Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,727,504	A→G	T132A (ACT→GCT)	lhr →	Lhr

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,727,504	0	A	G	98.6%	216.6 / ‑4.3	73	T132A (ACT→GCT)	lhr	Lhr
Reads supporting (aligned to +/- strand):  ref base A (1/0);  new base G (41/31);  total (42/31)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.57e-01

CAGCGCAACTTGCAGATCCCGTTGAAGGGTATTGCCGATGAACGGCGGCGGCGCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTACTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATCCGCCGGATATTCTGATCACCACACCCGAATCACTCTATCTGATG  >  NC_000913/1727414‑1727593                                                                                           |                                                                                          cAGCGCAACTTGCAGATCCCGTTGAAGGGTATTGCCGATGAACGGCGGCGGCGCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCt                                                                                         >  2:2345871/1‑93 (MQ=255)     gcAACTTGCAGATCCCGTTGAAGGGTATTGCCGATGAACGGCGGCGGCGCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCg                                                                                     >  1:4288495/1‑93 (MQ=255)     gcAACTTGCAGATCCCGTTGAAGGGTATTGCCGATGAACGGCGGCGGCGCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCg                                                                                     >  1:4098653/1‑93 (MQ=255)        aCTTGCAGATCCCGTTGAAGGGTATTGCCGATGAACGGCGGCGGCGCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATa                                                                                  >  1:2261676/1‑93 (MQ=255)        aCTTGCAGATCCCGTTGAAGGGTATTGCCGATGAACGGCGGCGGCGCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATa                                                                                  <  1:4079296/93‑1 (MQ=255)         cTTGCAGATCCCGTTGAAGGGTATTGCCGATGAACGGCGGCGGCGCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATAc                                                                                 >  1:4669389/1‑93 (MQ=255)              aGATCCCGTTGAAGGGTATTGCCGATGAACGGCGGCGGCGCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTg                                                                            >  1:2041632/1‑93 (MQ=255)               gATCCCGTTGAAGGGTATTGCCGATGAACGGCGGCGGCGCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGc                                                                           >  1:3071403/1‑93 (MQ=255)               gATCCCGTTGAAGGGTATTGCCGATGAACGGCGGCGGCGCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGc                                                                           >  1:4244699/1‑93 (MQ=255)                 tCCCGTTGAAGGGTATTGCCGATGAACGGCGGCGGCGCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGcac                                                                         >  1:2914266/1‑93 (MQ=255)                     gTTGAAGGTTATTGCCGATGAACGGCGGCGGCGCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGa                                                                     <  2:2519604/93‑1 (MQ=255)                      ttGAAGGGTATTGCCGATGAACGGCGGCGGCGCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGaa                                                                    <  1:477692/93‑1 (MQ=255)                      ttGAAGGGTATTGCCGATGAACGGCGGCGGCGCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGaa                                                                    <  1:3174790/93‑1 (MQ=255)                         aaGGGTATTGCCGATGAACGGCGGCGGCGCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACgc                                                                 <  1:1469159/93‑1 (MQ=255)                          aGGGTATTGCCGATGAACGGCGGCGGCGCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACgca                                                                <  1:1998702/93‑1 (MQ=255)                            ggTATTGCCGATGAACGGCGGCGGCGCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACgcagc                                                              <  1:695132/93‑1 (MQ=255)                             gTATTGCCGATGAACGGCGGCGGCGCGGCGAAACGGAAGTCAATCTTCGCGGAGGGATCCGTGCCGGCGATACGCCTGCACAGGAACgcagca                                                             >  1:33336/1‑93 (MQ=255)                              tATTGCCGATGAACGGCGGCGGCGCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCaa                                                            >  1:2025260/1‑93 (MQ=255)                              tATTGCCGATGAACGGCGGCGGCGCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCaa                                                            >  1:3188586/1‑93 (MQ=255)                               aTTGCCGATGAACGGCGGCGGCGCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCaaa                                                           >  2:4036104/1‑93 (MQ=255)                               aTTGCCGATGAACGGCGGCGGCGCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCaaa                                                           <  1:2800291/93‑1 (MQ=255)                                  gCCGATGAACGGCGGCGGCGCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTc                                                        <  2:1699997/93‑1 (MQ=255)                                  gCCGATGAACGGCGGCGGCGCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTc                                                        >  1:987730/1‑93 (MQ=255)                                    cGATGAACGGCGGCGGCGCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCAc                                                      >  2:3553389/1‑93 (MQ=255)                                        gAACGGCGGCGGCGCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGt                                                  >  1:2926833/1‑93 (MQ=255)                                        gAACGGCGGCGGCGCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGt                                                  <  1:3443364/93‑1 (MQ=255)                                        gAACGGCGGCGGCGCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGt                                                  >  2:3058225/1‑93 (MQ=255)                                          aCGGCGGCGGCGCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTaa                                                <  2:4279732/93‑1 (MQ=255)                                           cggcggcggCGCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAAt                                               <  1:2165258/93‑1 (MQ=255)                                             gcggcggcgCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATcc                                             >  1:3474217/1‑93 (MQ=255)                                               ggcggcgCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATccgc                                           <  1:3395311/93‑1 (MQ=255)                                               ggcggcgCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATccgc                                           <  1:1614409/93‑1 (MQ=255)                                                gcggcgcggcGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATccgcc                                          >  2:4414321/1‑93 (MQ=255)                                                    cgcggcgAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATCCGCCGGat                                      <  2:1414157/93‑1 (MQ=255)                                                     gcggcgAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATCCGCCGGata                                     >  2:3400054/1‑93 (MQ=255)                                                         cgAAACGGAAGTCAATCTTCGCGTAGTGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATCCGCCGGATATTCt                                 <  1:767686/93‑1 (MQ=255)                                                         cgAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATCCGCCGGATATTCt                                 <  1:1982591/93‑1 (MQ=255)                                                          gAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATCCGCCGGATATTCTg                                >  1:2496349/1‑93 (MQ=255)                                                          gAAACGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATCCGCCGGATATTCTg                                >  1:689284/1‑93 (MQ=255)                                                            aaCGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATCCGCCGGATATTCTGAt                              >  1:4328843/1‑93 (MQ=255)                                                            aaCGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATCCGCCGGATATTCTGAt                              >  2:2471072/1‑93 (MQ=255)                                                            aaCGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATCCGCCGGATATTCTGAt                              <  1:1074960/93‑1 (MQ=255)                                                             aCGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATCCGCCGGATATTCTGATc                             >  1:4543122/1‑93 (MQ=255)                                                             aCGGAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCCGCACAGGAACGCAGCCAACTCACCCGTAATCCGCCGGATATTCTGATc                             >  2:4142601/1‑93 (MQ=255)                                                               ggAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATCCGCCGGATATTCTGATcac                           >  2:2455024/1‑93 (MQ=255)                                                               ggAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATCCGCCGGATATTCTGATcac                           <  2:909257/93‑1 (MQ=255)                                                                gAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATCCGCCGGATATTCTGATcacc                          >  2:3191335/1‑93 (MQ=255)                                                                gAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATCCGCCGGATATTCTGATcacc                          >  2:1652306/1‑93 (MQ=255)                                                                gAAGTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATCCGCCGGATATTCTGATcacc                          >  1:1358934/1‑93 (MQ=255)                                                                 aaGTCAATCGTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATCCGCCGGATATTCTGATcacca                         <  2:3260138/93‑1 (MQ=255)                                                                   gTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATCCGCCGGATATTCTGATCACcaca                       >  1:2320992/1‑93 (MQ=255)                                                                   gTCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATCCGCCGGATATTCTGATCACcaca                       <  2:2293223/93‑1 (MQ=255)                                                                    tCAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATCCGCCGGATATTCTGATCACCacac                      <  1:529328/93‑1 (MQ=255)                                                                    tCAATCTTCGCGTAGGGATCCGTACTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATCCGCCGGATATTCTGATCACCacac                      >  2:2917436/1‑93 (MQ=255)                                                                     cAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATCCGCCGGATATTCTGATCACCACAcc                     <  2:1347122/93‑1 (MQ=255)                                                                     cAATCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATCCGCCGGATATTCTGATCACCACAcc                     >  1:4311708/1‑93 (MQ=255)                                                                       aTCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATCCGCCGGATATTCTGATCACCACAACCg                   >  2:2523148/1‑93 (MQ=255)                                                                        tCTTCGCGTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATCCGCCGGATATTCTGATCACCACACCCGa                  >  2:3375164/1‑93 (MQ=255)                                                                              cgTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATCCGCCGGATATTCTGATCACCACACCCGAATCAct            <  1:2974532/93‑1 (MQ=255)                                                                               gTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATCCGCCGGATATTCTGATCACCACACCCGAATCActc           <  1:1465931/93‑1 (MQ=255)                                                                               gTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATCCGCCGGATATTCTGATCACCACACCCGAATCActc           >  1:2220663/1‑93 (MQ=255)                                                                               gTAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATCCGCCGGATATTCTGATCACCACACCCGAATCActc           <  1:4481931/93‑1 (MQ=255)                                                                                tAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCCGCAAACTCACCCGTAATCCGCCGGATATTCTGATCACCCCACCCGAATCActct          >  2:3206202/1‑93 (MQ=255)                                                                                tAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATCCGCCGGATATTCTGATCACCACACCCGAATCActct          >  2:2451637/1‑93 (MQ=255)                                                                                tAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATCCGCCGGATATTCTGATCACCACACCCGAATCActct          >  2:397961/1‑93 (MQ=255)                                                                                tAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATCCGCCGGATATTCTGATCACCACACCCGAATCActct          <  1:2228468/93‑1 (MQ=255)                                                                                tAGGGATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATCCGCCGGATATTCTGATCACCACACCCGAATCActct          >  2:1326708/1‑93 (MQ=255)                                                                                    gATCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATCCGCCGGATATTCTGATCACCACACCCGAATCACTCTATCt      <  2:567639/93‑1 (MQ=255)                                                                                      tCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATCCGCCGGATATTCTGATCACCACACCCGAATCACTCTATCTGa    >  1:469497/1‑93 (MQ=255)                                                                                      tCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATCCGCCGGATATTCTGATCACCACACCCGAATCACTCTATCTGa    <  2:1112592/93‑1 (MQ=255)                                                                                      tCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATCCGCCGGATATTCTGATCACCACACCCGAATCACTCTATCTGa    <  2:1310030/93‑1 (MQ=255)                                                                                      tCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATCCGCCGGATATTCTGATCACCACACCCGAATCACTCTATCTGa    >  2:1895919/1‑93 (MQ=255)                                                                                      tCCGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATCAGCCGGATATTCTGATCACCACACCCGAATCACTCTATCTGa    >  1:363597/1‑93 (MQ=255)                                                                                       ccGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATCCGCCGGATATTCTGATCACCACACCCGAATCACTCTATCTGAt   <  1:1811824/93‑1 (MQ=255)                                                                                        cGTGCTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATCCGCCGGATATTCTGATCACCACACCCGAATCACTCTATCTGATg  <  2:2252844/93‑1 (MQ=255)                                                                                           |                                                                                          CAGCGCAACTTGCAGATCCCGTTGAAGGGTATTGCCGATGAACGGCGGCGGCGCGGCGAAACGGAAGTCAATCTTCGCGTAGGGATCCGTACTGGCGATACGCCTGCACAGGAACGCAGCAAACTCACCCGTAATCCGCCGGATATTCTGATCACCACACCCGAATCACTCTATCTGATG  >  NC_000913/1727414‑1727593

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑