Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,815,883	+C	coding (667/687 nt)	rph ←	truncated RNase PH

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,815,879	1	.	C	100.0%	154.1 / NA	42	E224G (GAA→GGA)	rph	truncated RNase PH
Reads supporting (aligned to +/- strand):  ref base . (0/0);  new base C (20/22);  total (20/22)

CAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATT‑CCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTC  >  NC_000913/3815741‑3816012                                                                                                                                            |                                                                                                                                      cAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGgattcgatt‑c                                                                                                                                      <  2:286808/140‑1 (MQ=255) cAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGgattcgatt‑c                                                                                                                                      <  2:767726/140‑1 (MQ=255) cAATAAACTGGCGCTGATATGATTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGgattcgatt‑c                                                                                                                                      <  1:863830/140‑1 (MQ=255)       aCTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATT‑ccccctc                                                                                                                                <  2:447470/140‑4 (MQ=255)         tGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATT‑ccccctcgg                                                                                                                              >  2:227044/1‑135 (MQ=255)          ggCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCCTCggg                                                                                                                              >  2:428906/1‑140 (MQ=255)                gATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCCTCGGGCCagag                                                                                                                        <  2:477046/140‑1 (MQ=255)                   atGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCCTCGGGCCAGAGCca                                                                                                                     <  1:341254/140‑1 (MQ=255)                     ggTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCCTCGGGCCAGAGCcaac                                                                                                                   >  2:567614/1‑140 (MQ=255)                           aTGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCCTCGGGCCAGAGCCAACAAGATg                                                                                                             >  2:605105/1‑140 (MQ=255)                           aTGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCCTCGGGCCAGAGCCAACAAGATg                                                                                                             >  1:251323/1‑140 (MQ=255)                                 tCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCCTCGGGCCAGAGCCAACAAGATGAGTAGc                                                                                                       >  2:569489/1‑140 (MQ=255)                                  cGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCCTCGGGCCAGAGCCAACAAGATGAGTAGct                                                                                                      >  2:707718/1‑140 (MQ=255)                                       ctcATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCa                                                                                                 >  2:178015/1‑140 (MQ=255)                                         cATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATg                                                                                               >  1:161786/1‑140 (MQ=255)                                               aCTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGaa                                                                                         >  2:690154/1‑140 (MQ=255)                                                    tCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCt                                                                                    <  1:567614/140‑1 (MQ=255)                                                    tCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCt                                                                                    >  1:869027/1‑140 (MQ=255)                                                        cAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGcc                                                                                <  2:865196/140‑1 (MQ=255)                                                        cAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGcc                                                                                <  2:253452/140‑1 (MQ=255)                                                             aaaaaaaaGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTg                                                                           >  1:217431/1‑140 (MQ=255)                                                               aaaaaaGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGcc                                                                         <  2:467205/140‑1 (MQ=255)                                                                  aaaGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTc                                                                      <  2:880085/140‑1 (MQ=255)                                                                  aaaGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTc                                                                      <  1:605105/140‑1 (MQ=255)                                                                    aGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTccc                                                                    <  2:4499/140‑1 (MQ=255)                                                                    aGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGAATTCGATTCCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTccc                                                                    <  1:88202/140‑1 (MQ=255)                                                                       cGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTg                                                                 >  1:565193/1‑140 (MQ=255)                                                                       cGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTg                                                                 <  1:707718/140‑1 (MQ=255)                                                                          cTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCAc                                                              >  2:306554/1‑140 (MQ=255)                                                                          cTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGACTTCTGCCGTCCCCTGCAc                                                              >  1:502738/1‑140 (MQ=255)                                                                                    gCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAatgatg                                                    <  2:565193/140‑1 (MQ=255)                                                                                       ttAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATgcgc                                                 >  1:934451/1‑140 (MQ=255)                                                                                       ttAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATgcgc                                                 >  2:889845/1‑140 (MQ=255)                                                                                       ttAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATgcgc                                                 <  1:227044/140‑1 (MQ=255)                                                                                             aTCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCt                                           <  1:305490/140‑1 (MQ=255)                                                                                                aGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCg                                        >  2:52153/1‑140 (MQ=255)                                                                                                    tGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGtca                                    <  1:52153/140‑1 (MQ=255)                                                                                                        aGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCAc                                <  1:690154/140‑1 (MQ=255)                                                                                                         gcgcCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACt                               <  2:161786/140‑1 (MQ=255)                                                                                                          cgccgcCTTCTGCGTCGCTACAATGGATTCGATTCCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTa                              >  1:266545/1‑140 (MQ=255)                                                                                                                  tCTGCGTCGCTACAATGGATTCGATTCCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATg                      <  1:178015/140‑1 (MQ=255)                                                                                                                    tGCGTCGCTACAATGGATTCGATTCCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCATCTTCGGTCATCACTACGTTCATGTc                    >  1:22781/1‑140 (MQ=255)                                                                                                                       gTCGCTACAATGGATTCGATTCCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGt                 <  2:217431/140‑1 (MQ=255)                                                                                                                       gTCGCTACAATGGATTCGATTCCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGt                 <  2:934451/140‑1 (MQ=255)                                                                                                                           cTACAATGGATTCGATTCCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTctct             >  2:165169/1‑140 (MQ=255)                                                                                                                                 tGGATTCGATTCCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGAGGCa       <  2:869027/140‑1 (MQ=255)                                                                                                                                 tGGATTCGATTCCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGACTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCa       <  2:502738/140‑1 (MQ=255)                                                                                                                                   gattcgattcCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCaga     >  1:659662/1‑140 (MQ=255)                                                                                                                                   gattcgattcCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCaga     >  1:652222/1‑140 (MQ=255)                                                                                                                                      tcgattcCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTc  >  1:783922/1‑140 (MQ=255)                                                                                                                                            |                                                                                                                                      CAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATT‑CCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTC  >  NC_000913/3815741‑3816012

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑