Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,815,844	A→G	pseudogene (38/48 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	3,815,844	0	A	G	100.0%	239.3 / NA	66	pseudogene (38/48 nt)	rph	ribonuclease PH (defective),enzyme, Degradation of RNA, RNase PH
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (33/33);  total (33/33)

ACACCTGCTTGCTAAGCGCAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAA‑AGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGG  >  NC_000913/3815717‑3815975                                                                                                                                 |                                                                                                                                    acacCTGCTTGCTAAGCGCAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAA‑AGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTc                                                                                                                          <  1:206796/139‑1 (MQ=255)       gcttgctAAGCGCAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAA‑AGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTCTg                                                                                                                        <  2:669902/135‑1 (MQ=255)       gcttgctAAGCGCAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAA‑AGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTCTg                                                                                                                        >  1:669902/1‑135 (MQ=255)                                  ggCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAA‑AGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCggg                                                                                         <  2:875257/139‑1 (MQ=255)                                           atGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAA‑AGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCca                                                                                <  1:26503/139‑1 (MQ=255)                                           atGGTTTCATGCCTTCGCCCCTCATCTTACTTTTCTACAGACAAAAAAA‑AGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCca                                                                                <  2:1207939/139‑1 (MQ=255)                                                   aTGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAA‑AGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTCTGCGTCGTTACAAt                                                                                                            >  2:836322/1‑103 (MQ=255)                                                   aTGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAA‑AGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTCTGCGTCGTTACAAt                                                                                                            <  1:836322/103‑1 (MQ=255)                                                     gCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAA‑AGGCGACTCACCAGTCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATGCCCCTCGGGCAAGAGCCAACAAGATGAg                                                                      <  1:1057397/139‑1 (MQ=255)                                                                tcATCTTACTTTTCTACAGACAAAAAAA‑AGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCGGcgcc                                                                                                                                >  2:605259/1‑70 (MQ=255)                                                                tcATCTTACTTTTCTACAGACAAAAAAA‑AGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCGGcgcc                                                                                                                                <  1:605259/70‑1 (MQ=255)                                                                tcATCTTACTTTTCTACAGACAAAAAAA‑AGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTCTGCGt                                                                                                                     <  1:1363019/81‑1 (MQ=255)                                                                tcATCTTACTTTTCTACAGACAAAAAAA‑AGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTCTGCGt                                                                                                                     >  2:1363019/1‑81 (MQ=255)                                                                       aCTTTTCTACAGACAAAAAAA‑AGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCGGcgcc                                                                                                                                >  2:1290404/1‑63 (MQ=255)                                                                       aCTTTTCTACAGACAAAAAAA‑AGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCGGcgcc                                                                                                                                <  1:1290404/63‑1 (MQ=255)                                                                       aCTTTTCTACAGACAAAAAAA‑AGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGaa                                                    >  2:1417654/1‑139 (MQ=255)                                                                         ttttCTACAGACAAAAAAATAGGCGCCTCATCGGTCGCCTTAAAATTCAGTTTGCCGGCGCCGCCTTTTGCGTCGTTACAATGATTTCGATTCCCCTCGGGCCAGGCCCAACAAGATGAGTAGCTCTTCATGGGTGAAc                                                   >  2:1197715/1‑139 (MQ=255)                                                                         ttttCTACAGACAAAAAAA‑AGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGc                                                                                        <  1:1363885/101‑1 (MQ=255)                                                                         ttttCTACAGACAAAAAAA‑AGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGc                                                                                        >  2:1363885/1‑101 (MQ=255)                                                                           ttCTACAGACAAAAAAA‑AGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTCTg                                                                                                                        <  2:951395/67‑1 (MQ=255)                                                                           ttCTACAGACAAAAAAA‑AGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTCTg                                                                                                                        >  1:951395/1‑67 (MQ=255)                                                                              tACAGACAAAAAAA‑AGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTCTGCGt                                                                                                                     <  1:1074199/67‑1 (MQ=255)                                                                              tACAGACAAAAAAA‑AGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTCTGCGt                                                                                                                     >  2:1074199/1‑67 (MQ=255)                                                                              tACAGACAAAAAAA‑AGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCg                                             >  2:1352970/1‑139 (MQ=255)                                                                                cAGACAAAAAAA‑AGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGc                                                                                        <  2:310864/94‑1 (MQ=255)                                                                                cAGACAAAAAAA‑AGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGc                                                                                        >  1:310864/1‑94 (MQ=255)                                                                                   aCAAAAAAA‑AGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTCTg                                                                                                                        >  1:1227031/1‑59 (MQ=255)                                                                                   aCAAAAAAA‑AGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTCTg                                                                                                                        <  2:1227031/59‑1 (MQ=255)                                                                                   aCAAAAAAA‑AGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTCTGCg                                                                                                                      >  1:293659/1‑61 (MQ=255)                                                                                   aCAAAAAAA‑AGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTCTGCg                                                                                                                      <  2:293659/61‑1 (MQ=255)                                                                                     aaaaaaa‑aGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAg                                                                   >  1:1231125/1‑110 (MQ=255)                                                                                     aaaaaaa‑aGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAg                                                                   <  2:1231125/110‑1 (MQ=255)                                                                                     aaaaaaa‑aGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTg                                      >  2:1364527/1‑139 (MQ=255)                                                                                          aa‑aGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTc                                 <  1:1352970/139‑1 (MQ=255)                                                                                              ggCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTCTg                                                                                                                        <  1:679416/49‑1 (MQ=255)                                                                                              ggCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTCTg                                                                                                                        >  2:679416/1‑49 (MQ=255)                                                                                              ggCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCcaac                                                                              >  2:176806/1‑91 (MQ=255)                                                                                              ggCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCcaac                                                                              <  1:176806/91‑1 (MQ=255)                                                                                              ggCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTcccc                              >  2:145362/1‑139 (MQ=255)                                                                                              ggCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTcccc                              <  2:1729/139‑1 (MQ=255)                                                                                                cGACTCATCAGTCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTc                                                                                                                          >  2:1003398/1‑45 (MQ=255)                                                                                                cGACTCATCAGTCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTc                                                                                                                          <  1:1003398/45‑1 (MQ=255)                                                                                                cGACTCATCAGTCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCt                                                                                             >  2:697776/1‑74 (MQ=255)                                                                                                cGACTCATCAGTCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCt                                                                                             <  1:697776/74‑1 (MQ=255)                                                                                                cGACTCATCAGTCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTg                            <  1:411206/139‑1 (MQ=255)                                                                                                  aCTCATCAGTCGCCTTAAAAATCAGTTTGCCGgcgc                                                                                                                                 <  1:1646064/36‑1 (MQ=255)                                                                                                  aCTCATCAGTCGCCTTAAAAATCAGTTTGCCGgcgc                                                                                                                                 >  2:1646064/1‑36 (MQ=255)                                                                                                      atcaGTCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTc                      >  1:859344/1‑139 (MQ=255)                                                                                                         aGTCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCt                                                                                             >  2:416962/1‑65 (MQ=255)                                                                                                         aGTCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCt                                                                                             <  1:416962/65‑1 (MQ=255)                                                                                                          gTCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAatg                  >  2:1394652/1‑139 (MQ=255)                                                                                                           tCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTCTGCGt                                                                                                                     >  2:1451713/1‑39 (MQ=255)                                                                                                           tCGCCTTAAAAATCAGTTTGCCGGCGCCGCCTTCTGCGt                                                                                                                     <  1:1451713/39‑1 (MQ=255)                                                                                                             gCCTTAAAAATCAGTTTGCCGGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAatgatg               >  1:25435/1‑139 (MQ=255)                                                                                                              ccTTAAAAATCAGTTTGCCGGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTg                            >  1:233095/1‑125 (MQ=255)                                                                                                              ccTTAAAAATCAGTTTGCCGGCGCCGCCTTCTGCGTCGTTACAATGGATGCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTg                            <  2:233095/125‑1 (MQ=255)                                                                                                                  aaaaaTCAGTTTGCCGGCGCCGCCTTCTGCGTCGTTACAATGgattcgatt                                                                                                  >  2:1291045/1‑51 (MQ=255)                                                                                                                  aaaaaTCAGTTTGCCGGCGCCGCCTTCTGCGTCGTTACAATGgattcgatt                                                                                                  <  1:1291045/51‑1 (MQ=255)                                                                                                                      aTCAGTTTGCCGGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCt      <  2:859344/139‑1 (MQ=255)                                                                                                                         aGTTTGCCGGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCg   >  2:1529858/1‑139 (MQ=255)                                                                                                                         aGTTTGCCGGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCg   >  2:390646/1‑139 (MQ=255)                                                                                                                          gTTTGCCGGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCgg  <  2:1742390/139‑1 (MQ=255)                                                                                                                           tttGCCGGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCag                                                                                     <  2:1312089/55‑1 (MQ=255)                                                                                                                           tttGCCGGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCag                                                                                     >  1:1312089/1‑55 (MQ=255)                                                                                                                             tGCCGGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGGGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCt                             >  2:817798/1‑109 (MQ=255)                                                                                                                             tGCCGGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGGGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCt                             <  1:817798/109‑1 (MQ=255)                                                                                                                                 |                                                                                                                                    ACACCTGCTTGCTAAGCGCAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAA‑AGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGG  >  NC_000913/3815717‑3815975

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑