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	96.7%	110.6 / ‑3.2	30	coding (671/687 nt)	rph	truncated RNase PH
Reads supporting (aligned to +/- strand):  ref base . (1/0);  new base C (11/18);  total (12/18)
Fisher's exact test for biased strand distribution p-value = 4.00e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATT‑CGATT‑CCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTC  >  NC_000913/3815743‑3816012                                                                                                                                           |                                                                                                                                      aTAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATT‑CGATT‑ccc                                                                                                                                    >  1:55913/1‑140 (MQ=255)    aaCTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATT‑CGATT‑ccccct                                                                                                                                 <  1:344767/140‑3 (MQ=255)     aCTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATT‑CGATT‑ccccctc                                                                                                                                <  1:109839/140‑4 (MQ=255)       tGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATT‑CGATT‑ccccctcgg                                                                                                                              >  1:84553/1‑135 (MQ=255)         gcgcTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATT‑CGATTCCCCCTCGGGc                                                                                                                             <  2:21061/140‑1 (MQ=255)         gcgcTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATT‑CGATTCCCCCTCGGGc                                                                                                                             <  2:645638/140‑1 (MQ=255)          cgcTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATT‑CGATTCCCCCTCGGGcc                                                                                                                            >  1:735348/1‑140 (MQ=255)                tatGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATT‑CGATTCCCCCTCGGGCCAGAGcc                                                                                                                      >  1:319202/1‑140 (MQ=255)                     tttCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCCAATC‑CCCCTCGGGCCAGAGCcaacaa                                                                                                                 >  1:716839/1‑140 (MQ=255)                      ttCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATT‑CGATTCCCCCTCGGGCCAGAGCCAACAAg                                                                                                                <  1:430988/140‑1 (MQ=255)                         aTGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATT‑CGATTCCCCCTCGGGCCAGAGCCAACAAGATg                                                                                                             >  1:393238/1‑140 (MQ=255)                              ttCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATT‑CGATTCCCCCTCGGGCCAGAGCCAACAAGATGAGTAg                                                                                                        <  1:313293/140‑1 (MQ=255)                              ttCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATT‑CGATTCCCCCTCGGGCCAGAGCCAACAAGATGAGTAg                                                                                                        <  1:27737/140‑1 (MQ=255)                              ttCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATT‑CGATTCCCCCTCGGGCCAGAGCCAACAAGATGAGTAg                                                                                                        <  1:855676/140‑1 (MQ=255)                                        aTCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATT‑CGATTCCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATgg                                                                                              <  2:454020/140‑1 (MQ=255)                                           ttACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATT‑CGATTCCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTg                                                                                           >  1:751637/1‑140 (MQ=255)                                                 ttCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATT‑CGATTCCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGc                                                                                     <  2:319202/140‑1 (MQ=255)                                                    tACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATT‑CGATTCCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTc                                                                                   <  2:796371/139‑1 (MQ=255)                                                    tACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATT‑CGATTCCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTc                                                                                   >  1:796371/1‑139 (MQ=255)                                                    tACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATT‑CGATTCCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCg                                                                                  >  2:159925/1‑140 (MQ=255)                                                         aCAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATT‑CGATTCCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTc                                                                             >  1:279051/1‑140 (MQ=255)                                                                  aGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATT‑CGATTCCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTccc                                                                    <  2:55913/140‑1 (MQ=255)                                                                  aGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATT‑CGATTCCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTccc                                                                    <  1:59123/140‑1 (MQ=255)                                                                       aCTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATT‑CGATTCCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCa                                                               <  2:751637/140‑1 (MQ=255)                                                                                  gCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATT‑CGATTCCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTc                                                           <  1:274697/133‑1 (MQ=255)                                                                                  gCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATT‑CGATTCCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTc                                                           >  2:274697/1‑133 (MQ=255)                                                                                     ttAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATT‑CGATTCCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTg                                                                 <  2:191789/124‑1 (MQ=255)                                                                                     ttAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATT‑CGATTCCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTg                                                                 >  1:191789/1‑124 (MQ=255)                                                                                     ttAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATT‑CGATTCCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATgcgc                                                 >  1:113852/1‑140 (MQ=255)                                                                                             cAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATT‑CGATTCCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTc                                         <  2:279051/140‑1 (MQ=255)                                                                                              aGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATT‑CGATTCCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCg                                        <  2:735348/140‑1 (MQ=255)                                                                                                             ccTTCTGCGTCGCTACAATGGATT‑CGATTCCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGtcatca                                 <  2:2046/132‑1 (MQ=255)                                                                                                             ccTTCTGCGTCGCTACAATGGATT‑CGATTCCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGtcatca                                 >  1:2046/1‑132 (MQ=255)                                                                                                                       cGCTACAATGGATT‑CGATTCCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGtct               <  2:84553/140‑1 (MQ=255)                                                                                                                                 gatt‑cgattcCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCaga     <  2:716839/140‑1 (MQ=255)                                                                                                                                 gatt‑cgattcCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCaga     >  2:168524/1‑140 (MQ=255)                                                                                                                                 gaat‑cgaat‑cCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGt                 <  2:181064/124‑1 (MQ=255)                                                                                                                                 gaat‑cgaat‑cCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGt                 >  1:181064/4‑127 (MQ=255)                                                                                                                                   tt‑cgattcCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGt                 >  2:721406/1‑126 (MQ=255)                                                                                                                                   tt‑cgattcCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGt                 <  1:721406/126‑1 (MQ=255)                                                                                                                                    t‑cgattcCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTc  >  1:814971/1‑140 (MQ=255)                                                                                                                                           |                                                                                                                                      ATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATT‑CGATT‑CCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTC  >  NC_000913/3815743‑3816012

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑