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	3,815,883	1	.	C	92.9%	29.9 / ‑2.7	14	coding (667/687 nt)	rph	truncated RNase PH
Reads supporting (aligned to +/- strand):  ref base . (1/0);  new base C (4/9);  total (5/9)
Fisher's exact test for biased strand distribution p-value = 3.57e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.73e-01

GGATTTCAGCGTAAACTCGCCAAACTTTAACACCTGCTTGCTAAGCGCAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCC‑CC‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCTTCGCCGTTCACAATTCCGACAGAAACTGCGGCTACCATCCCTTTCATCGGATTGGTTTTCAGCTTGC  >  NC_000913/3815688‑3816107                                                                                                                                                                                                      |                                                                                                                                                                                                                                 ggATTTCAGCGTAAACTCGCCAAACTTTAACACCTGCTTGCTAAGCGCAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCC‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTc                                                                                                                                                                            <  1:265440/251‑1 (MQ=255)                             aaCACCTGCTTGCTAAGCGCAAACTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCCTCGCTACAATGGATTCGATTCC‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATgcg                                                                                                                                                 <  1:548/250‑1 (MQ=255)                                                   aTTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCC‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGt                                                                                                                          <  1:354054/251‑1 (MQ=255)                                                      cAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCC‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCGCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCCCTTCAATGATGCGCCCGTCTTCGGTCATCACTACGttaa                                                                                                                       <  1:459036/251‑3 (MQ=255)                                                                                  gCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAACAGGCGACACATCCATCGCCCTCAAAATACGTTTGAAAGACCCGACCTGTGCGTAGCTACCATGGAATTGATTCC‑CCCTCGGGCCCCAGCCCACAAGATGAGAAGCCCTTCATGGGGGAAGGGCCCGCCTTCTGCCGTCCCCTGCCCCTCCATGATGCGCCCGCCTTCgg                                                                                                                                      >  1:261396/1‑208 (MQ=255)                                                                                                          cTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTcc‑ccctcgg                                                                                                                                                                                                                              <  1:41373/96‑6 (MQ=255)                                                                                                          cTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCNNCC‑TCgg                                                                                                                                                                                                                              >  2:41373/1‑96 (MQ=255)                                                                                                                                         gCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCC‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTcccc                                                                                                                                                                  >  1:42870/1‑125 (MQ=255)                                                                                                                                           cgtAAAAAGCAGTGTGCCAGCGCCGCCTTGAGCCTCGCGACAATGGATTCGATTCC‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTGCATGGGGGAACGGCTCGCCTTCGGCCGTCCCCTGCACATCAATGAGGCGcccttc                                                                                                                                           <  1:152779/144‑4 (MQ=255)                                                                                                                                           cTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATCCC‑CCCGCGGGCCAGAGCCAACAAGATGAGTATCTCTTCATGGGTGAACGGCTCGCCCTCCGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGc                                                                                                       <  1:80223/182‑1 (MQ=255)                                                                                                                                                      gTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCC‑CCCTCGGGCCCGAGACAACAAGGTGAGTAGCTCTCCATGGGTGAACGCCTCGCCTTCTGACGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGACCTCACTACGTTCATGTAGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCTTCGCCGTTCACAATTCCGACAGAAACTGCGGCTACCATCCCTTTc                        >  1:87241/1‑250 (MQ=255)                                                                                                                                                          gCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCC‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCTTCGCCGTTCACAATTCCGACAGAAACTGCGGCTACCATccc                            <  1:42484/242‑1 (MQ=255)                                                                                                                                                                     cTTCTNCANNGTNNCAANGGATTCGATTCC‑CCCTCGGGCCAGAGcc                                                                                                                                                                                                                     >  2:295093/1‑46 (MQ=255)                                                                                                                                                                     cTTCGGCGTCGCTACAATGGATTCGATTCC‑CCCTCGGGCCAGAGcc                                                                                                                                                                                                                     <  1:295093/46‑1 (MQ=255)                                                                                                                                                                               gCTACAATGGATTCGATTCC‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTAGTCCAGATCGCAAACCGCGTCGCCGTTCACAATTCCGACAGAAACTGCGGCTACCATCCCTTTCATCGGATTGGTTTTCAGCTTGc  <  1:434722/247‑1 (MQ=255)                                                                                                                                                                                            nattccc‑cc‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAAAGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCTTCGCCGTTCACAATTCCGACAGAAAc                                           >  1:63465/6‑192 (MQ=255)                                                                                                                                                                                                      |                                                                                                                                                                                                                                 GGATTTCAGCGTAAACTCGCCAAACTTTAACACCTGCTTGCTAAGCGCAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCC‑CC‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCTTCAACGTATTCCAGATCGCAAACCGCTTCGCCGTTCACAATTCCGACAGAAACTGCGGCTACCATCCCTTTCATCGGATTGGTTTTCAGCTTGC  >  NC_000913/3815688‑3816107

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑