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	94.7%	59.9 / ‑2.8	19	coding (671/687 nt)	rph	truncated RNase PH
Reads supporting (aligned to +/- strand):  ref base . (1/0);  new base C (7/11);  total (8/11)
Fisher's exact test for biased strand distribution p-value = 4.21e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.77e-01

ACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATT‑CC‑CCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCG  >  NC_000913/3815747‑3815995                                                                                                                                      |                                                                                                                      aCTGGCGCGGATATGCTTCCATCCCTTCGCCCCTCATCTTACTTTTCTACAGAC‑AAAAAAAGGCGACTCATCAGTCGTCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGgattcgatt‑c                                                                                                                      <  1:138272/133‑1 (MQ=255)      cgcTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGAC‑AAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATT‑cc‑ccct                                                                                                                <  2:25133/133‑3 (MQ=255)           atatGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGAC‑AAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCC‑CCTCGGGc                                                                                                            >  1:24491/1‑133 (MQ=255)              tGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGAC‑AAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCC‑CCTCGGGCCag                                                                                                         <  1:43303/133‑1 (MQ=255)                     aTGCCTTCGCTCCTCATCTTACTTTTCTACAGAC‑AAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCC‑CCTCGGGCCAGAGCcaac                                                                                                  <  2:448363/133‑1 (MQ=255)                           tCGCTCCTCATCTTATTTTTCTACGGAC‑AAAACAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCC‑CCTCGGGCCAGAGCCAACAAGATg                                                                                            <  2:149882/133‑1 (MQ=255)                                cctcATCTTACTTTTCTACAGAC‑AAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCC‑CCTCGGGCCAGAGCCAACAAGATGAGTAg                                                                                       <  2:50668/133‑1 (MQ=255)                                cctcATCTTACTTTTCTACAGAC‑AAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCC‑CCTCGGGCCAGAGCCAACAAGATGAGTAg                                                                                       <  2:368242/133‑1 (MQ=255)                                 ctcATCTTACTTTTCTACAGAC‑AAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATT‑CCGCCTCGGGGCAGCGCGAACAAGGTGAGTAGc                                                                                      >  1:149882/1‑133 (MQ=255)                                                      acaaaaaaaGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCC‑CCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTc                                                                  >  2:64406/3‑133 (MQ=255)                                                              aGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCC‑CCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTg                                                          <  1:64406/133‑1 (MQ=255)                                                                             cGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCC‑CCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACtt                                           <  2:384151/133‑1 (MQ=255)                                                                              gCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCC‑CCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTc                                          >  2:82100/1‑133 (MQ=255)                                                                              gCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCC‑CCTCGGGCCAGAGCCAACAAGATGAGTAGCTCATCATGGGTCAACGGCTGGCCTTCTGACGTCCCCTGCACTTc                                          >  2:167179/1‑133 (MQ=255)                                                                               ccTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCC‑CCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGTCTCTCCTTCTGCGGTCCACTGCACTTCa                                         >  2:214816/1‑133 (MQ=255)                                                                                          aGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCC‑CCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGcc                               >  1:74735/1‑132 (MQ=255)                                                                                          aGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCC‑CCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGcc                               <  2:74735/132‑1 (MQ=255)                                                                                          aGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCC‑CCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTCCATTTCAATGATGCGccc                              >  1:184464/1‑133 (MQ=255)                                                                                                    cgccgcCTTCTGCGTCGCCACATTGGATTCGATTCCC‑CCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGtc                    <  1:167179/133‑1 (MQ=255)                                                                                                                   cGCTACAATGGATTCGATTCCC‑CCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATg     <  2:24491/133‑1 (MQ=255)                                                                                                                      tACAATGGATTCGATTCCC‑CCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCg  <  1:271842/133‑1 (MQ=255)                                                                                                                                      |                                                                                                                      ACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATT‑CC‑CCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCG  >  NC_000913/3815747‑3815995

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑