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	97.3%	139.2 / ‑3.3	37	coding (671/687 nt)	rph	truncated RNase PH
Reads supporting (aligned to +/- strand):  ref base . (0/1);  new base C (18/18);  total (18/19)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.98e-01

AACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATT‑CCC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGA  >  NC_000913/3815746‑3816009                                                                                                                                        |                                                                                                                                     aaCTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATT‑ccc‑cct                                                                                                                               <  1:249962/140‑3 (MQ=255) aaCTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATT‑ccc‑cct                                                                                                                               <  1:435708/140‑3 (MQ=255)  accggCCCTGATATGGTTTCATGCCTTCGCTCCCCATCTTTCTTTTCCACCGACAAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATT‑ccc‑cct                                                                                                                               <  1:491251/137‑3 (MQ=255)       cgcTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCC‑C‑TCGGGcc                                                                                                                         >  1:452933/1‑140 (MQ=255)         cTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCC‑C‑TCGGGCCag                                                                                                                       >  1:236461/1‑140 (MQ=255)         cTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATT‑CCCGC‑TCGGGCCag                                                                                                                       <  1:196371/140‑1 (MQ=255)            atatGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCC‑C‑TCGGGCCAGAGc                                                                                                                    >  1:745550/1‑140 (MQ=255)              atGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAAGGGGCCTCTTCAGCCGCCTTAAAAATCAGTTTCCCAGCCCGGCCTTCTGCGTCCCTACATGGGTTTCAATT‑CCC‑CTTCGGGCAAGGGcc                                                                                                                   >  2:491251/1‑140 (MQ=255)                  tttCATGCCTTCGCTCCTCATCTTACTTTTCTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCC‑C‑TCGGGCCAGAGCcaacaa                                                                                                              >  1:478313/1‑140 (MQ=255)                   ttCATGCCTTCGCTCCTCATCTTACTTTTCTACAGTC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCC‑C‑TCGGGCCAGAGCCAACAAg                                                                                                             <  2:745550/140‑1 (MQ=255)                     cATGCCTTCGCTCCTCATCTTACTTTTCTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCC‑C‑TCGGGCCAGAGCCAACAAGAt                                                                                                           >  1:544336/1‑140 (MQ=255)                      aTGCCTTCGCTCCTCATCTTACTTTTCTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCC‑C‑TCGGGCCAGAGCCAACAAGATg                                                                                                          >  1:767908/1‑140 (MQ=255)                           ttCGCTCCTCATCTTACTTTTCTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAg                                                                                                     <  1:84823/140‑1 (MQ=255)                           ttCGCTCCTCATCTTACTTTTCTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAg                                                                                                     <  2:512876/140‑1 (MQ=255)                            tCGCTCCTCATCTTACTTTTCTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGc                                                                                                    >  1:821023/1‑140 (MQ=255)                                       cTTACTTTTCTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGt                                                                                         >  1:305106/1‑140 (MQ=255)                                        ttACTTTTCTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTg                                                                                        <  2:821023/140‑1 (MQ=255)                                          aCTTTTCTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGaa                                                                                      <  2:478313/140‑1 (MQ=255)                                          aCTTTTCTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGaa                                                                                      >  2:632802/1‑140 (MQ=255)                                          aCTTTTCTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGaa                                                                                      >  2:135716/1‑140 (MQ=255)                                          aCTTTTCTACAGAC‑‑AAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAAc                                                                                     >  2:726553/1‑140 (MQ=255)                                                     gAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCtt                                                                           <  2:277384/140‑1 (MQ=255)                                                                   cGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTg                                                              <  1:632802/140‑1 (MQ=255)                                                                   cGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTg                                                              <  2:570012/140‑1 (MQ=255)                                                                   cGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCACTACAATGGATTCGATTCCCC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTg                                                              >  2:566127/1‑140 (MQ=255)                                                                                gCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTg                                                              >  1:22781/1‑127 (MQ=255)                                                                                gCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTg                                                              <  2:22781/127‑1 (MQ=255)                                                                                gCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAatgatg                                                 <  2:305106/140‑1 (MQ=255)                                                                                 ccTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATgc                                                >  2:407755/1‑140 (MQ=255)                                                                                  cTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATgcg                                               <  2:236461/140‑1 (MQ=255)                                                                                    tAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGcc                                             >  1:455536/1‑140 (MQ=255)                                                                                     aaaaaTCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGccc                                            <  2:767908/140‑1 (MQ=255)                                                                                     aaaaaTCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGccc                                            <  1:404904/140‑1 (MQ=255)                                                                                     aaaaaTCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGccc                                            >  1:812160/1‑140 (MQ=255)                                                                                     aaaaaTCAGTTTGCCAGCGCCGCCTTCTGCGTCACTACAATGGATTCGATTCCCC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGccc                                            <  1:566127/140‑1 (MQ=255)                                                                                         aTCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCt                                        <  2:319070/140‑1 (MQ=255)                                                                                              tttGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGt                                   <  2:712779/140‑1 (MQ=255)                                                                                               ttGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCggac                                  <  2:452933/140‑3 (MQ=255)                                                                                                tGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGtca                                 <  2:274762/140‑1 (MQ=255)                                                                                                                   gTCGCTACAATGGATTCGATTCCCC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGt              >  1:657893/1‑140 (MQ=255)                                                                                                                            aTGGATTCGATTCCCC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGc     >  2:599127/1‑140 (MQ=255)                                                                                                                               gattcgattcCCC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCaga  >  1:523557/1‑140 (MQ=255)                                                                                                                                        |                                                                                                                                     AACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGAC‑AAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATT‑CCC‑C‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGA  >  NC_000913/3815746‑3816009

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: ‑