Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,815,908	Δ1 bp	pseudogene (642/669 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	3,815,908	0	T	.	100.0%	237.1 / NA	57	pseudogene (642/669 nt)	rph	ribonuclease PH (defective),enzyme, Degradation of RNA, RNase PH
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base . (29/28);  total (29/28)

CTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGC  >  NC_000913/3815784‑3816032                                                                                                                             |                                                                                                                             cTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAG‑AGCTCTTCATGGGTg                                                                                                               >  1:1182674/1‑139 (MQ=255)         tCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAG‑AGCTCTTCATGGGTGAACGGCTc                                                                                                       >  2:595132/1‑139 (MQ=255)         tCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAG‑AGCTCTTCATGGGTGAACGGCTc                                                                                                       >  2:368431/1‑139 (MQ=255)          cTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAG‑AGCTCTTCATGGGTGAACGGCTCg                                                                                                      >  2:31574/1‑139 (MQ=255)           tACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAG‑AGCTCTTCATGGGTGAACGGCTCGc                                                                                                     >  2:1594460/1‑139 (MQ=255)              aGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAG‑AGCTCTTCATGGGTGAACGGCTCGCCtt                                                                                                  <  2:1182674/139‑1 (MQ=255)                 cAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAG‑AGCTCTTCATGGGTGAACGGCTCGCCTTCTg                                                                                               <  1:1594460/139‑1 (MQ=255)                      aaaaGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAG‑AGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTc                                                                                          <  2:300516/139‑1 (MQ=255)                       aaaGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAG‑AGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTcc                                                                                         >  2:1633505/1‑139 (MQ=255)                          ggCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAG‑AGCTCtt                                                                                                                       >  2:1602167/1‑106 (MQ=255)                          ggCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAG‑AGCTCtt                                                                                                                       <  1:1602167/106‑1 (MQ=255)                           gCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAG‑AGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTg                                                                                     <  1:368431/139‑1 (MQ=255)                           gCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAG‑AGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTg                                                                                     <  1:595132/139‑1 (MQ=255)                              aCTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAG‑AGCTCTTCATGGGTg                                                                                                               >  1:780084/1‑110 (MQ=255)                              aCTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAG‑AGCTCTTCATGGGTg                                                                                                               <  2:780084/110‑1 (MQ=255)                                          ccTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAG‑AGCTCTTCATGGGTGAACGGCt                                                                                                        >  2:1002727/1‑105 (MQ=255)                                          ccTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAG‑AGCTCTTCATGGGTGAACGGCt                                                                                                        <  1:1002727/105‑1 (MQ=255)                                            ttAAAAATCAGTTTGTCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAG‑AGCTCTCCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGcc                                                                    >  1:1224607/1‑139 (MQ=255)                                             tAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAG‑AGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGccc                                                                   <  2:1224607/139‑1 (MQ=255)                                              aaaaaTCAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAG‑AGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCg                                                                  >  1:1566829/1‑139 (MQ=255)                                                    cAGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAG‑AGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCg                                                            <  1:1633505/139‑1 (MQ=255)                                                     aGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAG‑AGCTCTTCATGGGTGAACGGc                                                                                                         >  2:141211/1‑93 (MQ=255)                                                     aGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAG‑AGCTCTTCATGGGTGAACGGc                                                                                                         <  1:141211/93‑1 (MQ=255)                                                     aGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAG‑AGCTCTTCATGGGTGAACGGCTCGCCTTCTg                                                                                               <  2:1573697/103‑1 (MQ=255)                                                     aGTTTGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAG‑AGCTCTTCATGGGTGAACGGCTCGCCTTCTg                                                                                               >  1:1573697/1‑103 (MQ=255)                                                        ttGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAG‑AGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGtca                                                        <  2:1566829/139‑1 (MQ=255)                                                         tGCCAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAG‑AGCTCTTCATGGGGGAACGGCTCGCCTTCTGCCGGCCCCTGCACTTCAATGATGCGCCCGTCTTCGGtcat                                                       >  1:1294610/1‑139 (MQ=255)                                                           ccAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAG‑AGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGtcatca                                                     <  1:31574/139‑1 (MQ=255)                                                           ccAGCGCCGCCTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAG‑AGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGCCCCCTGCACTTCAATGATGCGCCCGTCTTCGGtcatca                                                     <  2:965257/139‑1 (MQ=255)                                                                 ccgccTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAG‑AGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGt                                               >  2:931719/1‑139 (MQ=255)                                                                 ccgccTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAG‑AGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGt                                               >  2:316265/1‑139 (MQ=255)                                                                    ccTTCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAG‑AGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCa                                            >  2:318686/1‑139 (MQ=255)                                                                      ttCTGCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAG‑AGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATg                                          <  2:1294610/139‑1 (MQ=255)                                                                          gCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAG‑AGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACt                                                   <  1:23566/126‑1 (MQ=255)                                                                          gCGTCGTTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAG‑AGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACt                                                   >  2:23566/1‑126 (MQ=255)                                                                             tcgttACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAG‑AGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGtct                                   <  1:318686/135‑1 (MQ=255)                                                                              cgttACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAG‑AGCTCTTCATGGGTGAACGGc                                                                                                         >  2:1183921/4‑68 (MQ=255)                                                                              cgttACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAG‑AGCTCTTCATGGGTGAACGGc                                                                                                         <  1:1183921/65‑1 (MQ=255)                                                                               gttACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAG‑AGCTCTTCATGGGTGAACGGCt                                                                                                        <  1:879396/66‑1 (MQ=255)                                                                               gttACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAG‑AGCTCTTCATGGGTGAACGGCt                                                                                                        >  2:879396/3‑68 (MQ=255)                                                                               gttACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAG‑AGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTctct                                 <  2:1477240/137‑1 (MQ=255)                                                                                ttACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAG‑AGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGt                                                          <  2:686698/112‑1 (MQ=255)                                                                                ttACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAG‑AGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGt                                                          >  1:686698/2‑113 (MQ=255)                                                                                        gattcgattcCCCTCGGGCCAGAGCCAACAAGATGAG‑AGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTcccc                                                                                       <  1:505217/76‑1 (MQ=255)                                                                                        gattcgattcCCCTCGGGCCAGAGCCAACAAGATGAG‑AGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTcccc                                                                                       >  2:505217/1‑76 (MQ=255)                                                                                          ttcgattcCCCTCGGGCCAGAGCCAACAAGATGAG‑AGCTCTTCa                                                                                                                     >  2:865156/1‑44 (MQ=255)                                                                                          ttcgattcCCCTCGGGCCAGAGCCAACAAGATGAG‑AGCTCTTCa                                                                                                                     <  1:865156/44‑1 (MQ=255)                                                                                          ttcgattcCCCTCGGGCCAGAGCCAACAAGATGAG‑AGCTCTTCATGGGTg                                                                                                               >  2:220149/1‑50 (MQ=255)                                                                                          ttcgattcCCCTCGGGCCAGAGCCAACAAGATGAG‑AGCTCTTCATGGGTg                                                                                                               <  1:220149/50‑1 (MQ=255)                                                                                          ttcgattcCCCTCGGGCCAGAGCCAACAAGATGAG‑AGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTc                      >  1:118040/1‑139 (MQ=255)                                                                                          ttcgattcCCCTCGGGCCAGAGCCAACAAGATGAG‑AGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTc                      >  1:983397/1‑139 (MQ=255)                                                                                            cgattcCCCTCGGGCCAGAGCCAACAAGATGAG‑AGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCtt                    <  2:983397/139‑1 (MQ=255)                                                                                                              agCCAACAAGATGAG‑AGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGc  >  1:1226718/1‑139 (MQ=255)                                                                                                                   acaaGATGAG‑AGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGtca                                                        >  2:1598755/1‑80 (MQ=255)                                                                                                                   acaaGATGAG‑AGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGtca                                                        <  1:1598755/80‑1 (MQ=255)                                                                                                                       gATGAG‑AGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAAc                <  2:1739873/116‑1 (MQ=255)                                                                                                                       gATGAG‑AGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAAc                >  1:1739873/1‑116 (MQ=255)                                                                                                                             |                                                                                                                             CTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGC  >  NC_000913/3815784‑3816032

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑