Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,816,407	G→A	pseudogene (143/669 nt)	rph ←	ribonuclease PH (defective);enzyme; Degradation of RNA; RNase PH

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,816,407	0	G	A	100.0%	220.3 / NA	55	pseudogene (143/669 nt)	rph	ribonuclease PH (defective);enzyme; Degradation of RNA; RNase PH
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (28/27);  total (28/27)

CACGGGCGATCAGACGCTGGATTTCCATTGTGCGTCCACCCTGCTTACCTTTCGCCGCTTCACGAGCGTTACGGGTGTGGGTAGAACGTGGCAGCATGCCGTACTCTGCGGTGATCCAGCCCTGGCCCTGACCTTTCAGGAAGCGCGGCACGCCTTCTTCAATAGAGGCGGTACACAACACTTTGGTATCGCCAAATTCGACCAGCACCGAGCCTTCTGCATGTTTTGTATAGTTACGAGTCAGGGTAACGGGACGCACCTGATTATTGCTACGGCCTGCTGGACGCATATT  >  NC_000913/3816261‑3816552                                                                                                                                                   |                                                                                                                                                  cACGGGCGATCAGACGCTGGATTTCCATTGTGCGTCCACCCTGCTTACCTTTCGCCGCTTCACGAGCGTTACGGGTGTGGGTAGAACGTGGCAGCATGCCGTACTCTGCGGTGATCCAGCCCTGGCCCTGACCTTTCAGGAAGCGCAGCAc                                                                                                                                               >  1:382309/1‑151 (MQ=255)  aCGGGCGATCAGACGCTGGATTTCCATTGTGCGTCCACCCTGCTTACCTTTCGCCGCTTCACGAGCGTTACGGGTGTGGGTAGAACGTGGCAGCATGCCGTACTCTGCGGTGATCCAGCCCTGGCCCTGACCTTTCAGGAAGCGCAGCACg                                                                                                                                              >  1:81240/1‑151 (MQ=255)  aCGGGCGATCAGACGCTGGATTTCCATTGTGCGTCCACCCTGCTTACCTTTCGCCGCTTCACGAGCGTTACGGGTGTGGGTAGAACGTGGCAGCATGCCGTACTCTGCGGTGATCCAGCCCTGGCCCTGACCTTTCAGGAAGCGCAGCACg                                                                                                                                              <  2:35742/151‑1 (MQ=255)         aTCAGACGCTGGATTTCCATTGTGCGTCCACCCTGCTTTCCTTTCGCCGCTTCACGAGCGTTACGGGTGTGGGTAGAACGTGGCAGCATGCCGTACTCTGCGGTGATCCAGCCCTGGCCCTGACCTTTCAGGAAGCGCAGCACGCcttctt                                                                                                                                       <  2:447681/151‑1 (MQ=255)          tCAGACGCTGGATTTCCATTGTGCGTCCACCCTGCTTACCTTTCGCCGCTTCACGAGCGTTACGGGTGTGGGTAGAACGTGGCAGCATGCCGTACTCTGCGGTGATCCAGCCCTGGCCCTGACCTTTCAGGAAGCGCAGCACGCCttcttc                                                                                                                                      >  2:598606/1‑151 (MQ=255)            cgaagCTGGATTTCCATGGTGCGTCCACCCTGCTTACCTTTCGCCGCTTCACGAGCGTTACGGGTGTGGGAAGAACGTGGCAGCATGCCGTATTCTGCGGTGATCCAGCTCTGGCACTGACCTTTCAGGAAGCGCAGGACGCcttctt                                                                                                                                       >  2:527768/5‑148 (MQ=255)            aGACGCTGGATTTCCATTGTGCGTCCACCCTGCTTACCTTTCGCCGCTTCACGAGCGTTACGGGTGTGGGTAGAACGTGGCAGCATGCCGTACTCTGCGGTGATCCAGCCCTGGCCCTGACCTTTCAGGAAGCGCAGCACGCCTTCTTCa                                                                                                                                     >  2:208176/1‑150 (MQ=255)                        tCCATTGTGCGTCCACCCTGCTTACCTTTCGCCGCTTCACGAGCGTTACGGGTGTGGGTAGAACGTGGCAGCATGCCGTACTCTGCGGTGATCCAGCCCTGGCCCTGACCTTTCAGGAAGCGCAGCACGCCTTCTTCAATAGAGGCGGTa                                                                                                                         >  2:236461/1‑150 (MQ=255)                         ccATTGTGCGTCCACCCTGCTTACCTTTCGCCGCTTCACGAGCGTTACGGGTGTGGGTAGAACGTGGCAGCATGCCGTACTCTGCGGTGATCCAGCCCTGGCCCTGACCTTTCAGGAAGCGCAGCACGCCTTCTTCAATAGAGGCGGTac                                                                                                                        >  2:117779/1‑150 (MQ=255)                          cATTGTGCGTCCACCCTGCTTACCTTTCGCCGCTTCACGAGCGTTACGGGTGTGGGTAGAACGTGGCAGCATGCCGTACTCTGCGGTGATCCAGCCCTGGCCCTGACCTTTCAGGAAGCGCAGCACGCCTTCTTCAATAGAGGCGGTacac                                                                                                                      <  1:761333/151‑1 (MQ=255)                            ttGTGCGTCCACCCTGCTTACCTTTCGCCGCTTCACGAGCGTTACGGGTGTGGGTAGAACGTGGCAGCATGCCGTACTCTGCGGTGATCCAGCCCTGGCCCTGACCTTTCAGGAAGCGCAGCACGCCTTCTTCAATAGAGGCGGTAcaca                                                                                                                     >  2:356593/1‑150 (MQ=255)                             tgtgCGTCCACCCTGCTTACCTTTCGCCGCTTCACGAGCGTTACGGGTGTGGGTAGAACGTGGCAGCATGCCGTACTCTGCGGTGATCCAGCCCTGGCCCTGACCTTTCAGGAAGCGCAGCACGCCTTCTTCAATAGAGGCGGTACacaa                                                                                                                    <  1:467834/150‑1 (MQ=255)                             tgtgCGTCCACCCTGCTTACCTTTCGCCGCTTCACGAGCGTTACGGGTGTGGGTAGAACGTGGCAGCATGCCGTACTCTGCGGTGATCCAGCCCTGGCCCTGACCTTTCAGGAAGCGCAGCACGCCTTCTTCAATAGAGGCGGTACacaa                                                                                                                    >  1:268746/1‑150 (MQ=255)                             tgtgCGTCCACCCTGCTTACCTTTCGCCGCTTCACGAGCGTTACGGGTGTGGGTAGAACGTGGCAGCATGCCGTACTCTGCGGTGATCCAGCCCTGGCCCTGACCTTTCAGGAAGCGCAGCACGCCTTCTTCAATAGAGGCGGTACacaa                                                                                                                    >  1:365443/1‑150 (MQ=255)                                  gTCCACCCTGCTTACCTTTCGCCGCTTCACGAGCGTTACGGGTGTGGGTAGAACGTGGCAGCATGCCGTACTCTGCGGTGATCCAGCCCTGGCCCTGACCTTTCAGGAAGCGCAGCACGCCTTCTTCAATAGAGGCGGTACACAACACttt                                                                                                              <  1:735847/151‑1 (MQ=255)                                    ccACCCTGCTTACCTTTCGCCGCTTCACGAGCGTTACGGGTGTGGGTAGAACGTGGCAGCATGCCGTACTCTGCGGTGATCCAGCCCTGGCCCTGACCTTTCAGGAAGCGCAGCACGCCTTCTTCAATAGAGGCGGTACACAACACTTTgg                                                                                                            <  1:516124/151‑1 (MQ=255)                                     cACCCTGCTTACCTTTCGCCGCTTCACGAGCGTTACGGGTGTGGGTAGAACGTGGCAGCATGCCGTACTCTGCGGTGATCCAGCCCTGGCCCTGACCTTTCAGGAAGCGCAGCACGCCTTCTTCAATAGAGGCGGTACACAACACTTTGGt                                                                                                           <  1:489399/151‑1 (MQ=255)                                        ccTGCTTACCTTTCGCCGCTTCACGAGCGTTACGGGTGTGGGTAGAACGTGGCAGCATGCCGTACTCTGCGGTGATCCAGCCCTGGCCCTGACCTTTCAGGAAGCGCAGCACGCCTTCTTCAATAGAGGCGGTACACAACACTTTGGTATc                                                                                                        <  1:215526/151‑1 (MQ=255)                                           gCTTACCTTTCGCCGCTTCACGAGCGTTACGGGTGTGGGTAGAACGTGGCAGCATGCCGTACTCTGCGGTGATCCAGCCCTGGCCCTGACCTTTCAGGAAGCGCAGCACGCCTTCTTCAATAGAGGCGGTACACAACACTTTGGTATCGcc                                                                                                     >  1:270702/1‑151 (MQ=255)                                           gCTTACCTTTCGCCGCTTCACGAGCGTTACGGGTGTGGGTAGAACGTGGCAGCATGCCGTACTCTGCGGTGATCCAGCCCTGGCCCTGACCTTTCAGGAAGCGCAGCACGCCTTCTTCAATAGAGGCGGTACACAACACTTTGGTATCGcc                                                                                                     >  2:578264/1‑151 (MQ=255)                                              tACCTTTCGCCGCTTCACGAGCGTTACGGGTGTGGGTAGAACGTGGCAGCATGCCGTACTCTGCGGTGATCCAGCCCTGGCCCTGACCTTTCAGGAAGCGCAGCACGCCTTCTTCAATAGAGGCGGTACACAACACTTTGGTATCGCCaa                                                                                                   >  2:574603/1‑150 (MQ=255)                                                ccTTTCGCCGCTTCACGAGCGTTACGGGTGTGGGTAGAACGTGGCAGCATGCCGTACTCTGCGGTGATCCAGCCCTGGCCCTGACCTTTCAGGAAGCGCAGCACGCCTTCTTCAATAGAGGCGGTACACAACACTTTGGTATCGCCAAAtt                                                                                                <  1:116609/151‑1 (MQ=255)                                                ccTTTCGCCGCTTCACGAGCGTTACGGGTGTGGGTAGAACGTGGCAGCATGCCGTACTCTGCGGTGATCCAGCCCTGGCCCTGACCTTTCAGGAAGCGCAGCACGCCTTCTTCAATAGAGGCGGTACACAACACTTTGGTATCGCCAAAt                                                                                                 <  1:324074/150‑1 (MQ=255)                                                 cTTTCGCCGCTTCACGAGCGTTACGGGTGTGGGTAGAACGTGGCAGCATGCCGTACTCTGCGGTGATCCAGCCCTGGCCCTGACCTTTCAGGAAGCGCAGCACGCCTTCTTCAATAGAGGCGGTACACAACACTTTGGTATCGCCAAATTc                                                                                               >  1:372994/1‑151 (MQ=255)                                                   ttCGCCGCTTCACGAGCGTTACGGGTGTGGGTAGAACGTGGCAGCATGCCGTACTCTGCGGTGATCCAGCCCTGGCCCTGACCTTTCAGGAAGCGCAGCACGCCTTCTTCAATAGAGGCGGTACACAACTCTTTGGTATCGCCAAATTCg                                                                                              <  1:576383/150‑1 (MQ=255)                                                    tCGCCGCTTCACGAGCGTTACGGGTGTGGGTAGAACGTGGCAGCATGCCGTACTCTGCGGTGATCCAGCCCTGGCCCTGACCTTTCAGGAAGCGCAGCACGCCTTCTTCAATAGAGGCGGTACACAACACTTTGGTATCGCCAAATTCGa                                                                                             <  2:710786/150‑1 (MQ=255)                                                      gccgcTTCACGAGCGTTACGGGTGTGGGTAGAACGTGGCAGCATGCCGTACTCTGCGGTGATCCAGCCCTGGCCCTGACCTTTCATGAAGCGCAGCACGCCTTCTTCAATAGATGCGGTACACAACACTTTGGTATCGCCAAATTCGGCCa                                                                                          <  1:29914/151‑1 (MQ=255)                                                       ccgcTTCACGAGCGTTACGGGTGTGGGTAGAACGTGGCAGCATGCCGTACTCTGCGGTGATCCAGCCCTGGCCCTGACCTTTCAGGAAGCGCAGCACGCCTTCTTCAATAGAGGCGGTACACAACACTTTGGTATCGCCAAATTCGAcc                                                                                           >  1:238643/1‑149 (MQ=255)                                                          cTTCACGAGCGTTACGGGTGTGGGTAGAACGTGGCAGCATGCCGTACTCTGCGGTGATCCAGCCCTGGCCCTGACCTTTCAGGAAGCGCAGCACGCCTTCTTCAATAGAGGCGGTACACAACACTTTGGTATCGCCAAATTCGACCCGccc                                                                                      >  2:741949/1‑149 (MQ=255)                                                            tCACGAGCGTTACGGGTGTGGGTAGAACGTGGCAGCATGCCGTACTCTGCGGTGATCCAGCCCTGGCCCTGACCTTTCAGGAAGCGCAGCACGCCTTCTTCAATAGAGGCGGTACACAACACTTTGGTATCGCCAAATTCGACCAGCAc                                                                                      <  1:557032/149‑1 (MQ=255)                                                                 aGCGTTACGGGTGTGGGTAGAACGTGGCAGCATGCCGTACTCTGCGGTGATCCAGCCCTGGCCCTGACCTTTCAGGAAGCGCAGCACGCCTTCTTCAATAGAGGCGGTACACAACACTTTGGTATCGCCAAATTCGACCAGCACCGAGCCt                                                                               >  1:638591/1‑151 (MQ=255)                                                                   cGTTACGGGTGTGGGTAGAACGTGGCAGCATGCCGTACTCTGCGGTGATCCAGCCCTGGCCCTGACCTTTCAGGAAGCGCAGCACGCCTTCTTCAATAGAGGCGGTACACAACACTTTGGTATCGCCAAATTCGACCAGCACCGAGCCTTc                                                                             <  1:363938/151‑1 (MQ=255)                                                                      tACGGGTGTGGGTAGAACGTGGCAGCATGCCGTACTCTGCGGTGATCCAGCCCTGGCCCTGACCTTTCAGGAAGCGCAGCACGCCTTCTTCAATAGAGGCGGTACACAACACTTTGGTATCGCCAAATTCGACCAGCACCGAGCCTTCTg                                                                           <  1:327393/150‑1 (MQ=255)                                                                      tACGGGTGTGGGTAGAACGTGGCAGCATGCCGTACTCTGCGGTGATCCAGCCCTGGCCCTGACCTTTCAGGAAGCGCAGCACGCCTTCTTCAATAGAGGCGGTACACAACACTTTGGTATCGCCAAATTCGACCAGCACCGAGCCTTCTGc                                                                          >  2:477974/1‑151 (MQ=255)                                                                            tgtgGGTAGAACGTGGCAGCATGCCGTACTCTGCGGTGATCCAGCCCTGGCCCTGACCTTTCAGGAAGCGCAGCACGCCTTCTTCAATAGAGGCGGTACACAACACTTTGGTATCGCCAAATTCGACCAGCACCGAGCCTTCTGCATGttt                                                                    >  1:439402/1‑151 (MQ=255)                                                                             gtgGGTAGAACGTGGCAGCATGCCGTACTCTGCGGTGATCCAGCCCTGGCCCTGACCTTTCAGGAAGCGCAGCACGCCTTCTTCAATAGAGGCGGTACACAACACTTTGGTATCGCCAAATTCGACCAGCACCGAGCCTTCTGCATGtttt                                                                   <  2:344814/151‑1 (MQ=255)                                                                                         tGGCAGCATGCCGTGCTCTGCGGTGATCCAGCCCTGGCCCTGACCTTGCAGGAAGCGCATCACGCCTTCTTCAATAGAGGCGGTACACAACACTTTGGTATCGCCAAAGTCGACCAGCACCGAGCCTTCTGCAGGTTTTGTATAGTTACg                                                        <  1:432251/150‑1 (MQ=255)                                                                                          ggCAGCATGCCGTACTCTGCGGTGATCCAGCCCTGGCCCTGACCTTTCAGGAAGCGCAGCACGCCTTCTTCAATAGAGGCGGTACACAACACTTTGGTATCGCCAAATTCGACCAGCACCGAGCCTTCTGCATGTTTTGTATAGTTACg                                                        >  1:28867/1‑149 (MQ=255)                                                                                               caTGCCGTACTCTGCGGTGATCCAGCCCTGGCCCTGACCTTTCAGGAAGCGCAGCACGCCTTCTTCAATAGAGGCGGTACACAACACTTTGGTATCGCCAAATTCGACCAGCACCGAGCCTTCTGCATGTTTTGTATAGTTACGAGTCAgg                                                 >  1:5355/1‑151 (MQ=255)                                                                                                        ctctGCGGTGATCCAGCCCTGGCCCTGACCTTTCAGGAAGCGCAGCACGCCTTCTTCAATAGAGGCGGTACACAACACTTTGGTATCGCCAAATTCGACCAGCACCGAGCCTTCTGCATGTTTTGTATAGTTACGAGTCAGGGTAACgg                                          <  1:125482/149‑1 (MQ=255)                                                                                                         tctGCGGTGATCCAGCCCTGGCCCTGACCTTTCAGGAAGCGCAGCACGCCTTCTTCAATAGAGGCGGTACACAACACTTTGGTATCGCCAAATTCGACCAGCACCGAGCCTTCTGCATGTTTTGTATAGTTACGAGTCAGGGTAACGGGAc                                       >  1:320427/1‑151 (MQ=255)                                                                                                          ctGCGGTGATCCAGCCCTGGCCCTGACCTTTCAGGAAGCGCAGCACGCCTTCTTCAATAGAGGCGGTACACAACACTTTGGTATCGCCAAATTCGACCAGCACCGAGCCTTCTGCATGTTTTGTATAGTTACGAGTCAGGGTAACGGGAc                                       >  1:213081/1‑150 (MQ=255)                                                                                                                 gATCCAGCCCTGGCCCTGACCTTTCAGGAAGCGCAGCACGCCTTCTTCAATAGAGGCGGTACACAACACTTTGGTATCGCCAAATTCGACCAGCACCGAGCCTTCTGCATGTTTTGTATAGTTACGAGTCAGGGTAACGGGACGCACCTGa                               <  1:222813/151‑1 (MQ=255)                                                                                                                 gATCCAGCCCTGGCCCTGACCTTTCAGGAAGCGCAGCACGCCTTCTTCAATAGAGGCGGTACACAACACTTTGGTATCGCCAAATTCGACCAGCACCGAGCCTTCTGCATGTTTTGTATAGTTACGAGTCAGGGTAACGGGACGCACCTGa                               <  2:646934/151‑1 (MQ=255)                                                                                                                    ccAGCCCTGGCCCTGACCTTTCAGGAAGCGCAGCACGCCTTCTTCAATAGAGGCGGTACACAACACTTTGGTATCGCCAAATTCGACCAGCACCGAGCCTTCTGCATGTTTTGTATAGTTACGAGTCAGGGTAACGGGACGCACCTGatt                             <  2:283337/150‑1 (MQ=255)                                                                                                                     cAGCCCTGGCCCTGACCTTTCAGGAAGCGCAGCACGCCTTCTTCAATAGAGGCGGTACACAACACTTTGGTATCGCCAAATTCGACCAGCACCGAGCCTTCTGCATGTTTTGTATAGTTACGAGTCAGGGTAACGGGACGCACCTGattat                           >  1:36261/1‑151 (MQ=255)                                                                                                                      aGCCCTGGCCCTGACCTTTCAGGAAGCGCAGCACGCCTTCTTCAATAGAGGCGGTACACAACACTTTGGTATCGCCAAATTCGACCAGCACCGAGCCTTCTGCATGTTTTGTATAGTTACGAGTCAGGGTAACGGGACGCACCTGattatt                          >  1:18359/1‑151 (MQ=255)                                                                                                                            ggccctgACCTTTCAGGAAGCGCAGCACGCCTTCTTCAATAGAGGCGGTACACAACACTTTGGTATCGCCAAATTCGACCAGCACCGAGCCTTCTGCATGTTTTGTATAGTTACGAGTCAGGGTAACGGGACGCACCTGATTATTGCTACg                    <  1:672375/151‑1 (MQ=255)                                                                                                                                  gcccTTTCAGGAAGCGCAGCACGCCTTCTTCAATAGAGGCGGTACACAACACTTTGGGATTGCCCAATTCGACCAGCACCGAACCTGCTGCATGTTTTGTATAGTTGCGATGCAGGGGAACGGGACGCACCTGCTTATAGGGACGGCctg               >  2:316399/3‑150 (MQ=255)                                                                                                                                  gACCTTTCAGGAAGCGCAGCACGCCTTCTTCAATAGAGGCGGTACACAACACTTTGGTATCGCCAAATTCGACCAGCACCGAGCCTTCTGCATGTTTTGTATAGTTACGAGTCAGGGTAACGGGACGCACCTGATTATTGCTACGGCctgc              <  1:389546/151‑1 (MQ=255)                                                                                                                                     cTTTCAGGAAGCGCAGCACGCCTTCTTCAATAGAGGCGGTACACAACACTTTGGTATCGCCAAATTCGACCAGCACCGAGCCTTCTGCATGTTTTGTATAGTTACGAGTCAGGGTAACGGGACGCACCTGATTATTGCTACGGCCTGCTgg           >  2:607957/1‑151 (MQ=255)                                                                                                                                         cAGGAAGCGCAGCACGCCTTCTTCAATAGAGGCGGTACACAACACTTTGGTATCGCCAAATTCGACCAGCACCGAGCCTTCTGCATGTTTTGTATAGTTACGAGTCAGGGTAACGGGACGCACCTGATTATTGCTACGGCCTGCTGGACg        <  2:188380/150‑1 (MQ=255)                                                                                                                                          aGGAAGCGCAGCACGCCTTCTTCAATAGAGGCGGTACACAACACTTTGGTATCGCCAAATTCGACCAGCACCGAGCCTTCTGCATGTTTTGTATAGTTACGAGTCAGGGTAACGGGACGCACCTGATTATTGCTACGGCCTGCTGGACGCa      <  2:490947/151‑1 (MQ=255)                                                                                                                                           ggAAGCGCAGCACGCCTTCTTCAATAGAGGCGGTACACAACACTTTGGTATCGCCAAATTCGACCAGCACCGAGCCTTCTGCATGTTTTGTATAGTTACGAGTCAGGGTAACGGGACGCACCTGATTATTGCTACGGCCTGCTGGACGCat     >  1:292920/1‑151 (MQ=255)                                                                                                                                              aGCGCAGCACGCCTTCTTCAATAGAGGCGGTACACAACACTTTGGTATCGCCAAATTCGACCAGCACCGAGCCTTCTGCATGTTTTGTATAGTTACGAGTCAGGGTAACGGGACGCACCTGATTATTGCTACGGCCTGCTGGACGCATAtt  <  2:16025/151‑1 (MQ=255)                                                                                                                                                   |                                                                                                                                                  CACGGGCGATCAGACGCTGGATTTCCATTGTGCGTCCACCCTGCTTACCTTTCGCCGCTTCACGAGCGTTACGGGTGTGGGTAGAACGTGGCAGCATGCCGTACTCTGCGGTGATCCAGCCCTGGCCCTGACCTTTCAGGAAGCGCGGCACGCCTTCTTCAATAGAGGCGGTACACAACACTTTGGTATCGCCAAATTCGACCAGCACCGAGCCTTCTGCATGTTTTGTATAGTTACGAGTCAGGGTAACGGGACGCACCTGATTATTGCTACGGCCTGCTGGACGCATATT  >  NC_000913/3816261‑3816552

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑