTTTTTAGCGCCGga                                                                                                          >  1:737293/1‑139 (MQ=255)                            cacaAATCCCCAGTTGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGGTCACCTTTTTGCACACCTGATCCATCAGTTTTTTTAGCGCCGga                                                                                                          <  2:147979/139‑1 (MQ=255)                                 aTCCCCAGTTGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGGTCACCTTTTTGCACACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGaa                                                                                                     <  1:543559/139‑1 (MQ=255)                                   ccccAGTTGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGGTCACCTTTTTGCACACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAg                                                                                                   <  2:199420/139‑1 (MQ=255)                                      cAGTTGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGGTCACCTTTTTGCACACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTga                                                                                                >  2:1272327/1‑139 (MQ=255)                                        gTTGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGGTCACCTTTTTGCACACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTgaga                                                                                              <  1:460595/139‑1 (MQ=255)                                               tgcCAGCCAGAGTTGAAAATCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGGTCACCTTTTTGCACACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTc                                                                                       <  1:18770/139‑1 (MQ=255)                                                gccagccaGAGTTGAAAATCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGGTCACCTTTTTGCACACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCg                                                                                      <  2:319618/139‑1 (MQ=255)                                                gccagccaGAGTTGAAAATCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGGTCACCTTTTTGCACACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCg                                                                                      <  1:10249/139‑1 (MQ=255)                                                gccagccaGAGTTGAAAATCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGGTCACCTTTTTGCACACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCg                                                                                      <  2:926475/139‑1 (MQ=255)                                                   agccagAGTTGAAAATCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCCGCGAATGGTCACCTTTTTGCACACCTGATCCATCAGTTTTTTTAGCGCGGGAGAGAAAGTGAGATCGGTGGGCTg                                                                                   >  1:783767/1‑139 (MQ=255)                                                     ccagAGTTGAAAATCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGGTCACCTTTTTGCACACCTGATCCATCAGTTTTTTTAGCGCCGgaga                                                                                                        >  2:175029/1‑116 (MQ=255)                                                     ccagAGTTGAAAATCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGGTCACCTTTTTGCACACCTGATCCATCAGTTTTTTTAGCGCCGgaga                                                                                                        <  1:175029/116‑1 (MQ=255)                                                     ccagAGTTGAAAATCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGGTCACCTTTTTGCACACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCGCTGCa                                                                                 <  1:341664/139‑1 (MQ=255)                                                     ccagAGTTGAAAATCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGGTCACCTTTTTGCACACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCGCTGCa                                                                                 <  1:1112154/139‑1 (MQ=255)                                                      cagAGTTGAAAATCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGGTCACCTTTTTGCACACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCGCTGCAt                                                                                >  1:496255/1‑139 (MQ=255)                                                        gagTTGAAAATCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGGTCACCTTTTTGCACACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCGCTGCATcc                                                                              >  1:713264/1‑139 (MQ=255)                                                           ttGAAAATCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGGTCACCTTTTTGCACACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCGCTGCATccacc                                                                           <  1:1272327/139‑1 (MQ=255)                                                              aaaaTCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGGTCACCTTTTTGCACACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCGCTGCATCCACCACg                                                                        >  1:1048516/1‑139 (MQ=255)                                                                     cACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGGTCACCTTTTTGCACACCTGATCCGTCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCGCTGCATCCACCACGCCAGTaa                                                                 >  1:833194/1‑139 (MQ=255)                                                                     cACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGGTCACCTTTTTGCACACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCGCTGCATCCACCACGCCAGTaa                                                                 >  2:820668/1‑139 (MQ=255)                                                                     cACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGGTCACCTTTTTGCACACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCGCTGCATCCACCACGCCAGTaa                                                                 >  1:232775/1‑139 (MQ=255)                                                                       cGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGGTCACCTTTTTGCACACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCGCTGCATCCACCACGCCAGTAAAt                                                               <  2:1213152/139‑1 (MQ=255)                                                                            gATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGGTCACCTTTTTGCACACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCGCTGCATCCACCACGCCAGTAAATCAATg                                                          >  1:654425/1‑139 (MQ=255)                                                                              tCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGGTCACCTTTTTGCACACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCGCTGCATCCACCACGCCAGTAAATCAATGcc                                                        <  1:371859/139‑1 (MQ=255)                                                                                      tctTCGGCAAACCGCTGACGATTGATGCAGCGAATGGTCACCTTTTTGCACACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCGCTGCATCCACCACGCCAGTAAATCAATGCCTTTGTGAt                                                >  2:260835/1‑139 (MQ=255)                                                                                          cGGCAAACCGCTGACGATTGATGCAGCGAATGGTCACCTTTTTGCACACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCGCTGCATCCACCACGCCAGTAAATCAATGCCTTTGTGATAAcc                                            >  1:1048150/1‑139 (MQ=255)                                                                                          cGGCAAACCGCTGACGATTGATGCAGCGAATGGTCACCTTTTTGCACACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCGCTGCATCCACCACGCCAGTAAATCAATGCCTTTGTGATAAcc                                            >  2:707759/1‑139 (MQ=255)                                                                                          cGGCAAACCGCTGACGATTGATGCAGCGAATGGTCACCTTTTTGCACACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCGCTGCATCCACCACGCCAGTAAATCAATGCCTTTGTGATAAcc                                            >  1:1148400/1‑139 (MQ=255)                                                                                            gCAAACCGCTGACGATTGATGCAGCGAATGGTCACCTTTTTGCACACCTGATCCA‑‑AGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCGCTGCATCCACCACGCCAGTAAATCAATGCCTTTGTGATAACCCAgt                                        <  1:557203/139‑1 (MQ=255)                                                                                                           ttGATGCAGCGAATGGTCACCTTTTTGCACACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCGCTGCATCCACCACGCCAGTAAATCAATGCCTTTGTGATAACCCAGTTGTTCAATATgcg                           <  2:713264/139‑1 (MQ=255)                                                                                                           ttGATGCAGCGAATGGTCACCTTTTTGCACACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCGCTGCATCCACCACGCCAGTAAATCAATGCCTTTGTGATAACCCAGTTGTTCAATATgcg                           <  2:764698/139‑1 (MQ=255)                                                                                                            tGATGCAGCGAATGGTCACCTTTTTGCACACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCGCTGCATCCACCACGCCAGTAAATCAATGCCTTTGTGATAACCCAGTTGTTCAATATgcgc                          >  2:895918/1‑139 (MQ=255)                                                                                                              aTGCAGCGAATGGTCACCTTTTTGCACACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCGCTGCATCCACCACGCCAGTAAATCAATGCCTTTGTGATAACCCAGTTGTTCAATATGCGCgg                        <  2:1062443/139‑1 (MQ=255)                                                                                                                   gCGAATGGTCACCTTTTTGCACACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCGCTGCATCCACCACGCCAGTAAATCAATGCCTTTGTGATAACCCAGTTGTTCAatat                              <  2:1235609/128‑1 (MQ=255)                                                                                                                   gCGAATGGTCACCTTTTTGCACACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCGCTGCATCCACCACGCCAGTAAATCAATGCCTTTGTGATAACCCAGTTGTTCAatat                              >  1:1235609/1‑128 (MQ=255)                                                                                                                    cGAATGGTCACCTTTTTGCACACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCGCTGCATCCACCACGCCAGTAAATCAATGCCTTTGTGATAACCCa                                          <  2:1056095/115‑1 (MQ=255)                                                                                                                    cGAATGGTCACCTTTTTGCACACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCGCTGCATCCACCACGCCAGTAAATCAATGCCTTTGTGATAACCCa                                          >  1:1056095/1‑115 (MQ=255)                                                                                                                      aaTGGTCACCTTTTTGCACACCTGATCCATCAGTTTTTTTAGCGCCGgag                                                                                                         >  1:142310/1‑50 (MQ=255)                                                                                                                      aaTGGTCACCTTTTTGCACACCTGATCCATCAGTTTTTTTAGCGCCGgag                                                                                                         <  2:142310/50‑1 (MQ=255)                                                                                                                      aaTGGTCACCTTTTTGCACACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCGCTGCATCCACCACGCCAGTAAATCAATGCCTTTGTGATAACCCAGTTGTTCAATATGCGCGGCATACCAc                >  1:504266/1‑139 (MQ=255)                                                                                                                          gTCACCTTTTTGCACACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCGCTGCATCCACCACGCCAGTAAATCAATGCCTTTGTGATAACCCAGTTGTTCAATATGCGCGGCATACCACGGtt            >  1:31764/1‑139 (MQ=255)                                                                                                                                   ttGCACACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCGCTGCATCCACCACGCCAGTAAATCAATGCCtt                                                      <  2:1184187/88‑1 (MQ=255)                                                                                                                                   ttGCACACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCGCTGCATCCACCACGCCAGTAAATCAATGCCtt                                                      >  1:1184187/1‑88 (MQ=255)                                                                                                                                    tGCACACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCGCTGCATCCACCACGCCAGTAAATCAATGCCTTTGTGATAACCCAGTTGTTCAATATGCGCGGCATACCACGGTTTGCCGTGTgg  >  2:563478/1‑139 (MQ=255)                                                                                                                                    tGCACACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCGCTGCATCCACCACGCCAGTAAATCAATGCCTTTGTGATAACCCAGTTGTTCAATATGCGCGGCATACCACGGTTTGCCGTGTgg  <  1:370555/139‑1 (MQ=255)                                                                                                                                       |                                                                                                                                        GGTCGCGAATTCATGTTCGGTAAACGGCACAAATCCCCAGTTGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGGTCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCGCTGCATCCACCACGCCAGTAAATCAATGCCTTTGTGATAACCCAGTTGTTCAATATGCGCGGCATACCACGGTTTGCCGTGTGG  >  NC_000913/3129460‑3129729

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑