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	95.7%	155.4 / ‑0.0	47	coding (671/687 nt)	rph	truncated RNase PH
Reads supporting (aligned to +/- strand):  ref base . (1/1);  new base C (18/26);  total (20/27)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.92e-01

AACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCG‑ATT‑CCCC‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAG  >  NC_000913/3815746‑3816008                                                                                                                                        |                                                                                                                                   aaCTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCG‑ATT‑ccccct                                                                                                                              >  2:902929/1‑138 (MQ=255)      gcgcTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCG‑ATTCCCCC‑TCGGGc                                                                                                                         <  1:185343/140‑1 (MQ=255)           gATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCG‑ATTCCCCC‑TCGGGCCagag                                                                                                                    <  1:39432/140‑1 (MQ=255)           gATATGGTTTCATGCATTCGCTGCTAATCTTGCTTTTTTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCG‑ATTCCCCC‑TCGGGCCagag                                                                                                                    <  1:314472/140‑1 (MQ=255)             tatGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCGGCCTTCTGGGTCCCTAGAATGGATTGG‑ATTACCCC‑TCGGGCCAGAGcc                                                                                                                  >  2:400879/1‑140 (MQ=255)             tatGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCG‑ATTCCCCC‑TCGGGCCAGAGcc                                                                                                                  <  1:902929/140‑1 (MQ=255)                ggTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGATACAATGCATTAGAATC‑CCCC‑CCGGGCCAGAGCcaac                                                                                                               >  1:415273/1‑140 (MQ=255)                      aTGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCG‑ATTCCCCC‑TCGGGCCAGAGCCAACAAGATg                                                                                                         >  2:253361/1‑140 (MQ=255)                      aTGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCG‑ATTCCCCC‑TCGGGCCAGAGCCAACAAGATg                                                                                                         >  1:548058/1‑140 (MQ=255)                      aTGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCG‑ATTCCCCC‑TCGGGCCAGAGCCAACAAGATg                                                                                                         >  1:897207/1‑140 (MQ=255)                       tGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCG‑ATTCCCCC‑TCGGGCCAGAGCCAACAAGATGa                                                                                                        >  2:60608/1‑140 (MQ=255)                        gCCTTCGCTCCTCATCTTACTTTGCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCG‑ATTCCCCC‑TCGGGCCAGAGCCAACAAGATGAg                                                                                                       <  1:694249/140‑1 (MQ=255)                         ccTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCG‑ATTCCCCC‑TCGGGCCAGAGCCAACAAGATGAGt                                                                                                      <  1:595330/140‑1 (MQ=255)                           ttCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCG‑ATTCCCCC‑TCGGGCCAGAGCCAACAAGATGAGTAg                                                                                                    >  1:211253/1‑140 (MQ=255)                           ttCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCG‑ATTCCCCC‑TCGGGCCAGAGCCAACAAGATGAGTAg                                                                                                    <  2:897207/140‑1 (MQ=255)                           ttCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCG‑ATTCCCCC‑TCGGGCCAGAGCCAACAAGATGAGTAg                                                                                                    <  1:871218/140‑1 (MQ=255)                           ttCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCG‑ATTCCCCC‑TCGGGCCAGAGCCAACAAGATGAGTAg                                                                                                    <  1:60608/140‑1 (MQ=255)                            tCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCG‑ATTCCCCC‑TCGGGCCAGAGCCAACAAGATGAGTAGc                                                                                                   >  1:755818/1‑140 (MQ=255)                                  ctcATCTTACTTTTCTACAGACAAAAAAATGGCGACTTATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCG‑ATTCCCCC‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCa                                                                                             <  1:400879/140‑1 (MQ=255)                                    cATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCG‑ATTCCCCC‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATg                                                                                           >  1:709352/1‑140 (MQ=255)                                            ttttCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCG‑ATTCCCCC‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCtt                                                                                               <  2:963754/128‑1 (MQ=255)                                            ttttCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCG‑ATTCCCCC‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCtt                                                                                               >  1:963754/1‑128 (MQ=255)                                            ttttCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCG‑ATTCCCCC‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACg                                                                                   >  2:202269/1‑140 (MQ=255)                                                   cAGACAAAAAAAAGGCGCCTCAACAGTCGCCGTAAAAATAAGTTTGCCTGCGCCGCCTTCTGCGTCGCTACAATGGATTCG‑ATTCCCCC‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGcc                                                                            <  2:355087/140‑1 (MQ=255)                                                      aCAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCG‑ATTCCCCC‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTc                                                                         >  2:584093/1‑140 (MQ=255)                                                        aaaaaaaaGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCG‑ATTCCCCC‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTg                                                                       >  1:564782/1‑140 (MQ=255)                                                        aaaaaaaaGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCG‑ATTCCCCC‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTg                                                                       >  2:703851/1‑140 (MQ=255)                                                          aaaaaaGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCG‑ATTCCCCC‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGcc                                                                     <  1:159542/140‑1 (MQ=255)                                                           aaaaaGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCG‑ATTCCCCC‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCg                                                                    <  1:703851/140‑1 (MQ=255)                                                                ggCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCG‑ATTCCCCC‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTcccc                                                               >  1:1000836/1‑140 (MQ=255)                                                                  cGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCG‑ATTCCCCC‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTg                                                             <  2:211253/140‑1 (MQ=255)                                                                  cGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCG‑ATTCCCCC‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTg                                                             <  1:898664/140‑1 (MQ=255)                                                                  cGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCG‑ATTCCCCC‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTg                                                             <  2:564782/140‑1 (MQ=255)                                                                  cGACTCATCAGTCGCCTGAAAATTCAGTTTGCCAGCGCCTCCTTCTGCGTCGCTACAATGGATTCG‑ATTCCCCC‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTg                                                             <  2:331103/140‑1 (MQ=255)                                                                        atcaGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCG‑ATTCCCCC‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTc                                                       >  1:542364/1‑140 (MQ=255)                                                                                ccTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCG‑ATTCCCCC‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGGACGGCTCGCCTTCTGCGGTCCGCTGCACTTCAATGATgc                                               >  2:268093/1‑140 (MQ=255)                                                                                ccTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCG‑ATTCCCCC‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAAAGGCTCGCTTTCAGCCGTCCCCAGCACTTCAATGATgc                                               >  1:421416/1‑140 (MQ=255)                                                                                 cTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCG‑ATTCCCCC‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATgcg                                              <  1:253361/140‑1 (MQ=255)                                                                                 cTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCG‑ATTCCCCC‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCCGCACTTCAATGATgcg                                              >  1:243868/1‑140 (MQ=255)                                                                                        aTCAGTTTGCCAGCGCCGCCTTATGCGTCGCTACACTGGATTCG‑ATTCCCCC‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCt                                       <  2:415273/140‑1 (MQ=255)                                                                                           aGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCG‑ATTCCCCC‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCg                                    <  1:607131/140‑1 (MQ=255)                                                                                           aGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCG‑ATTCCCCC‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCg                                    >  1:120655/1‑140 (MQ=255)                                                                                             tttGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCG‑ATTCCCCC‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGt                                  <  2:755818/140‑1 (MQ=255)                                                                                                     cgccgcCTTCTGCGTCGCTACAATGGATTCG‑ATTCCCCC‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTa                          <  2:1000836/140‑1 (MQ=255)                                                                                                                tcctCGCTACCATGGATTCG‑ATTCCCCC‑TCGGGCCAGAGCCAACAAGATGACTAGCTCTTCATGGGTGACCGGCTCGCCTTCTGCCGTCCCCTGCCCTTCAATGATGCGCCCGTCTTCGCTCATCACTACCTTCATGTCg               <  2:548058/137‑1 (MQ=255)                                                                                                                gCGTCGCTACAATGGATTCG‑ATTCCCCC‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCg               <  1:584093/140‑1 (MQ=255)                                                                                                                      cTACAATGGATTCG‑ATTCCCCC‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTctct         <  2:542364/140‑1 (MQ=255)                                                                                                                            tGGATTCG‑ATT‑CCCCATCGGGCCAGTGCCCACAAGATCAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCa   <  1:268093/140‑1 (MQ=255)                                                                                                                             ggATTCG‑ATTCCCCC‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCag  <  2:607158/140‑1 (MQ=255)                                                                                                                                        |                                                                                                                                   AACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCG‑ATT‑CCCC‑TCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAG  >  NC_000913/3815746‑3816008

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑