Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	KT2440	1,637,682	T→C	8.5%	K39R (AAG→AGG)	lon_1 ←	Lon protease

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	KT2440	1,637,682	0	T	C	8.5%	138.4 / 4.2	47	K39R (AAG→AGG)	lon_1	Lon protease
Reads supporting (aligned to +/- strand):  ref base T (18/25);  new base C (2/2);  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 = 8.24e-01

CCAGGCAGTGGTCCGGTGACTTGGCTACCAGGTCGAGCGTTTCGGCCCAGGGCTCTTCATTGACGATCACCGGCAGTACCTGGGCCGGGAAGAACGGGCGGTTGTGGATCGGGATGACGTAGACCTTGTCCGGCAGCTGTTGACCGGGCAGGGCGAGGGCGTGGCTGACTTCGGCCTGGAGGGTGTGTTCGACTTCGCTGTGTTCGTCAGGGTGTTCGGGGAAATCCTGCTGGTCGCTCATGGGGCACCTGCGTGAATGA  >  KT2440/1637557‑1637816                                                                                                                              |                                                                                                                                       ccAGGCAGTGGTCCGGTGACTTGGCTACCAGGTCGAGCGTTTCGGCCCAGGGCTCTTCATTGACGATCACCGGCTGTACCTGGGCCGGGAAGAACGGGCGGTTGTGGATCGGGATGACGTAGACCTTGTCCGGCa                                                                                                                               <  8:142710/135‑1 (MQ=255) ccAGGCAGTGGTCCGGTGACTTGGCTACCAGGTCGAGCGTTTCGGCCCAGGGCTCTTCATTGACGATCACCGGCAGTACCTGGGCCGGGAAGAACGGGCGGTTGTGGATCGGGATGACGTAGACCTTGTCCGGCa                                                                                                                               >  1:201027/1‑135 (MQ=255)       aGTTGTCCGGTGACTTGGCTACCAGGTCGAGCGTTTCGGCCCAGGGCTCTTCATTGACGATCACCGGCAGTACCTGGGCCGGGAAGAACGGGCGGTTGTGGATCGGGATGACGTAGACCTTGTCCGGCAGCTGtt                                                                                                                         <  3:8102/135‑1 (MQ=255)            tCCGGTGACTTGGCTACCAGGTCGAGCGTTTCGGCCCAGGGCTCTTCATTGACGATCACCGGCAGTACCTGGGCCGGGAAGAACGGGCGGTTGTGGATCGGGATGACGTAGACCTTGTCCGGCAGCTGTTGACCg                                                                                                                    <  5:132134/135‑1 (MQ=255)                   aCTTGGCTACCAGGTCGAGCGTTTCGGCCCAGGGCTCTTCATTGACGATCACCGGCAGTACCTGGGCCGGGAAGAACGGGCGGTTGTGGATCGGGATGACGTAGACCTTGTACGGCAGCTGGTGACCGGCCaggg                                                                                                             >  3:164031/1‑135 (MQ=255)                                gTCGAGCGTTTCGGCCCAGGGCTCTTCATTGACGATCACCGGCAGTACCTGGGCCGGGAAGAACGGGCGGTTGTGGATCGGGATGACGTAGACCTTGTCCGGCAGCTGTTGCCCGGGCAGGGCGAGGGCGTGGCt                                                                                                >  7:186213/1‑135 (MQ=255)                                gTCGAGCGTTTCGGCCCAGGGCTCTTCATTGACGATCACCGGCAGTACCTGGGCCGGGAAGAACGGGCGGTTGTGGATCGGGATGACGTAGACCTTGTCCGGCAGCTGTTGACCGGGCAGGGCGAGGGCGTGGCt                                                                                                >  4:57341/1‑135 (MQ=255)                                 tCGAGCGTTTCGGCCGAGGGCTCTTCATTGACGATCACCGGCAGTACCTGGGCCGGGAAGAACGGGCGGTTGTGGATCGGGATGACGTAGACCTTGTCCGGCAGCTGTTGACCGGGCAGGGCGAGGGCGTGGCTg                                                                                               <  4:99492/135‑1 (MQ=255)                                 tCGAGCGTTTCGGCCCAGGGCTCTTCATTGACGATCACCGGCAGTACCTGGGCCGGGAAGAACGGGCGGTTGTGGATCGGGATGACGTAGACCTTGTCCGGCAGCTGTTGACCGGGCAGGGCGAGGGCGTGGCTg                                                                                               <  5:4809/135‑1 (MQ=255)                                  cGAGCGTTTCGGCCCAGGGCTCTTCATTGACGAGCACCGGCAGTACCTGGGCCGGGAAGAACGGGCGGTTGTGGATCGGGATGACGTAGACCTTGTCCGGCAGCTGTTGACCGGGCAGGGCGAGGGCGTGGCTGa                                                                                              <  8:195094/135‑1 (MQ=255)                                   gAGCGTTTCGGCCCAGGGCTCTTCATTGACGATCACCGGCAGTACCTGGGCCGGGAAGAACGGGCGGTTGTGGATCGGGATGACGTAGACCTTGTCCGGCAGCTGTTGACCGGGCAGGGCGAGGGCGTGGCTGAc                                                                                             <  7:96267/135‑1 (MQ=255)                                       gTTTCGGCCCAGGGCTCTTCATTGACGATCACCGGCAGTACCTGGGCCGGGAAGAACGGGCGGTTGTGGATCGGGATGACGTAGACCTTGTCCGGCAGCTGTTGCCCGGGCAGGGCGAGGGCGTGGCTGACTTCg                                                                                         >  1:133614/1‑135 (MQ=255)                                       gTTTCGGCCCAGGGCTCTTCATTGACGATCACCGGCAGTACCTGGGCCGGGAAGAACGGGCGGTTGTGGATCGGGATGACGTAGACCTTGTCCGGCAGCTGTTGCCCGGGCAGGGCGAGGGCGTGGCGGACTTCg                                                                                         >  5:35970/1‑135 (MQ=255)                                           cGGCCCAGGGCTCTTCATTGACGATCACCGGCAGTACCTGGGCCGGGAAGAACGGGCGGTTGTGGATCGGGATGACGTAGACCTTGTCCGGCAGCTGTTGACCGGGCAGGGCGAGGGCGTGGCTGACTTCGGCCt                                                                                     >  2:50759/1‑135 (MQ=255)                                             gCCCAGGGCTCTTCATTGACGATCACCGGCAGTACCTGGGCCGGGAAGAACGGGCGGTTGTGGATCGGGATGACGTAGACCTTGTCCGGCAGCTGTTGACCGGGCAGGGCGAGGGCGTGGCTGACTTCGGCCt                                                                                     >  1:12635/1‑133 (MQ=255)                                             gCCCAGGGCTCTTCATTGACGATCACCGGCAGTACCTGGGCCGGGAAGAACGGGCGGTTGTGGATCGGGATGACGTAGACCTTGTCCGGCAGCTGTTGACCGGGCAGGGCGAGGGCGTGGCTGACTTCGGCCTgg                                                                                   <  5:132844/135‑1 (MQ=255)                                             gCCCAGGGCTCTTCATTGACGATCACCGGCAGTACCTGGGCCGGGAAGAACGGGCGGTTGTGGATCGGGATGACGTAGACCTTGTCCGGCAGCTGTTGACCGGGCAGGGCGAGGGCGTGGCTGACTTCGGCCTgg                                                                                   <  4:276722/135‑1 (MQ=255)                                                     ctctTCATTGACGATCACCGGCAGTACCTGGGCCGGGAAGAACGGGCGGTTGTGGATCGGGATGACGTAGACCTTGTCCGGCAGCTGTTGACCGGGCAGGGCGAGGGCGTGGCTGACTTCGGCCTGGAGGgtgtg                                                                           >  7:41070/1‑135 (MQ=255)                                                      tctTCATTGACGATCACCGGCAGTACCTGGGCCGGGAAGAACGGGCGGTTGTGTATCGGGATGACGTAGACCCTGTCCGGCAGCTCTTGACCGGGCAGGGAGAGGGCGTGGCTGACTTCGGCATGGAGGgtgtgt                                                                          >  2:87057/1‑135 (MQ=255)                                                      tctTCATTGACGATCACCGGCAGTACCTGGGCCGGGAAGAACGGGCGGTTGTGGATCGGGATGACGTAGACCTTGTCCGGCAGCTGTTGACCGGGCAGGGCGAGGGCGTGGCTGACTTCGGCCTGGAGGgtgtgt                                                                          >  4:8489/1‑135 (MQ=255)                                                      tctTCATTGACGATCACCGGCAGTACCTGGGCCGGGAAGAACGGGCGGTTGTGGATCGGGATGACGTAGACCCTGTCCGGCAGCTGTTGAACGGGCAGGGCGAGGGCGTGGCTGACTTCGGCCTGGAGGgtgtgt                                                                          >  2:91129/1‑135 (MQ=255)                                                         tCATTGACGATCACCGGCAGTACCTGGGCCGGGAAGAACGGGCGGTTGTGGATCGGGATGACGTAGACCTTGTCCGGCAGCTGTTGACCGGGCAGGGCGAGGGCGTGGCTGACTTCGGCCTGGAGGGTGTGtt                                                                         <  5:123245/133‑1 (MQ=255)                                                           aTTGACGATCACCGGCAGTACCTGGGCCGGGAAGAACGGGCGGTTGTGGATCGGGATGACGTAGACCTTGTCCGGCAGCTGTTGACCGGGCAGGGCGAGGGCGTGGCTGACTTCGGCCTGGAGGGTGTGTTCGAc                                                                     >  2:150051/1‑135 (MQ=255)                                                            ttGACGATCACCGGCAGTACCTGGGCCGGGAAGAACGGGCGGTTGTGGATCGGGATGACGTAGACCTTGTCCGGCAGCTGTTGACCGGGCAGGGCGAGGGCGTGGCTGACTTCGGCCTGGAGGGTGTGTTCGACt                                                                    <  1:49528/135‑1 (MQ=255)                                                                cGATCACCGGCAGTACCTGGGCCGGGAAGAACGGGCNGTTGTGGATCGGGATGACGTAGACCCTGTCCGGCAGCTGTTGACCGGGCAGGGCGAGGGCGTGGCTGACTTCGGCCTGGAGGGTGTGTTCGACTTCGc                                                                <  1:91129/135‑1 (MQ=255)                                                                cGATCACCGGCAGTACCTGGGCCGGGAAGAACGGGCGGTTGTGGATCGGGATGACGTAGACCTTGTCCGGCAGCTGTTGACCGGGCAGGGCGAGGGCGTGGCTGACTTCGGCCTGGAGGGTGTGTTCGACTTCGc                                                                <  3:201092/135‑1 (MQ=255)                                                                cGATCACCGGCAGTACCTGGGCCGGGAAGAACGGGCGGTTGTGGATCGGGATGACGTAGACCTTGTCCGGCAGCTGTTGACCGGGCAGGGCGAGGGCGTGGCTGACTTCGGCCTGGAGGGTGTGTTCGACTTCGc                                                                <  1:150051/135‑1 (MQ=255)                                                                cGATCACCGGCAGTACCTGGGCCGGGAAGAACGGGCGGTTGTGGATCGGGATGACGTAGACCCTGTCCGGCAGCTGTTGACCGGGCAGGGCGAGGGCGTGGCTGACTTCGGCCTGGAGGGTGTGTTCGACTTCGc                                                                <  1:87057/135‑1 (MQ=255)                                                                     aCCGGCAGTACCTGGGCCGGGAAGAACGGGCGGTTGTGGATCGGGATGACGTAGACCTTGTCCGGCAGCTGTTGACCGGGCAGGGCGAGGGCGTGGCTg                                                                                               >  7:262773/1‑99 (MQ=255)                                                                     aCCGGCAGTACCTGGGCCGGGAAGAACGGGCGGTTGTGGATCGGGATGACGTAGACCTTGTCCGGCAGCTGTTGACCGGGCAGGGCGAGGGCGTGGCTg                                                                                               <  8:262773/99‑1 (MQ=255)                                                                                  gggCCGGGAAGAACGGGCGGTAGTGGATCGGGATGACGTAGACCTTGTCCGGCAGCTGTTGACCGGGCAGGGCGAGGGCGTGGCTGACTTCGGCCTGGAGGGTGTCTTCGACTTCGCTGTGTTCGTCAGGGTGtt                                              >  1:244250/1‑135 (MQ=255)                                                                                       gggAAGAACGCGCGGTTGTGGATCGGGATGACGTAGACCTTGTCCGGCAGCTGTTGACCGGGCAGGGCGAGGGCGTGGCTGACTTCGGCCTGGAGGGTGTGTTCGACTTCGCTGTGTTCGTCAGGGTGTTCggg                                          >  3:127245/1‑134 (MQ=255)                                                                                          aagaaCGGGCGGTTGTGGATCGGGATGACGTAGACCTTGTCCGGCAGCTGTTGACCGGGCAGGGCGAGGGCGTGGCTGACTTCGGCCTGGAGGGTGTGTTCGACt                                                                    <  2:12044/105‑1 (MQ=255)                                                                                          aagaaCGGGCGGTTGTGGATCGGGATGACGTAGACCTTGTCCGGCAGCTGTTGACCGGGCAGGGCGAGGGCGTGGCTGACTTCGGCCTGGAGGGTGTGTTCGACt                                                                    >  1:12044/1‑105 (MQ=255)                                                                                                gggCGGTTGTGGATCGGGATGACGTAGACCTTGTCCGGCAGCTGTTGACCGGGCAGGGCGAGGGCGTg                                                                                                   <  1:114289/68‑1 (MQ=255)                                                                                                gggCGGTTGTGGATCGGGATGACGTAGACCTTGTCCGGCAGCTGTTGACCGGGCAGGGCGAGGGCGTg                                                                                                   >  2:114289/1‑68 (MQ=255)                                                                                                 ggCGGTTGTGGATCGGGATGACGTAGACCTTGTCCGGCAGCTGTTGACCGGGCAGGGCGAGGGCGTGGCTGACTTCGGCCTGGAGGGTGTGTTCGACTTCGCTGTGTTCGTCAGGGTGTTCGGGGAAATCctgct                               <  1:148658/135‑1 (MQ=255)                                                                                                 ggCGGTTGTGGATCGGGATGACGTAGACCTTGTCCGGCAGCTGTTGACCGGGCAGGGCGAGGGCGTGGCTGACTTCGGCCTGGAGGGTGTGTTCGACTTCGCTGTGTTCGTCAGGGTGTTCGGGGAAATCctgct                               <  3:57341/135‑1 (MQ=255)                                                                                                         tgGATCGGGATGACGTAGACCTTGTCCGGCAGCTGTTGACCGGGCAGGGCGAGGGCGTGGCTGACTTCGGCCTGGAGGGTGTGTTCGACTTCGCTGTGTTCGTCAGGGTGTTCGGGGAAATCCTGCTGGTCGCTc                       <  3:8489/135‑1 (MQ=255)                                                                                                              cGGGATGACGTAGACCTTGTCCGGCAGCTGTTGACCGGGCAGGGCGAGGGCGTGGCTGACTTCGGCCTGGAGGGTGTGTTCGACTTCGCTGTGTTCGTCAGGGTGTTCGGGGAAATCCTGCTGGTCGCTCATggg                  >  5:125213/1‑135 (MQ=255)                                                                                                                 gaggACGTAGACCTTGTCCGGCAGCTGTTGACCGGGCAGGGCGAGGGCGTGGCTGACTTCGGCCTGGAGGGTGTGTTCGACTTCGCTGTGTTCGTCAGGGTGTTCGGGGAAATCCTGCTGGTCGCTCATGGGGCa               <  8:210092/132‑1 (MQ=255)                                                                                                                   tGACGTAGACCTTGTCCGGCAGCTGTTGACCGGGCAGGGCGAGGGCGTGGCTGACTTCGGCCTGGAGGGTGTGTTCGACTTCGCTGTGTTCGTCAGGGTGTTCggg                                          >  7:108587/1‑106 (MQ=255)                                                                                                                   tGACGTAGACCTTGTCCGGCAGCTGTTGACCGGGCAGGGCGAGGGCGTGGCTGACTTCGGCCTGGAGGGTGTGTTCGACTTCGCTGTGTTCGTCAGGGTGTTCggg                                          <  8:108587/106‑1 (MQ=255)                                                                                                                      cGTAGACCTTGTCCGGCAGCTGTTGACCGGGCAGGGCGAGGGCGTGGCTGACTTCGGCCTGGAGGGTGTGTTCGACTTCGCTGTGTTCGTCAGGGTGTTCGGGGAAATCCTGCTGGTCGCTCATGGGGCACCTGc          <  4:127245/135‑1 (MQ=255)                                                                                                                      cGTAGACCTTGTCCGGCAGCTGGTGACCGGGCAGGGCGAGGGCGTGGCTGACTTCGGCCTGGAGGGTGTGTTCGACTTGGCTGTGTTCGTCAGGGTGTTCGGGGAAATCCTGCTGGTCGCTCATGGGGCACCTGc          <  8:57329/135‑1 (MQ=255)                                                                                                                           aCCTTGTCCGGCAGCTGTTGACCGGGCAGGGCGAGGGCGTGGCTGACTTCGGCCTGGAGGGTGTGTTCGACTTCGCTGTGTTCGTCAGGGTGTTCGGGGAAATCCTGCTGGTCGCTCATGGGGCACCTGCGTGaa     <  3:90424/135‑1 (MQ=255)                                                                                                                           aCCTTGTCCGGCAGCTGTTGACCGGGCAGGGCGAGGGCGTGGCTGACTTCGGCCTGGAGGGTGTGTTCGACTTCGCTGTGTTCGTCAGGGTGTTCGGGGAAATCCTGCTGGTCGCTCATGGGGCACCTGCGTGaa     <  1:50759/135‑1 (MQ=255)                                                                                                                              ttGTCCGGCAGCTGTTGACCGGGCAGGGCGAGGGCGTGGCTGACTTCGGCCTgg                                                                                   >  1:126206/1‑54 (MQ=255)                                                                                                                              ttGTCCGGCAGCTGTTGACCGGGCAGGGCGAGGGCGTGGCTGACTTCGGCCTgg                                                                                   <  2:126206/54‑1 (MQ=255)                                                                                                                              ttGTCCGGCAGCTGTTGACCGGGCAGGGCGAGGGCGTGGCTGACTTCGGCCTGGAGGGTGTGTTCGACTTCGCTGTGTTCGt                                                       <  4:257876/82‑1 (MQ=255)                                                                                                                              ttGTCCGGCAGCTGTTGACCGGGCAGGGCGAGGGCGTGGCTGACTTCGGCCTGGAGGGTGTGTTCGACTTCGCTGTGTTCGt                                                       >  3:257876/1‑82 (MQ=255)                                                                                                                              ttGTCCGGCAGCTGTTGACCGGGCAGGGCGAGGGCGTGGCTGACTTCGGCCTGGAGGGTGTGTTCGACTTCGCTGTGTTCGTCAGGGTGTTCGGGGAAATCCTGCTGGTCGCTCAt                     <  2:170515/116‑1 (MQ=255)                                                                                                                              ttGTCCGGCAGCTGTTGACCGGGCAGGGCGAGGGCGTGGCTGACTTCGGCCTGGAGGGTGTGTTCGACTTCGCTGTGTTCGTCAGGGTGTTCGGGGAAATCCTGCTGGTCGCTCAt                     >  1:170515/1‑116 (MQ=255)                                                                                                                              ttGTCCGGCAGCTGTTGACCGGGCAGGGCGAGGGCGTGGCTGACTTCGGCCTGGAGGGTGTGTTCGACTTCGCTGTGTTCGTCAGGGTGTTCGGGGAAATCCTGCTGGTCGCTCATGGGGCACCTGCGTGAATGa  >  7:83845/1‑135 (MQ=255)                                                                                                                              ttGTCCGGCAGCTGTTGACCGGGCAGGGCGAGGGCGTGGCTGACTTCGGCCTGGAGGGTGTGTTCGACTTCGCTGTGTTCGTCAGGGTGTTCGGGGAAATCCTGCTGGTCGCTCATGGGGCACCTGCGTGAATGa  >  6:189577/1‑135 (MQ=255)                                                                                                                              ttGTCCGCCAGCTGTTGCCCGGGCAGGGCGAGCGCGTGGCTGACTTCGGCCTCGAGGGTGTGTTCGACTTCGCTGTGTTCGTCAGCGTCTTCGCGCAAATCCTGCTGGTCGCTCATGGGGCACCTGAGTGAAtc   >  7:127625/1‑133 (MQ=255)                                                                                                                              |                                                                                                                                       CCAGGCAGTGGTCCGGTGACTTGGCTACCAGGTCGAGCGTTTCGGCCCAGGGCTCTTCATTGACGATCACCGGCAGTACCTGGGCCGGGAAGAACGGGCGGTTGTGGATCGGGATGACGTAGACCTTGTCCGGCAGCTGTTGACCGGGCAGGGCGAGGGCGTGGCTGACTTCGGCCTGGAGGGTGTGTTCGACTTCGCTGTGTTCGTCAGGGTGTTCGGGGAAATCCTGCTGGTCGCTCATGGGGCACCTGCGTGAATGA  >  KT2440/1637557‑1637816

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑