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	94.9%	138.3 / ‑0.1	39	coding (671/687 nt)	rph	truncated RNase PH
Reads supporting (aligned to +/- strand):  ref base . (0/2);  new base C (16/21);  total (16/23)
Fisher's exact test for biased strand distribution p-value = 5.03e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.89e-01

AACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑T‑C‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTC  >  NC_000913/3815746‑3816012                                                                                                                                        |                                                                                                                                       aaCTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑T‑c‑cccct                                                                                                                                 >  1:34211/1‑138 (MQ=255)  aCTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑T‑CGCCCTc                                                                                                                                 <  1:428500/140‑1 (MQ=255)   cTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑T‑c‑cccctcg                                                                                                                               >  2:160719/1‑136 (MQ=255)      gcgcTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCACTACAATGGATTCGAT‑TCC‑CCCTCGGGc                                                                                                                             <  1:549146/140‑1 (MQ=255)       cgcTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCC‑CCCTCGGGcc                                                                                                                            >  1:101358/1‑140 (MQ=255)       cgcTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCC‑CCCTCGGGcc                                                                                                                            >  1:594307/1‑140 (MQ=255)       cgcTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCC‑CCCTCGGGc                                                                                                                             <  1:220161/139‑1 (MQ=255)       cgcTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCC‑CCCTCGGGc                                                                                                                             >  2:220161/1‑139 (MQ=255)             tatGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCC‑CCCTCGGGCCAGAGcc                                                                                                                      <  1:746945/140‑1 (MQ=255)              atGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCC‑CCCTCGGGCCAGAGCca                                                                                                                     <  2:218976/140‑1 (MQ=255)                     cATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCC‑CCCTCGGGCCAGAGCCAACAAGAt                                                                                                              <  2:302527/140‑1 (MQ=255)                      aTGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATCC‑C‑CCCTCGGGCCAGAGCCAACAAGATg                                                                                                             <  2:698855/140‑1 (MQ=255)                      aTGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCC‑CCCTCGGGCCAGAGCCAACAAGATg                                                                                                             >  1:125221/1‑140 (MQ=255)                      aTGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCC‑CCCTCGGGCCAGAGCCAACAAGATg                                                                                                             >  2:251103/1‑140 (MQ=255)                      aTGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCC‑CCCTCGGGCCAGAGCCAACAAGATg                                                                                                             >  1:59580/1‑140 (MQ=255)                      aTGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCC‑CCCTCGGGCCAGAGCCAACAAGATg                                                                                                             >  1:555839/1‑140 (MQ=255)                      aTGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCC‑CCCTCGGGCCAGAGCCAACAAGATg                                                                                                             >  1:267346/1‑140 (MQ=255)                       tGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCC‑CCCTCGGGCCAGAGCCAACAAGATGa                                                                                                            >  1:196039/1‑140 (MQ=255)                           ttCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCC‑CCCTCGGGCCAGAGCCAACAAGATGAGTAg                                                                                                        <  2:34211/140‑1 (MQ=255)                            tCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCC‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGc                                                                                                       >  1:453826/1‑140 (MQ=255)                             cGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCC‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGct                                                                                                      <  2:456060/140‑1 (MQ=255)                                          aCTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCC‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCa                                                                                                 <  1:411093/132‑1 (MQ=255)                                          aCTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCC‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCa                                                                                                 >  2:411093/1‑132 (MQ=255)                                                   cAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCC‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGcc                                                                                <  2:453826/140‑1 (MQ=255)                                                     gACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCC‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCtt                                                                              <  1:399216/140‑1 (MQ=255)                                                      aCAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCC‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTc                                                                             >  2:657658/1‑140 (MQ=255)                                                             aaaGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCC‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTc                                                                      <  2:594307/140‑1 (MQ=255)                                                                ggCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCC‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTcccc                                                                   <  2:267346/140‑1 (MQ=255)                                                                                 cTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCC‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATgcg                                                  <  2:59580/140‑1 (MQ=255)                                                                                  ttAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCC‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATgcgc                                                 >  1:534209/1‑140 (MQ=255)                                                                                    aaaaaTCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCC‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGccc                                               >  2:726337/1‑140 (MQ=255)                                                                                           aGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCC‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCg                                        <  1:501752/140‑1 (MQ=255)                                                                                             tttGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCC‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGt                                      <  2:196039/140‑1 (MQ=255)                                                                                               tGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCC‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTc                                         <  1:711444/135‑1 (MQ=255)                                                                                               tGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCC‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTc                                         >  2:711444/1‑135 (MQ=255)                                                                                                   aGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCC‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCAc                                <  1:657658/140‑1 (MQ=255)                                                                                                    gcgcCGCCTTCTGCGTCGCTACAATGGATTCGAT‑TCC‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACt                               <  2:125221/140‑1 (MQ=255)                                                                                                      gccgccTTCTGCGTCGCTACAATGGATTCGAT‑TCC‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTAc                             <  1:726337/140‑1 (MQ=255)                                                                                                        cgccTTCTGCGTCGCTACAATGGATTCGAT‑TCC‑CCCTCGGGCCTGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGt                           <  1:160719/140‑1 (MQ=255)                                                                                                                gCGTCGCTACAATGGATTCGAT‑TCC‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCg                   <  2:611176/140‑1 (MQ=255)                                                                                                                    cGCTACAATGGATTCGAT‑TCC‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGtct               >  1:348588/1‑140 (MQ=255)                                                                                                                              gattcgat‑tcC‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCaga     <  2:348588/140‑1 (MQ=255)                                                                                                                                 tcgat‑tcC‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTc  >  2:768099/1‑140 (MQ=255)                                                                                                                                        |                                                                                                                                       AACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGAT‑T‑C‑CCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTC  >  NC_000913/3815746‑3816012

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑