Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	461,007	T→G	I707S (ATC→AGC)	lon →	Lon protease

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	461,007	0	T	G	95.2%	105.1 / ‑5.6	44	I707S (ATC→AGC)	lon	Lon protease
Reads supporting (aligned to +/- strand):  ref base T (1/1);  new base G (20/20);  total (21/23)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.91e-01

CATCCACGTCCACGTACCGGAAGGTGCGACGCCGAAAGATGGTCCGAGTGCCGGTATTGCTATGTGCACCGCGCTGGTTTCTTGCCTGACCGGTAACCCGGTTCGTGCCGATGTGGCAATGACCGGTGAGATCACTCTGCGTGGTCAGGTACTGCCGATCGGTGGTTTGAAAGAAAAACTCCTGGCAGCGCATCGCGGCGGGATTAAAACAGTGCTAATTCCGTTCGAAAATAAACGCGATCTGGAAGAGATTCCTGACAACGT  >  NC_000913/460876‑461139                                                                                                                                    |                                                                                                                                     cATCCATGTCCACGTACCGTAAGGTGCGACGCCGAAAGATGGTGCGAGTGCCAGTATTGCTATGTGCACCGCGCTGGTTTCTTGCCTGACCGGTAACCCGGTTCGTGCCGATGTGGTAATGACCGGTGAGAGCACTCTGCGTg                                                                                                                           <  1:159582/143‑1 (MQ=255)    ccacgtccacgtACCGGAAGGTGCGACGCCGAAAGATGGTCCGAGTGCCGGTATTGCTATGTGCACCGCGCTGGATTCTTGCCTGACCGCTAACCCGGTTCGTGACGAAGTCGCAATGAACGGTCAGAGCAGTCGGCGCGGtg                                                                                                                        >  2:722416/1‑142 (MQ=255)      acgtccacgtACCGGAAGGTGCGACGCCGAAAGATGGTCCGAGTGCCGGTATTGCTATGTGCACCGCGCTGGTTTCTTGAATGAATGATAACCCGGTTCGTGCCGATGTGGCAATGACCGGTGAGAGAACTGTGCGAgggccg                                                                                                                      >  2:474372/1‑139 (MQ=255)       cgtccccgtACCGGAAGGTGCGACGCCCAAAAAACATCATTTGGCTGGTATTGCTATGTGCACCGCGCTGGTTTCTTGCCTGACCGGTAACCCGGTTCGTGCCGATGTGGCAATGACCGGTGAGAGCACTCTGCGTGGTCAgg                                                                                                                     <  1:539564/143‑1 (MQ=255)            acgtACCGGAAGGTGCGACGCCGAAAGATGGTCCGAGTGCCGGTATTGCTATGTGCACCGCGCTGGTTTCTTGCCTGACCGGTAACCCGGTTCGGGCCGATGTGGCAATGACCGGTGAGAGCCCTCCGCGTGGTCAGGCACTg                                                                                                                >  2:41675/1‑143 (MQ=255)            acgtACCGGAAGGTGCGACGCCGAAAGATGGTCCGAGTGCCGGTAGTGCAATGTGCACCGCGCTGGTTTCTTGCATGACCGGTAACCCGGTTCGTGCCGATGTGGCAATGACCGGTGAGATCACACTGCGTGGTGAGCTACTg                                                                                                                >  2:673662/1‑143 (MQ=255)             cgtACCGGAAGGTGCGACGCCTAAAGATGGTCCGAGTGCCGGTATTGCTCTGTGCACCGCGCTGGTTTCTTGCCTGACCGGTAACCCGGTTCGTGCCGATGTGGCACTGCCCGGTGAGCGCTCTCTGCGTGGGCTGGTACTGc                                                                                                               >  1:35531/1‑143 (MQ=255)               tACCGGAAGGTGCGACGCCGAAAGATGGTCCGAGTGCCGGTATTGCTATGTGCACCGCGCTGGTTTCTTGCCTGACCGGTAACCCGGTTCGTGCCGATGTGGCAATGACCGGTGAGAGCACTCTGCGTGGGCAGGTACTGCCg                                                                                                             >  1:375689/1‑143 (MQ=255)                   ggcaGGTGCCACGCCGAACGATGGTACGAGTGCCGGTATTGCTATGTGCACCGCGCTGGTTTCTTGCCGGACCGGTAACCCGGTTCGTGCCGATGTGGCAATGACCGGTGAGAGCACTCTGCGTGGTCAGGTACTGCCGATCg                                                                                                         <  2:104668/140‑1 (MQ=255)                   ggAAGGTGCGACGCCGAAAGATGGTCCGAGTGCCGGTATTGCTATGTGCACCGCGCTGGTTTCTTGCCTGACCGGTAACCCGGTTCGTGCCGATGTGGCAATGACCGGTGAGAGCACTCTGCGTGGTCAGGTACTGCCGATCg                                                                                                         >  1:711914/1‑143 (MQ=255)                   ggAAGGTGCGACGCCGAAAGATGGTCCGAGTGCCGGTATTGCTATGTGCACCGCGCTGGTTTCTTGCCTGACCGGTAACCCGGTTCGTGCCGATGTGGCAATGACAGGTGAGAGCACTCTGGGTGGACAGGTAATACCGAtag                                                                                                         >  1:46727/1‑141 (MQ=255)                      aGGTGCGACGCCGAATTATGGTCCGAGTGCCGGTATTGCTATGTGCACCGCGCTGGTTTCTTGCCTGACCGGTAACCCGGTTCGTGCCGATGTGGCAATGACCGGTGAGAGCACTCTGCGTGGTCAGGTACTGCCGATCggtg                                                                                                      <  1:668038/143‑1 (MQ=255)                        gTGCGACGCCGAAAGATGGTCCGAGTGCCCGTATTGCTATGTGCACCGCGCTGGTTTCTTGCCTGACCGGTAGCGCGGTTCGTGCCGATGCGGCCATGACGAGGGAGAGCACTCTGCGTGGTCAGGTACTGACGAACggcagt                                                                                                    >  2:299060/1‑139 (MQ=255)                         gcggaggCCAAAAGATGGTCCGAGTGCAGGTATTGCTATGTGCACCGCGCTGGTTTCTTGCCTGACCGTTAACCCGGTTCGTGCCGATGTGGCAATGACCGGTGAGAGCACTCTGCGTGGTCAGGTACTGCCGATCGGTGGtt                                                                                                   <  1:670786/137‑1 (MQ=255)                           cGACGCCGAAAGATGGTCCGAGTGCCGGTATTGCTATGTGCACCGCGCTGGTTTCTTGCCTGACCGGTAACCCGGTTCGTGCCGATGTGGCAATGACCGGTGAGAGCACTCTGCGTGGTCAGGTACTGCCGATCGGTGGTATg                                                                                                 >  2:45664/1‑143 (MQ=255)                                       ttGGTCCTAGTTACGGTTTTTCTTTTTGAATCGTGTTAGTTTCTTGCCTGACCGGTAACCCGGTTCGCGCCGATGGGGCAATGACCGGTGAGAGCACTCTGCGTGGTCAGGTACTGCCGATCGGTGGTTTGAAAGAAAAACTc                                                                                     <  1:609562/142‑1 (MQ=255)                                           tCCGAGTGCCGGCATTGCTATATGCACCACGCTGGATTCTTGCCTGACCGGTAACCCGGTTCGTGCCGATATGGCCATGACCGGTGAGAGCACTCTGCGTGGTCAGGTACAGCCGATCGGTGGTACGAAAGAAAAACTCCTgc                                                                                 >  2:58423/1‑142 (MQ=255)                                           gccGAGTGCCGGTATTGCTATGTGCACCGCGCTGGTTTCTTGCCTGACCGGTAACCCGGTTCGTGCCGATGTGGCAATGACCGGTGAGAGCACTCTGCGTGGTCAGGTACTGCCGATCGGTGGTTTGAAAGAAAAACTCCTgg                                                                                 <  1:355696/142‑1 (MQ=255)                                            ccGAGTGCCGGTATTGCTATGTGCACCGCGCTGGTTTCTTGCCTGACCGGTAACCCGGTTCGTGCCGATGTGGCAATGACCGGTGAGAGCACTCTGCGTGGTCAGGTACTGCCGATCGGTGGTTTGACCGAGAACGTCCTGGc                                                                                >  1:256217/1‑143 (MQ=255)                                              gAGTGCCGGTATTGCTATGTGCACCGCGCTGGTTTCTCGGCCGCCACGTGACCCGGTTAGTGCCGATGTGGCAATGACCGGTGAGAGCACCCTGCGTGGTCAGGTACTTCCGATCGGTGGTTTGAAAGAAAAACTCCTGGCAg                                                                              <  1:714611/143‑1 (MQ=255)                                                          gtcTATTTGCACGTCGCTGGTTTTTTGTCTGGCCGGTAAGCCGGTTCGTGCCGATGTGGCAATGAGCGGTGAGATCATGCTGCGTGGTCAGGTACTGCCGATCGGTGGTTTGAAAGAAAAACTCCTGGCAGCGCATCgcggcg                                                                  <  2:18312/141‑1 (MQ=255)                                                                   cACCGCGCTGGTTTCTTGCCTGACCGGTAACCCGGTTCGTGCCGATGTGGCAATGACCGGTGAGAGCACTCTGCGTGGTCAGGTACTGCCGATCGGTGGTTTGAAAGAAAAACTCCTGGCAGCGCATCGCGGCGGGATTcaaa                                                         >  2:485934/1‑143 (MQ=255)                                                                   cACCGCGCTGGTTTCTTGCCTGACCGGTAACCCGGTTCGTGCCGATGTGGCAATGACCGGTGAGAGCACTCTGCGTGGTCAGGTACTGCCGATCGGTGGTTTGAAAGAAAAACTCATGGCAGCGCATCGCGACGGGATTaaaa                                                         >  1:199343/1‑143 (MQ=255)                                                                       tcgttGGTTTCTTGCCTGACCGGTAACCCGGTTCGTGCCGATTTTGCAATGACCGGTGAGAGCACTCTGCGTGGGCAGGTACTGCCGATCGGTGGTTTGAAAGAAAAACTCCTGGCAGCGCATCGCGGCGGGATTAAAACAGt                                                     <  1:630378/139‑1 (MQ=255)                                                                            ggactcgtGCCAGACCGGGAAACCGGTTCGGGCTGAGGTGGCAATGACCGGTGAGAGCCCTCTGTGTCCTCCACTACAAACGCTCGGCTTTATCAAATAAAAACTCCTGGCAGCGCATCGCGGCGGGATTAAAACAGTGCTaa                                                <  1:180702/136‑1 (MQ=255)                                                                             gTTTCTTGCCTGACCGGTAACCCGGTTCGTGCCGATGTGGCAATGACCGGTGAGAGCTCTCTGCGTGGTCAGGTCCTGCCGATCGGTGGGTTGATAGAATACCTCCTGGCAGCGCATCGCGGCGGGGCTAAAACAGTGCTCAt                                               >  1:780473/1‑143 (MQ=255)                                                                              tttCTGGCTGGACCGGTAACCGTGTTCGTGCCGATGTGGCAATGACCGGTGAGAGCACTCTGCGTGGTCAGGTACTGCCGATCGGTGGTTTGAAAGAAAAACTCCTGGCAGCGCATCGCGGCGGGATTAAAACAGTGCTAAtt                                              <  2:261813/143‑1 (MQ=255)                                                                                  ttGCCGGACCGGTAGCCCGGTGCGTGCCGATGTGGCAATGACCGGTGAGAGCACTCTGCGTGGTCAGGTACTGCCGATCGGTGGTTTGAAAGAAAAACTCCTGGCAGCGCATCGCGGCGGGATTAAAACAGTGCTAATTCCGt                                          <  1:463178/143‑1 (MQ=255)                                                                                   tGCCGGACCGGTACGCGGGTGCGTGCCGATGTGGTAACGACCGGTGAGAGCACTCTGCGTGGTCAGGTACTGACGATCGGTGGTTTGAAAGAAAAACTCCTGGCAGGGCATCGCGGCGGGATTAAAACAGTGCTAATTCCGtt                                         <  2:80900/143‑1 (MQ=255)                                                                                   ggCCAGACCGTTGTCCCGGTTCGTGCCGATGGGGACATGACCGGGGAGAGCACTCTGCGGGGTCAGGTACTGCCGATCGGTGGTTTAAAAGAAAAACTCCTGGCAGCGCATCGCGGCGGGATTAAAACAGTGCTAATTCCGtt                                         <  2:78646/142‑1 (MQ=255)                                                                                    gCCTGACCGGTAACCCGGTTCGTGCCGATGTGGCAATGACCGGTGAGAGCACTCTGCGTGGTCAGGTACTGCCGATCGGTGGTTTgaa                                                                                               >  1:517927/1‑88 (MQ=255)                                                                                    gCCTGACCGGTAACCCGGTTCGTGCCGATGTGGCAATGACCGGTGAGAGCACTCTGCGTGGTCAGGTACTGCCGATCGGTGGTTTgaa                                                                                               <  2:517927/88‑1 (MQ=255)                                                                                           cGGTAACCCGGTTCGTGCCGATGTGGCAATGACCGGTGAGAGCACTCTGCGTGGACAGGTACTGCCGATCGGTGGTTTGAAAGAAAAACTCCTGGCAGCGCATCGCGGCGGGATTAAAACAGTGCTAATTCCGTTCGAAAATa                                 >  1:410783/1‑143 (MQ=255)                                                                                            ggtatatcGGTTCGTGCCGATGTGGGGAGGGCGGGAAAAAACACGCAGCGTGGTCAGGTACTGCCGATCGGTGGTTTGAAAGAAAAACTCCTGGCAGCGCATCGCGGCGGGATTAAAACAGTGCTAATTCCGTTCGAAAATaa                                <  1:141902/136‑1 (MQ=255)                                                                                                aCCCGGTTCGTGCCGATGTGGCAATGACCTGTTAGAGCACTCTGCGTGGTCAGGTACTGCCGATCGGTGAGTTGAAAGAAAAACACCTGGCAGCGCATCGCGGCGGGATTAAAACAGTGCTAATTCCGTTCGAAAATAAAcgc                            <  1:69878/143‑1 (MQ=255)                                                                                                  gtgttgcGTGCGGATGTGGAAATGAACGGGGAGAGCACACGGCGTGGTCAGGGACTGCCGATCGGTGGTTTGAAAGAAAAACTCCTGGCAGCGCATCGCGGCGGGATTAAAACAGTGCTAATTCCGTTCGAAAATAAACGCGa                          <  1:218752/137‑1 (MQ=255)                                                                                                     gTTCGTGCCGATGTGGCAATGACCGGTGAGAGCACTCTGCGTGGTCAGGTACTGCCGATCGGTGGTTTGAAAGAAAAACTCCTGGCAGCGCATCGCGGCGGGATTAAAACAGTGCTAATTCCGGTCGAAAATAAACGCGATCt                       >  1:734465/1‑143 (MQ=255)                                                                                                        cGTGCCGATGTGGCAATGACCGGTGAGAGCACTCTGCGTGGTCAGGTACTGCCGATCGGTGGTTTGAAAGAAAAACTCCTAGCAGCGCATCGCGGCGGGATTAAAACAGTGCTAATTCCGTTCGAAAATAAACGAGAtaagga                    >  1:396008/1‑138 (MQ=255)                                                                                                           gCCGATGTGGCAATGACTGGTGAGAGCACTCTGCTTGGTCAGGTACTGCTGATCGGTGGTTTGAAAGAAAAACTTCTGGCAGCGCATCGCGGCGGGATTAAAACAGGGCGAATTGCGTTCGAAAATAAACGCGATCTGGAaga                 <  1:121679/143‑1 (MQ=255)                                                                                                           gCCGATGGGGCAATGCCCGGTGAGCCCAATCTGCGTGGTCAGGTACTGCCGATCGGGGGTGTGAAAGAAAAACTCCTGGCAGCGCATCGCGGCGGGATTAAAACAGTGCTAATTCCGTTCGAAAATAAACGCGATCTGGAaga                 <  1:176306/143‑1 (MQ=255)                                                                                                             tgttgtgGCAATGACCGGTGAGAGCACTCTGCGTGGTCAGGTACTGCCGAGCGGTGGTTTGAAAGAAAACCTCCTGGCAGCGCATCGCGGCGGGATTAAAACAGTGCTAATTCCGTTCGAAAATAAACGCGATCTGGAAgaga               <  1:137967/140‑1 (MQ=255)                                                                                                                tgtgGTAAGGGCCGGTGAGAGAACTCTGCGTGGGCAGGTACTGCCGATCGGCGGTTTGAAAGAAAAACTCCCGGCAGCGCATCGCGGCGGGATTAAAACAGTGCTAATTCCGTTCGAAAATAAACGCGATCTGGAAGAGATTc            <  1:557336/143‑1 (MQ=255)                                                                                                                    gCAATGACCGGTGAGAGCACTCTGCGTGGTCAGGTACTGCCGATCGGTGGTTTGAAAGAAAAACTCCTGGCAGCGCATCGCGGCGGGATTAAAAAAGTGCTAATTCAGTTCGAAAATAAACGCGAACTGGAAGAGATTCCAGa        >  2:437548/1‑143 (MQ=255)                                                                                                                          aCCGGTGAGAGCACTCTGCGTGGTCAGGTACTGCCGATCGGTGGTTTGAAAGAAAAACTCCTGGCAGCGCATCGCGGCGGGATTAAAACAGTGCTAATTCCGTTCGAAAATAAACGCGATCTGGAAGAGATTCCTGACAACGt  >  1:474080/1‑143 (MQ=255)                                                                                                                                    |                                                                                                                                     CATCCACGTCCACGTACCGGAAGGTGCGACGCCGAAAGATGGTCCGAGTGCCGGTATTGCTATGTGCACCGCGCTGGTTTCTTGCCTGACCGGTAACCCGGTTCGTGCCGATGTGGCAATGACCGGTGAGATCACTCTGCGTGGTCAGGTACTGCCGATCGGTGGTTTGAAAGAAAAACTCCTGGCAGCGCATCGCGGCGGGATTAAAACAGTGCTAATTCCGTTCGAAAATAAACGCGATCTGGAAGAGATTCCTGACAACGT  >  NC_000913/460876‑461139

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑