Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,129,541	C→T	pseudogene (603/1101 nt)	yghO ←	pseudogene, IS‑interrupted

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,129,541	0	C	T	100.0%	172.3 / NA	54	pseudogene (603/1101 nt)	yghO	pseudogene, IS‑interrupted
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (28/26);  total (28/26)

ATAGATCATATCGTCCGGCACCAGATATTTAAGTTGATCGCCCATGGTCGCGAATTCATGTTCGGTAAACGGCACAAATCCCCAGTTGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGGTCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCGCTGCATCCACCACGCCAGTAAATCAATGCC  >  NC_000913/3129415‑3129675                                                                                                                               |                                                                                                                                       ataGATCAGATCGTCCGGCACCAGATATTTAAGTTGATCGCCCATGGTCGCGAATTCATGTTCGGTAAACGGCACAAATCCCCAGTTGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGTATCTCTTCGGCa                                                                                                                            <  2:820171/139‑1 (MQ=255)        atatCGTCCGGCACCAGATATTTAAGTTGATCGCCCATGGTCGCGAATTCATGTTCGGTAAACGGCACAAATCCCCAGTTGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGTATCTCTTCGGCAAACCGCt                                                                                                                     <  1:635260/139‑1 (MQ=255)          atCGTCCGGCACCAGATATTTAAGTTGATCGCCCATGGTCGCGAATTCATGTTCGGTAAACGGCACAAATCCCCAGTTGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGTATCTCTTCGGCAAACCg                                                                                                                       <  1:694969/135‑1 (MQ=255)          atCGTCCGGCACCAGATATTTAAGTTGATCGCCCATGGTCGCGAATTCATGTTCGGTAAACGGCACAAATCCCCAGTTGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGTATCTCTTCGGCAAACCg                                                                                                                       >  2:694969/1‑135 (MQ=255)          atCGTCCGGCACCAGATATTTAAGTTGATCGCCCATGGTCGCGAATTCATGTTCGGTAAACGGCACAAATCCCCAGTTGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGTATCTCTTCGGCAAACCGCTGa                                                                                                                   >  1:86075/1‑139 (MQ=255)          atCGTCCGGCACCAGATATTTAAGTTGATCGCCCATGGTCGCGAATTCATGTTCGGTAAACGGCACAAATCCCCAGTTGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGTATCTCTTCGGCAAACCGCTGa                                                                                                                   >  2:361176/1‑139 (MQ=255)          atCGTCCGGCACCAGATATTTAAGTTGATCGCCCATGGTCGCGAATTCATGTTCGGTAAACGGCACAAATCCCCAGTTGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGTATCTCTTCGGCAAACCGCTGa                                                                                                                   >  1:1339858/1‑139 (MQ=255)          atCGTCCGGCACCAGATATTTAAGTTGATCGCCCATGGTCGCGAATTCATGTTCGGTAAACGGCACAAATCCCCAGTTGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGTATCTCTTCGGCAAACCGCTGa                                                                                                                   >  1:759623/1‑139 (MQ=255)              tCCGGCACCAGATATTTAAGTTGATCGCCCATGGTCGCGAATTCATGTTCGGTAAACGGCACAAATCCCCAGTTGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGTATCTCTTCGGCAAACCGCTGACGAt                                                                                                               <  1:732378/139‑1 (MQ=255)              tCCGGCACCAGATATTTAAGTTGATCGCCCATGGTCGCGAATTCATGTTCGGTAAACGGCACAAATCCCCAGTTGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGTATCTCTTCGGCAAACCGCTGACGAt                                                                                                               >  2:12500/1‑139 (MQ=255)              tCCGGCACCAGATATTTAAGTTGATCGCCCATGGTCGCGAATTCATGTTCGGTAAACGGCACAAATCCCCAGTTGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGTATCTCTTCGGCAAACCGCTGACGAt                                                                                                               >  2:732378/1‑139 (MQ=255)               ccGGCACCAGATATTTAAGTTGATCGCCCATGGTCGCGAATTCATGTTCGGTAAACGGCACAAATCCCCAGTTGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGTATCTCTTCGGCAAACCGCTGACGAtt                                                                                                              >  1:219190/1‑139 (MQ=255)               ccGGCACCAGATATTTAAGTTGATCGCCCATGGTCGCGAATTCATGTTCGGTAAACGGCACAAATCCCCAGTTGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGTATCTCTTCGGCAAACCGCTGACGAtt                                                                                                              >  2:119688/1‑139 (MQ=255)                        gATATTTAAGTTGATCGCCCATGGTCGCGAATTCATGTTCGGTAAACGGCACAAATCCCCAGTTGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGTATCTCTTCGGCAAACCGCTGACGATTGATGCAGCg                                                                                                     >  1:1247316/1‑139 (MQ=255)                        gATATTTAAGTTGATCGCCCATGGTCGCGAATTCATGTTCGGTAAACGGCACAAATCCCCAGTTGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGTATCTCTTCGGCAAACCGCTGACGATTGATGCAGCg                                                                                                     >  2:10956/1‑139 (MQ=255)                              tAAGTTGATCGCCCATGGTCGCGAATTCATGTTCGGTAAACGGCACAAATCCCCAGTTGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGTATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGGt                                                                                               <  1:119688/139‑1 (MQ=255)                               aaGTTGATCGCCCATGGTCGCGAATTCATGTTCGGTAAACGGCACAAATCCCCAGTTGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGTATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGGTc                                                                                              <  2:86075/139‑1 (MQ=255)                                    gATCGCCCATGGTCGCGAATTCATGTTCGGTAAACGGCACAAATCCCCAGTTGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGTATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGGTCACCtt                                                                                         >  1:879366/1‑139 (MQ=255)                                     aTCGCCCATGGTCGCGAATTCATGTTCGGTAAACGGCACAAATCCCCAGTTGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGTATCTCTTCGGCAAACCg                                                                                                                       >  1:381637/1‑108 (MQ=255)                                     aTCGCCCATGGTCGCGAATTCATGTTCGGTAAACGGCACAAATCCCCAGTTGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGTATCTCTTCGGCAAACCg                                                                                                                       <  2:381637/108‑1 (MQ=255)                                     aTCGCCCATGGTCGCGAATTCATGTTCGGTAAACGGCACAAATCCCCAGTTGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGTATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGGTCACCttt                                                                                        >  1:362662/1‑139 (MQ=255)                                        gCCCATGGTCGCGAATTCATGTTCGGTAAACGGCACAAATCCCCAGTTGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGTATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGGTCACCTTTTTg                                                                                     <  2:219190/139‑1 (MQ=255)                                        gCCCATGGTCGCGAATTCATGTTCGGTAAACGGCACAAATCCCCAGTTGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGTATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGGTCACCTTTTTg                                                                                     <  1:12500/139‑1 (MQ=255)                                         cccATGGTCGCGAATTCATGTTCGGTAAACGGCACAAATCCCCAGTTGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGTATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATAGTCACCTTTTTgc                                                                                    <  2:1247316/139‑1 (MQ=255)                                            aTGGTCGCGAATTCATGTTCGGTAAACGGCACAAATCCCCAGTTGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGTATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGGTCACCTTTTTGCGCa                                                                                 >  1:1054942/1‑139 (MQ=255)                                                   cgAATTCATGTTCGGTAAACGGCACAAATCCCCAGTTGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGTATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGGTCACCTTTTTGCGCACCTGATc                                                                          >  2:532684/1‑139 (MQ=255)                                                          aTGTTCGGTAAACGGCACAAATCCCCAGTTGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGTATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGGTCACCTTTTTGCGCACCTGATCCATCAGt                                                                   <  2:1054942/139‑1 (MQ=255)                                                            gTTCGGTAAACGGCACAAATCCCCAGTTGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGTATCTCTTCGGCAACCCGCTGACGATTGATGCAGCGAATGGTCACCTTTTTg                                                                                     >  2:796719/1‑119 (MQ=255)                                                            gTTCGGTAAACGGCACAAATCCCCAGTTGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGTATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGGTCACCTTTTTg                                                                                     <  1:796719/119‑1 (MQ=255)                                                             ttCGGTAAACGGCACAAATCCCCAGTTGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGTATCTCTTCGGCa                                                                                                                            <  1:484974/79‑1 (MQ=255)                                                             ttCGGTAAACGGCACAAATCCCCAGTTGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGTATCTCTTCGGCa                                                                                                                            >  2:484974/1‑79 (MQ=255)                                                               cGGTAAACGGCACAAATCCCCAGTTGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGTATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGGTCACCTTTTTGCGCACCTGATCCATCAGtttttt                                                              <  1:532684/139‑1 (MQ=255)                                                                  tAAACGGCACAAATCCCCAGTTGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGTATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGGTCACCTTTTTg                                                                                     >  1:674092/1‑113 (MQ=255)                                                                  tAAACGGCACAAATCCCCAGTTGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGTATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGGTCACCTTTTTg                                                                                     <  2:674092/113‑1 (MQ=255)                                                                    aaCGGCACAAATCCCCAGTTGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGTATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGGTCACCTTTTTg                                                                                     >  1:34/1‑111 (MQ=255)                                                                    aaCGGCACAAATCCCCAGTTGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGTATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGGTCACCTTTTTg                                                                                     <  2:34/111‑1 (MQ=255)                                                                     aCGGCACAAATCCCCAGTTGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGTATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGGTCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAgcgc                                                        <  1:113578/139‑1 (MQ=255)                                                                         cacaAATCCCCAGTTGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGTATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGGTCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCGga                                                    <  2:879366/139‑1 (MQ=255)                                                                          acaAATCCCCAGTTGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGTATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGGTCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCGgag                                                   >  1:129437/1‑139 (MQ=255)                                                                                      ttGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGTATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGGTCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGAt                                       >  1:604560/1‑139 (MQ=255)                                                                                         tgctgcCAGCCAGAGTTGAAAATCTCACGCAGGATCTGTATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGGTCACCTTTTTgcgc                                                                                  <  2:1009210/93‑1 (MQ=255)                                                                                         tgctgcCAGCCAGAGTTGAAAATCTCACGCAGGATCTGTATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGGTCACCTTTTTgcgc                                                                                  >  1:1009210/1‑93 (MQ=255)                                                                                                agccagAGTTGAAAATCTCACGCAGGATCTGTATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGGTCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCGCTg                             >  1:1166882/1‑139 (MQ=255)                                                                                                  ccagAGTTGAAAATCTCACGCAGGATCTGTATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGGTCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCGCTGCa                           <  2:604560/139‑1 (MQ=255)                                                                                                   cagAGTTGAAAATCTCACGCAGGATCTGTATCTCTTCGGCaaa                                                                                                                          >  2:358507/1‑43 (MQ=255)                                                                                                   cagAGTTGAAAATCTCACGCAGGATCTGTATCTCTTCGGCaaa                                                                                                                          <  1:358507/43‑1 (MQ=255)                                                                                                       gTTGAAAATCTCACGCAGGATCTGTATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGGTCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCGCTGCATccac                      <  1:361176/139‑1 (MQ=255)                                                                                                           aaaaTCTCACGCAGGATCTGTATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGGTCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCGCTGCATCCACCACg                  <  1:433647/139‑1 (MQ=255)                                                                                                                  cACGCAGGATCTGTATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGGTCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCGgagag                                                 <  1:137121/101‑1 (MQ=255)                                                                                                                  cACGCAGGATCTGTATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGGTCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCGgagag                                                 >  2:137121/1‑101 (MQ=255)                                                                                                                     gCAGGATCTGTATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGGTCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCGCTGCATCCACCACGCCAGTAAATc        >  2:282678/1‑139 (MQ=255)                                                                                                                       aGGATCTGTATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGGTCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCGCTGCATCCACCACGCCAGTAAATCaa      <  2:759623/139‑1 (MQ=255)                                                                                                                          aTCTGTATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGGTCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCGCTGCATCCACCACGCCAGTAAATCAATGc   >  2:621429/1‑139 (MQ=255)                                                                                                                           tCTGTATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGGTCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCGCTGCATCCACCACGCCAGTAAATCAATGcc  <  1:282678/139‑1 (MQ=255)                                                                                                                               |                                                                                                                                       ATAGATCATATCGTCCGGCACCAGATATTTAAGTTGATCGCCCATGGTCGCGAATTCATGTTCGGTAAACGGCACAAATCCCCAGTTGTGCTGCCAGCCAGAGTTGAAAATCTCACGCAGGATCTGCATCTCTTCGGCAAACCGCTGACGATTGATGCAGCGAATGGTCACCTTTTTGCGCACCTGATCCATCAGTTTTTTTAGCGCCGGAGAGAAAGTGAGATCGGTTCGCTGCATCCACCACGCCAGTAAATCAATGCC  >  NC_000913/3129415‑3129675

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: ‑