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%	182.0 / NA	58	pseudogene (563/1101 nt)	yghO	pseudogene, IS‑interrupted
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (28/30);  total (28/30)

GATCGCCCATGGTCGCGAATTCATGTTCGGTAAACGGCACAAATCCCCAGTTGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGGTCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCGCTGCATCCACCACGCCAGTAAATCAATGCCTTTGTGATAACCCAGTTGTTCAATATGCGCGGCATACCA  >  NC_000913/3129450‑3129714                                                                                                                                    |                                                                                                                                      gATCGCCCATGGTCGCGAATTCATGTTCGGTAAACGGCACAAATCCCCAGTTGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCtt                                                                                                                                >  2:1152680/1‑139 (MQ=255) gATCGCCCATGGTCGCGAATTCATGTTCGGTAAACGGCACAAAGCCCCAGTTGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCtt                                                                                                                                <  2:854877/139‑1 (MQ=255)  aTCGCCCATGGTCGCGAATTCATGTTCGGTAAACGGCACAAATCCCCAGTTGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCttt                                                                                                                               >  1:1062499/1‑139 (MQ=255)  aTCGCCCATGGTCGCGAATTCATGTTCGGTAAACGGCACAAATCCCCAGTTGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCttt                                                                                                                               >  2:266487/1‑139 (MQ=255)    cGCCCATGGTCGCGAATTCATGTTCGGTAAACGGCACAAATCCCCAGTTGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCttttt                                                                                                                             >  1:999931/1‑139 (MQ=255)    cGCCCATGGTCGCGAATTCATGTTCGGTAAACGGCACAAATCCCCAGTTGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCttttt                                                                                                                             >  1:453688/1‑139 (MQ=255)           ggTCGCGAATTCATGTTCGGTAAACGGCACAAATCCCCAGTTGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCAcc                                                                                                                      <  1:1152680/139‑1 (MQ=255)                    ttCATGTTCGGTAAACGGCACAAATCCCCAGTTGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCACCTGATCCATc                                                                                                             <  1:224236/139‑1 (MQ=255)                         gTTCGGTAAACGGCACAAATCCCCAGTTGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCACCTGATCCATCAGttt                                                                                                        >  2:1031859/1‑139 (MQ=255)                                 aaCGGCACAAATCCCCAGTTGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTgcgc                                                                                                                         >  1:736363/1‑114 (MQ=255)                                 aaCGGCACAAATCCCCAGTTGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTgcgc                                                                                                                         <  2:736363/114‑1 (MQ=255)                                    ggCACAAATCCCCAGTTGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCg                                                                                             <  2:217318/139‑1 (MQ=255)                                    ggCACAAATCCCCAGTTGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCg                                                                                             <  2:443742/139‑1 (MQ=255)                                      cacaAATCCCCAGTTGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCGga                                                                                           >  2:1051835/1‑139 (MQ=255)                                        caAATCCCCAGTTGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTgcgc                                                                                                                         <  1:45221/107‑1 (MQ=255)                                        caAATCCCCAGTTGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTgcgc                                                                                                                         >  2:45221/1‑107 (MQ=255)                                        caAATCCCCAGTTGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCGgaga                                                                                         <  1:1051835/139‑1 (MQ=255)                                         aaaTCCCCAGTTGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCGgagag                                                                                        <  1:198714/139‑1 (MQ=255)                                             ccccAGTTGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAg                                                                                    >  1:457418/1‑139 (MQ=255)                                                  gTTGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTgaga                                                                               <  2:721319/139‑1 (MQ=255)                                                  gTTGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTgaga                                                                               >  1:1109576/1‑139 (MQ=255)                                                      tgctgcCAGCCAGAGTTGAAAATCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCTCCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCgg                                                                           >  2:778317/1‑139 (MQ=255)                                                      tgctgcCAGCCAGAGTTGAAAATCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCAGAGAGAAAGTGAGATCgg                                                                           >  2:629902/1‑139 (MQ=255)                                                       gctgcCAGCCAGAGTTGAAAATCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGt                                                                          <  1:778317/139‑1 (MQ=255)                                                        ctgcCAGCCAGAGTTGAAAATCTCACGCAGGATCGGCATCCCTTCGGCAAACCGCTGACGTTTGTTGGAGCGATTGATCACCTTTTTGCGCACCTGACCGATCAGTTTTTTTAGCGCCGGAGAGAAAGGTAGATCGGta                                                                         >  2:339796/1‑138 (MQ=255)                                                          gccagccaGAGTTGAAAATCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCg                                                                       <  2:457418/139‑1 (MQ=255)                                                             agccagAGTTGAAAATCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCGCTg                                                                    >  2:715719/1‑139 (MQ=255)                                                             agccagAGTTGAAAATCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCGCTg                                                                    >  2:289966/1‑139 (MQ=255)                                                                 agagTTGAAAATCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCAGAGAGAAAGTGAGATCGGTTCGCTGCATc                                                                <  1:629902/139‑1 (MQ=255)                                                                    gTTGAAAATCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCGCTGCATccac                                                             <  1:740589/139‑1 (MQ=255)                                                                         aaaTCTCACGCAGGGTCTGCATCTCTTCGGAAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCGCTGCATCCACCACGc                                                        <  1:339796/139‑1 (MQ=255)                                                                             ctcACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCGCTGCATCCACCACGCCAGt                                                    <  1:115407/139‑1 (MQ=255)                                                                                    aGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCGCTGCATCCACCACGCCAGTAAATCaa                                             <  2:453688/139‑1 (MQ=255)                                                                                    aGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCGCTGCATCCACCACGCCAGTAAATCaa                                             <  1:266487/139‑1 (MQ=255)                                                                                       aTCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTg                                                                                                                            <  2:1030606/57‑1 (MQ=255)                                                                                       aTCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTg                                                                                                                            >  1:1030606/1‑57 (MQ=255)                                                                                            cATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCACCTGATCCCTCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCGCTGCATCCACCACGCCAGTAAATCAATGCCTTtg                                     >  2:102060/1‑139 (MQ=255)                                                                                             aTCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCGCTGCATCCACCACGCCAGTAAATCAATGCCTTtgt                                    <  1:289966/139‑1 (MQ=255)                                                                                                tctTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCACCTGATCCATc                                                                                                             <  1:487633/63‑1 (MQ=255)                                                                                                tctTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCACCTGATCCATc                                                                                                             >  2:487633/1‑63 (MQ=255)                                                                                                tctTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCGCTGCATCCACCACGCCAGTAAATCAATGCCTTTGTGAt                                 >  2:1203811/1‑139 (MQ=255)                                                                                                tctTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCGCTGCATCCACCACGCCAGTAAATCAATGCCTTTGTGAt                                 >  1:730609/1‑139 (MQ=255)                                                                                                tctTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCGCTGCATCCACCACGCCAGTAAATCAATGCCTTTGTGAt                                 >  2:37637/1‑139 (MQ=255)                                                                                                 ctTCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCGCTGCATCCACCACGCCAGTAAATCAATGCCTTTGTGATa                                >  1:680131/1‑139 (MQ=255)                                                                                                  ttCGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCGCTGCATCCACCACGCCAGTAAATCAATGCCTTTGTGATaa                               >  1:713092/1‑139 (MQ=255)                                                                                                    cGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCGCTGCATCCACCACg                                                         <  2:839633/111‑1 (MQ=255)                                                                                                    cGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCGCTGCATCCACCACg                                                         >  1:839633/1‑111 (MQ=255)                                                                                                    cGGCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCACCTGATCCATCAGTGTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCGCTGCATCCACCACGCCAGTAAATCAATGCCTTTGTGATAAcc                             <  2:939804/139‑1 (MQ=255)                                                                                                      gCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCGCTGCATCCACCACGCCAGTAAATCAATGCCTTTGTGATAACCCa                           <  2:730609/139‑1 (MQ=255)                                                                                                      gCAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCGCTGCATCCACCACGCCAGTAAATCAATGCCTTTGTGATAACCCa                           <  1:1203811/139‑1 (MQ=255)                                                                                                       cAAACCGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCGCTGCATCCACCACGCCAGTAAATCAATGCCTTTGTGATAACCCAg                          <  2:1062499/139‑1 (MQ=255)                                                                                                           ccGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCGCTGCATCCACCACGCCAGTAAATCAATGCCTTTGTGATAACCCAgttgt                      <  2:747813/139‑1 (MQ=255)                                                                                                            cGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCGCTGCATCCACCACGCCAGTAAATCAAt                                            <  1:1153468/116‑1 (MQ=255)                                                                                                            cGCTGACGATTGATGCAGCGAATGATCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCGCTGCATCCACCACGCCAGTAAATCAAt                                            >  2:1153468/1‑116 (MQ=255)                                                                                                                       gATGCAGCGAATGATCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCGCTGCATCCACCACGCCAGTAAATCAATGCCTTTGTGATAACCCAGTTGTTCAATATGcgcg          <  2:680131/139‑1 (MQ=255)                                                                                                                             gCGAATGATCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCGCTGCATCCACCACGCCAGTAAATCAATGCCTTTGTGATAACCCAGTTGTTCAATATGCGCGGCATAc    >  1:985277/1‑139 (MQ=255)                                                                                                                              cGAATGATCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCGCTGCATCCACCACGCCAGTAAATCAATGCCTTTGTGATAACCCAGTTGTTCAATATGCGCGGCATAcc   <  2:412268/139‑1 (MQ=255)                                                                                                                               gAATGATCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCGCTGCATCCACCACGCCAGTAAATCAATGCCTTTGTGATAACCCAGTTGTTCAATATGCGCGGCATACCa  >  2:1104677/1‑139 (MQ=255)                                                                                                                                    |                                                                                                                                      GATCGCCCATGGTCGCGAATTCATGTTCGGTAAACGGCACAAATCCCCAGTTGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGGTCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCGCTGCATCCACCACGCCAGTAAATCAATGCCTTTGTGATAACCCAGTTGTTCAATATGCGCGGCATACCA  >  NC_000913/3129450‑3129714

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: ‑