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	91.9%	118.9 / 3.5	38	coding (671/687 nt)	rph	truncated RNase PH
Reads supporting (aligned to +/- strand):  ref base . (2/1);  new base C (13/21);  total (16/22)
Fisher's exact test for biased strand distribution p-value = 5.54e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.27e-01

TGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATT‑CC‑CC‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGT  >  NC_000913/3815749‑3816011                                                                                                                                    |                                                                                                                                       tGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCCTCGGTACAATGGAATCGATT‑cc‑ccctcgg                                                                                                                              >  1:316276/1‑135 (MQ=255)   gcgcTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCC‑CC‑TCGGGc                                                                                                                            <  1:6880/140‑1 (MQ=255)    cgcTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCC‑CC‑TCGGGcc                                                                                                                           >  2:820935/1‑140 (MQ=255)    cgcTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCC‑CC‑TCGGGcc                                                                                                                           >  2:629234/1‑140 (MQ=255)     gcTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCC‑CC‑TCGGGCCa                                                                                                                          <  2:53216/140‑1 (MQ=255)        gATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCC‑CC‑TCGGGCCagag                                                                                                                       <  1:174660/140‑1 (MQ=255)         atatGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCC‑CC‑TCGGGCCag                                                                                                                         <  1:213641/137‑1 (MQ=255)         atatGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTACC‑CC‑TCGGGCCag                                                                                                                         >  2:213641/1‑137 (MQ=255)          tatGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCC‑CC‑TCGGGCCAGAGcc                                                                                                                     <  2:90253/140‑1 (MQ=255)             ggTTTCATGCCTTCGCTCCTCAACTTACTTTCCTACAGACAAAAAAAACGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCC‑CC‑TCGGGCCAGAGCcaac                                                                                                                  <  2:225693/140‑1 (MQ=255)                ttCATGCCTTCGCTCCTCATCTTACCTTTCTACAGACTAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCC‑CC‑TCGGGCCAGAGCCAACAAg                                                                                                               <  1:243557/140‑1 (MQ=255)                 tCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCC‑CC‑TCGGGCCAGAGCca                                                                                                                    >  2:191866/1‑134 (MQ=255)                 tCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCC‑CC‑TCGGGCCAGAGCca                                                                                                                    <  1:191866/134‑1 (MQ=255)                   aTGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCC‑CC‑TCGGGCCAGAGCcaac                                                                                                                  <  2:85944/134‑1 (MQ=255)                   aTGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCC‑CC‑TCGGGCCAGAGCcaac                                                                                                                  >  1:85944/1‑134 (MQ=255)                    tGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCC‑CC‑TCGGGCCAGAGCCAACAAGATGa                                                                                                           >  1:748125/1‑140 (MQ=255)                        ttCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCC‑CC‑TCGGGCCAGAGCCAACAAGATGAGTAg                                                                                                       <  1:820935/140‑1 (MQ=255)                                           ttCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATT‑CCACC‑TCGGGCAAGAGCCAAGAAGATGAGTAGCTATTCATGGGTGAACGGc                                                                                    >  2:407076/1‑140 (MQ=255)                                              tACAGACAAAAAAAAGTCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCC‑CC‑TCGGGCCAAAGCCCACAAGATGAGTATCTCTTCATGGGTGAACGGCTCg                                                                                 >  2:382394/1‑140 (MQ=255)                                                               cGACTCATCAGTCGCTCCAAAAATCAGTTTTTCTGTGCCTCCTTCTGCTTCGCTACAATGGATTCGATTCCC‑CC‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTg                                                                <  2:398769/140‑1 (MQ=255)                                                               cGACTCATCAGTCGCCTTAAAATTCTGTTCGCCAGCGACGCCTTCTGCGTCGCTACAATGGATTCGATTCCC‑CC‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTg                                                                <  1:246376/140‑1 (MQ=255)                                                               cGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCC‑CC‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTc                                                                     <  1:752716/135‑1 (MQ=255)                                                               cGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCC‑CC‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTc                                                                     >  2:752716/1‑135 (MQ=255)                                                               cGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCC‑CC‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTg                                                                <  1:860777/140‑1 (MQ=255)                                                                 aCTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCC‑CC‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCa                                                              <  2:748125/140‑1 (MQ=255)                                                                            gCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCC‑CC‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAatgatg                                                   >  2:179931/1‑140 (MQ=255)                                                                            gCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCC‑CC‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAatgatg                                                   >  1:824494/1‑140 (MQ=255)                                                                              cTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCC‑CC‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCa                                                              <  2:76029/127‑1 (MQ=255)                                                                              cTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCC‑CC‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCa                                                              >  1:76029/1‑127 (MQ=255)                                                                               ttAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCC‑CC‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATgcgc                                                >  1:40478/1‑140 (MQ=255)                                                                                     aTCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCC‑CC‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCt                                          <  2:40478/140‑1 (MQ=255)                                                                                     aTCAGTTTGCCAGCGACGCCTTATGTGTCGCTACAATTGATTCGATTCCC‑CC‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTACTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCt                                          <  1:407076/140‑1 (MQ=255)                                                                                        aGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCC‑CC‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCg                                       >  2:197531/1‑140 (MQ=255)                                                                                          tttGCCAGCGCCGCCTTCTGCGGCGCTACAAAGGAGTCGTTTCCC‑CC‑TTGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGt                                     <  2:348074/140‑1 (MQ=255)                                                                                             gCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCC‑CC‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGtcat                                  <  2:824494/140‑1 (MQ=255)                                                                                                             gCGTCGCTACAATGGATTCGATTCCC‑CC‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCg                  <  1:179931/140‑1 (MQ=255)                                                                                                              cGTCGCTACAATGGATTCGATT‑CC‑CCTTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCTTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACt                              <  2:715011/127‑1 (MQ=255)                                                                                                              cGTCGCTACAATGGATTCGATT‑CC‑CCTTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACt                              >  1:715011/1‑127 (MQ=255)                                                                                                                 cGCTACAATGGATTCGATTCCC‑CC‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGtct              <  2:686777/140‑1 (MQ=255)                                                                                                                        aTGGATTCGATTCCC‑CC‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGc       >  1:840505/1‑140 (MQ=255)                                                                                                                        aTGGATTCGATTCCC‑CC‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGc       >  1:777475/1‑140 (MQ=255)                                                                                                                         tGGATTCGATTCCC‑CC‑TCGGGCCAGAGCCAACATGTTGAATAGCTCTTTATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCa      <  2:372850/140‑1 (MQ=255)                                                                                                                           gattcgattcCC‑CC‑TCGGGCCACAGCCAACAAGATGAGTAGCTCTTCACGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCaga    <  2:316276/140‑1 (MQ=255)                                                                                                                             ttcgattcCC‑CC‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGt  >  1:784164/1‑140 (MQ=255)                                                                                                                                    |                                                                                                                                       TGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATT‑CC‑CC‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGT  >  NC_000913/3815749‑3816011

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑