Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,129,581	G→A	pseudogene (563/1101 nt)	yghO ←	pseudogene, IS‑interrupted

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,129,581	0	G	A	100.0%	168.1 / NA	52	pseudogene (563/1101 nt)	yghO	pseudogene, IS‑interrupted
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (23/29);  total (23/29)

GATCGCCCATGGTCGCGAATTCATGTTCGGTAAACGGCACAAATCCCCAGTTGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGGTCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCGCTGCATCCACCACGCCAGTAAATCAATGCCTTTGTGATAACCCAGTTGTTCAATATGCGC  >  NC_000913/3129450‑3129705                                                                                                                                    |                                                                                                                             gATCGCCCATGGTCGCGAATTCATGTTCGGTAAACGGCACAAATCCCCAGTTGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCtt                                                                                                                       >  1:510129/1‑139 (MQ=255)  aTCGCCCATGGTCGCGAATTCATGTTCGGTAAACGGCACAAATCCCCAGTTGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCttt                                                                                                                      >  2:71746/1‑139 (MQ=255)     gCCCATGGTCGCGAATTCATGTTCGGTAAACGGCACAAATCCCCAGTTGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTg                                                                                                                   <  1:806434/139‑1 (MQ=255)       ccATGGTCGCGAATTCATGTTCGGTAAACGGCACAAATCCCCAGTTGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTgcg                                                                                                                 <  2:905347/139‑1 (MQ=255)         aTGGTCGCGAATTCATGTTCGGTAAACGGCACAAATCCCCAGTTGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCa                                                                                                               <  2:1189570/139‑1 (MQ=255)                 gAATTCATGTTCGGTAAACGGCACAAATCCCCAGTTGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCACCTGATcc                                                                                                       >  2:666962/1‑139 (MQ=255)                     tCATGTTCGGTAAACGGCACAAATCCCCAGTTGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCACCTGATCCATCa                                                                                                   <  2:60832/139‑1 (MQ=255)                               tAAACGGCACAAATCCCCAGTTGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAg                                                                                         >  2:1309645/1‑139 (MQ=255)                                  aCGGCACAAATCCCCAGTTGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAgcgc                                                                                      <  2:475385/139‑1 (MQ=255)                                  aCGGCACAAATCCCCAGTTGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAgcgc                                                                                      >  2:1135253/1‑139 (MQ=255)                                    ggCACAAATCCCCAGTTGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCg                                                                                    <  2:1386965/139‑1 (MQ=255)                                    ggCACAAATCCCCAGTTGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCg                                                                                    >  1:607259/1‑139 (MQ=255)                                    ggCACAAATCCCCAGTTGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCg                                                                                    <  1:1309645/139‑1 (MQ=255)                                      cacaAATCCCCAGTTGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCGga                                                                                  >  1:85300/1‑139 (MQ=255)                                        caAATCCCCAGTTGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCGgaga                                                                                <  1:71746/139‑1 (MQ=255)                                                     gtgCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCGgag                                                                                 >  2:70273/1‑125 (MQ=255)                                                     gtgCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCGgag                                                                                 <  1:70273/125‑1 (MQ=255)                                                          gccagccaGAGTTGAAAATCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCg                                                              <  1:1135253/139‑1 (MQ=255)                                                          gccagccaGAGTTGAAAATCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCg                                                              <  2:510129/139‑1 (MQ=255)                                                             agccagAGTTGAAAATCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTa                                                                                          <  1:1232493/108‑1 (MQ=255)                                                             agccagAGTTGAAAATCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTa                                                                                          >  2:1232493/1‑108 (MQ=255)                                                             agccagAGTTGAAAATCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCGCTg                                                           >  1:713369/1‑139 (MQ=255)                                                                       gAAAATCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCGCTGCATCcaccac                                                 <  2:607259/139‑1 (MQ=255)                                                                         aaaTCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCGCTGCATCCACCACGc                                               <  2:244679/139‑1 (MQ=255)                                                                          aaTCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCGgagag                                                                               >  2:309367/1‑106 (MQ=255)                                                                          aaTCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCGgagag                                                                               <  1:309367/106‑1 (MQ=255)                                                                             ctcACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCGCTGCATCCACCACGCCAGt                                           <  2:85300/139‑1 (MQ=255)                                                                             ctcACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCGCTGCATCCACCACGCCAGt                                           <  1:965004/139‑1 (MQ=255)                                                                                     ggATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCGCTGCATCCACCACGCCAGTAAATCAAt                                   <  1:166541/139‑1 (MQ=255)                                                                                          tGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCa                                                                                                               >  2:1035550/1‑58 (MQ=255)                                                                                          tGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCa                                                                                                               <  1:1035550/58‑1 (MQ=255)                                                                                          tGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCGCTGCATCCACCACGCCAGTAAATCAATGCCtt                              >  2:1334483/1‑139 (MQ=255)                                                                                            cATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCttt                                                                                                                      <  2:1383891/49‑1 (MQ=255)                                                                                            cATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCttt                                                                                                                      >  1:1383891/1‑49 (MQ=255)                                                                                              tctcTTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCGCTGCATCCACCACGCCAGTAAATCAATGCCTTtgtg                          >  1:1202992/1‑139 (MQ=255)                                                                                               ctctTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCGCTGCATCCACCACGCCAGTAAATCAATGCCTTTGTGa                         <  2:1202992/139‑1 (MQ=255)                                                                                                 ctTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTgc                                                                                                                  <  2:601999/48‑1 (MQ=255)                                                                                                 ctTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTgc                                                                                                                  >  1:601999/1‑48 (MQ=255)                                                                                                 ctTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAgcgc                                                                                      >  2:172332/1‑76 (MQ=255)                                                                                                 ctTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAgcgc                                                                                      <  1:172332/76‑1 (MQ=255)                                                                                                  ttCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCACCT‑ATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCGCTGCATCCACCACGCCAg                                            >  2:182822/1‑116 (MQ=255)                                                                                                  ttCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCACCT‑ATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCGCTGCATCCACCACGCCAg                                            <  1:182822/116‑1 (MQ=255)                                                                                                      gCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCGCTGCATCCACCACGCCAGTAAATCAATGCCTTTGTGATAACCCa                  <  1:1334483/139‑1 (MQ=255)                                                                                                         aaCCGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCGgaga                                                                                >  2:421210/1‑74 (MQ=255)                                                                                                         aaCCGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCGgaga                                                                                <  1:421210/74‑1 (MQ=255)                                                                                                          aCCGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCGCTGCATCCACCACGCCAGTAAATCAATGCCTTTGTGATAACCCAgttg              <  2:713369/139‑1 (MQ=255)                                                                                                                      tGATGCAGCGAATGATCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCGCTGCATCCACCACGCCAGTAAATCAAt                                   >  2:52124/1‑106 (MQ=255)                                                                                                                      tGATGCAGCGAATGATCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCGCTGCATCCACCACGCCAGTAAATCAAt                                   <  1:52124/106‑1 (MQ=255)                                                                                                                      tGATGCAGCGAATGATCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCGCTGCATCCACCACGCCAGTAAATCAATGCCTTTGTGATAACCCAGTTGTTCAATATgcgc  >  2:358269/1‑139 (MQ=255)                                                                                                                      tGATGCAGCGAATGATCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCGCTGCATCCACCACGCCAGTAAATCAATGCCTTTGTGATAACCCAGTTGTTCAATATgcgc  >  2:1432173/1‑139 (MQ=255)                                                                                                                           cAGCGAATGATCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCGCTGCATccac                                                    <  1:150172/84‑1 (MQ=255)                                                                                                                           cAGCGAATGATCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCGCTGCATccac                                                    >  2:150172/1‑84 (MQ=255)                                                                                                                                    |                                                                                                                             GATCGCCCATGGTCGCGAATTCATGTTCGGTAAACGGCACAAATCCCCAGTTGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGGTCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCGCTGCATCCACCACGCCAGTAAATCAATGCCTTTGTGATAACCCAGTTGTTCAATATGCGC  >  NC_000913/3129450‑3129705

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑