Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	461,186	C→A	L767M (CTG→ATG)	lon →	Lon protease

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	461,186	0	C	A	97.1%	108.2 / ‑2.7	34	L767M (CTG→ATG)	lon	Lon protease
Reads supporting (aligned to +/- strand):  ref base C (1/0);  new base A (19/14);  total (20/14)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.16e-01

AAACTCCTGGCAGCGCATCGCGGCGGGATTAAAACAGTGCTAATTCCGTTCGAAAATAAACGCGATCTGGAAGAGATTCCTGACAACGTAATTGCCGATCTGGACATTCATCCTGTGAAGCGCATTGAGGAAGTTCTGACTCTGGCGCTGCAAAATGAACCGTCTGGTATGCAGGTTGTGACTGCAAAATAGTGACCTCGCGCAAAATGCACTAATAAAAACAGGGCTGGCAGGCTAATTCGGGCTTGCCAGCCTTTTTTTGTCTCG  >  NC_000913/461051‑461317                                                                                                                                        |                                                                                                                                    aaaCTCCTGGCAGCGCATCGCGGCGGGATTAAAACAGTGCTAATTCCGTTCGAAAATAAACGCGATCTGGAAGAGATTCCTGACAACGTAATTGCCGATCTGGACATTCATCCTGTGAAGCGCATTGAGGAAGTTATGAc                                                                                                                                 >  1:171519/1‑140 (MQ=255)        tGGCAGCGCATCGCGGCGGGATTAAAACAGTGCTAATTCCGTTCGAAAATAAACGCGATCTGGAAGAGATTCCTGACAACGTAATTGCCGATCTGGACATTCATCCTGTGAAGCGCATTGAGGAAGTTATGACTCTGgcg                                                                                                                          <  1:180130/140‑1 (MQ=255)         ggCAGCGCATCGCGGCGGGATTAAAACAGTGCTAATTCCGTTCGAAAATAAACGCGATCTGGAAGAGATTCCTGACAACGTAATTGCCGATCTGGACATTCATCCTGTGAAGCGCATTGAGGAAGTTATGACTCTGgcgc                                                                                                                         >  1:708090/1‑140 (MQ=255)              cgcATCGCGGCGGGATTAAAACAGTGCTAATTCCGTTCGAAAATAAACGCGATCTGGAAGAGATTCCTGACAACGTAATTGCCGATCTGGACATTCATCCTGTGAAGCGCATTGAGGAAGTTATGACTCTGGCGCTGCaa                                                                                                                    >  1:506789/1‑140 (MQ=255)                 aTCGCGGCGGGATTAAAACAGTGCTAATTCCGTTCGAAAATAAACGCGATCTGGAAGAGATTCCTGACAACGTAATTGCCGATCTGGACATTCATCCTGTGAAGCGCATTGAGGAAGTTATGACTCTGGCGCTGCAAAAt                                                                                                                 >  1:633597/1‑140 (MQ=255)                    gcggcgGGATTAAAACAGTGCTAATTCCGTTCGAAAATAAACGCGATCTGGAAGAGATTCCTGACAACGTAATTGCCGATCTGGACATTCATCCTGTGAAGCGCATTGAGGAAGTTATGACTCTGGCGCTGCAAAATGaa                                                                                                              <  2:708090/140‑1 (MQ=255)                      ggcggGATTAAAACAGTGCTAATTCCGTTCGAAAATAAACGCGATCTGGAAGAGATTCCTGACAACGTAATTGCCGATCTGGACATTCATCCTGTGAAGCGCATTGAGGAAGTTATGACTCTGGCGCTGCAAAATGAAcc                                                                                                            <  1:622034/140‑1 (MQ=255)                                aaaCAGTGCTAATTCCGTTCGAAAATAAACGCGATCTGGAAGAGATTCCTGACAACGTAATTGCCGATCTGGACATTCATCCTGTGAAGCGCATTGAGGAAGTTATGACTCTGGCGCTGCAAAATGAACCGTCTGGTATg                                                                                                  <  2:296326/140‑1 (MQ=255)                                        cTAATTCCGTTCGAAAATAAACGCGATCTGGAAGAGATTCCTGACAACGTAATTGCCGATCTGGACATTCATCCTGTGAAGCGCATTGAGGAAGTTATGACTCTGGCGCTGCAAAATGAACCGTCTGGTATGCAGGTtgt                                                                                          <  2:455323/140‑1 (MQ=255)                                                gTTCGAAAATAAACGCGATCTGGAAGAGATTCCTGACAACGTAATTGCCGATCTGGACATTCATCCTGTGAAGCGCATTGAGGAAGTTCTGACTCTGGCGCTGCAAAATGAACCGTCTGGTATGCAGGTTGTGACTGCaa                                                                                  >  1:577483/1‑140 (MQ=255)                                                gTTCGAAAATAAACGCGATCTGGAAGAGATTCCTGACAACGTAATTGCCGATCTGGACATTCATCCTGTGAAGCGCATTGAGGAAGTTATGACTCTGGCGCTGCAAAATGAACCGTCTGGTATGCAGGTTGTGACTGCaa                                                                                  >  2:480058/1‑140 (MQ=255)                                                                 aTCTGGAAGAGATTCCTGACAACGTAATTGCCGATCTGGACATTCATCCTGTGAAGCGCATTGAGGAAGTTATGACTCTGGCGCTGCAAAATGAACCGTCTGGTATGCAGGTTGTGACTGCAAAATAGTGACCTCGCGCa                                                                 <  2:633597/140‑1 (MQ=255)                                                                        agagATTCCTGACAACGTAATTGCCGATCTGGACATTCATCCTGTGAAGCGCATTGAGGAAGTTATGACTCTGGCGCTGCAAAATGAACCGTCTGGTATGCAGGTTGTGACTGCAAAATAGTGACCTCGCGCAAAATGCa                                                          <  1:651468/140‑1 (MQ=255)                                                                            aTTCCTGACAACGTAATTGCCGATCTGGACATTCATCCTGTGAAGCGCATTGAGGAAGTTATGACTCTGGCGCTGCAAAATGAACCGTCTGGTATGCAGGTTGTGACTGCAAAATAGTGACCTCGCGCAAAATGCACtaa                                                      >  2:223968/1‑140 (MQ=255)                                                                            aTTCCTGACAACGTAATTGCCGATCTGGACATTCATCCTGTGAAGCGCATTGAGGAAGTTATGACTCTGGCGCTGCAAAATGAACCGTCTGGTATGCAGGTTGTGACTGCAAAATAGTGACCTCGCGCAAAATGCACtaa                                                      >  1:487488/1‑140 (MQ=255)                                                                            aTTCCTGACAACGTAATTGCCGATCTGGACATTCATCCTGTGAAGCGCATTGAGGAAGTTATGACTCTGGCGCTGCAAAATGAACCGTCTGGTATGCAGGTTGTGACTGCAAAATAGTGACCTCGCGCAAAATGCACt                                                        >  2:792353/1‑138 (MQ=255)                                                                            aTTCCTGACAACGTAATTGCCGATCTGGACATTCATCCTGTGAAGCGCATTGAGGAAGTTATGACTCTGGCGCTGCAAAATGAACCGTCTGGTATGCAGGTTGTGACTGCAAAATAGTGACCTCGCGCAAAATGCACt                                                        >  2:8933/1‑138 (MQ=255)                                                                            aTTCCTGACAACGTAATTGCCGATCTGGACATTCATCCTGTGAAGCGCATTGAGGAAGTTATGACTCTGGCGCTGCAAAATGAACCGTCTGGTATGCAGGTTGTGACTGCAAAATAGTGACCTCGCGCAAAATGCACt                                                        <  1:792353/138‑1 (MQ=255)                                                                            aTTCCTGACAACGTAATTGCCGATCTGGACATTCATCCTGTGAAGCGCATTGAGGAAGTTATGACTCTGGCGCTGCAAAATGAACCGTCTGGTATGCAGGTTGTGACTGCAAAATAGTGACCTCGCGCAAAATGCACt                                                        <  1:8933/138‑1 (MQ=255)                                                                              tCCTGACAACGTAATTGCCGATCTGGACATTCATCCTGTGAAGCGCATTGAGGAAGTTATGACTCTGGCGCTGCAAAATGAACCGTCTGGTATGCAGGTTGTGACTGCAAAATAGTGACCTCGCGCAAAATGCACtaata                                                    >  1:334870/1‑140 (MQ=255)                                                                                              gCCGATCTGGACATTCATCCTGTGAAGCGCATTGAGGAAGTTATGACTCTGGCGCTGCAAAATGAACCGTCTGGTATGCAGGTTGTGACTGCAAAATAGTGACCTCGCGCAAAATGCACTAATAAAAACAGGGCTGGCAg                                    >  1:75588/1‑140 (MQ=255)                                                                                               ccGATCTGGACATTCATCCTGTGAAGCGCATTGAGGAAGTTATGACTCTGGCGCTGCAAAATGAACCGTCTGGTATGCAGGTTGTGACTGCAAAATAGTGACCTCGCGCAAAATGCACTAATAAAAACAGGGCTGGCAgg                                   <  2:506789/140‑1 (MQ=255)                                                                                                       gACATTCATCCTGTGAAGCGCATTGAGGAAGTTATGACTCTGGCGCTGCAAAATGAACCGTCTGGTATGCAGGTTGTGACTGCAAAATAGTGACCTCGCGCAAAATGCACTAATAAAAACAGGGCTGGCAGGCTatt                              <  2:135034/137‑3 (MQ=255)                                                                                                       gACATTCATCCTGTGAAGCGCATTGAGGAAGTTATGACTCTGGCGCTGCAAAATGAACCGTCTGGTATGCAGGTTGTGACTGCAAAATAGTGACCTCGCGCAAAATGCACTAATAAAAACAGGGCTGGCAGGCTatt                              >  1:135034/1‑135 (MQ=255)                                                                                                       gACATTCATCCTGTGAAGCGCATTGAGGAAGTTATGACTCTGGCGCTGCAAAATGAACCGTCTGGTATGCAGGTTGTGACTGCAAAATAGTGACCTCGCGCAAAATGCACTAATAAAAACAGGGCTGGCAGGCTAATTCg                           >  2:528829/1‑140 (MQ=255)                                                                                                                 cTGTGATGCGCATTGAGGAAGTTATGACTCTGGCGCTGCAAAATGAACCGTCTGGTATGCAGGTTGTGACTGCAAAATAGTGACCTCGCGCAAAATGCACTAATAAAAACAGGGCTGGCAGGCTAATTCGGGCTTGCCAg                 >  1:739934/1‑140 (MQ=255)                                                                                                                    tgAAGCGCATTGAGGAAGTTATGACTCTGGCGCTGCAAAATGAACCGTCTGGTATGCAGGTTGTGACTGCAAAATAGTGACCTCGCGCAAAATGCACTAATAAAAACAGGGCTGGCAGGCTAATTCGGGCTTGCCAGCCt              >  1:531145/1‑140 (MQ=255)                                                                                                                         cgcATTGAGGAAGTTATGACTCTGGCGCTGCAAAATGAACCGTCTGGTATGCAGGTTGTGACTGCAAAATAGTGACCTCGCGCAAAATGCACTAATAAAAACAGGGCTGGCAGGCTAATTCGGGCTTGCCAGCCtttttt         >  2:325918/1‑140 (MQ=255)                                                                                                                         cgcATTGAGGAAGTTATGACTCTGGCGCTGCAAAATGAACCGTCTGGTATGCAGGTTGTGACTGCAAAATAGTGACCTCGCGCAAAATGCACTAATAAAAACAGGGCTGGCAGGCTAATTCGGGCTTGCCAGCCtttttt         >  1:601927/1‑140 (MQ=255)                                                                                                                         cgcATTGAGGAAGTTATGACTCTGGCGCTGCAAAATGAACCGTCTGGTATGCAGGTTGTGACTGCAAAATAGTGACCTCGCGCAAAATGCACTAATAAAAACAGGGCTGGCAGGCTAATTCGGGCTTGCCAGCCtttttt         >  1:561612/1‑140 (MQ=255)                                                                                                                           cATTGAGGAAGTTATGACTCTGGCGCTGCAAAATGAACCGTCTGGTATGCAGGTTGTGACTGCAAAATAGTGACCTCGCGCAAAATGCACTAATAAAAACAGGGCTGGCAGGCTAATTCGGGCTTGCCAGCCTTTTTTTg       >  1:161461/1‑140 (MQ=255)                                                                                                                            aTTGAGGAAGTTATGACTCTGGCGCTGCAAAATGAACCGTCTGGTATGCAGGTTGTGACTGCAAAATAGTGACCTCGCGCAAAATGCACTAATAAAAACAGGGCTGGCAGGCTAATTCGGGCTTGCCAGCCTTTTTTTGt      <  2:171519/140‑1 (MQ=255)                                                                                                                            aTTGAGGAAGTTATGACTCTGGCGCTGCAAAATGAACCGTCTGGTATGCAGGTTGTGACTGCAAAATAGTGACCTCGCGCAAAATGCACTAATAAAAACAGGGCTGGCAGGCTAATTCGGGCTTGCCAGCCTTTTTTTGt      <  2:487488/140‑1 (MQ=255)                                                                                                                                aGGAAGTTATGACTCTGGCGCTGCAAAATGAACCGTCTGGTATGCAGGTTGTGACTGCAAAATAGTGACCTCGCGCAAAATGCACTAATAAAAACAGGGCTGGCAGGCTAATTCGGGCTTGCCAGCCTTTTTTTGTCTCg  <  2:161461/140‑1 (MQ=255)                                                                                                                                        |                                                                                                                                    AAACTCCTGGCAGCGCATCGCGGCGGGATTAAAACAGTGCTAATTCCGTTCGAAAATAAACGCGATCTGGAAGAGATTCCTGACAACGTAATTGCCGATCTGGACATTCATCCTGTGAAGCGCATTGAGGAAGTTCTGACTCTGGCGCTGCAAAATGAACCGTCTGGTATGCAGGTTGTGACTGCAAAATAGTGACCTCGCGCAAAATGCACTAATAAAAACAGGGCTGGCAGGCTAATTCGGGCTTGCCAGCCTTTTTTTGTCTCG  >  NC_000913/461051‑461317

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 24 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑