Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	CP006584	3,028,824	G→A	L110L (CTG→CTA)	LY180_14390 →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP006584	3,028,824	0	G	A	96.4%	77.1 / NA	28	L110L (CTG→CTA)	LY180_14390	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (0/0);  major base A (12/15);  minor base C (1/0);  total (13/15)
Fisher's exact test for biased strand distribution p-value = 4.64e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GGGATGCACTGGATGTGGCGCGAACACAGGCAGCGCTGTGGCAGACATGGCTGCTGCCGGTGACGGCAAATACGCCGGTCGGGGAAGACCCCGGCTACCACGACGATTTCCTGCGTATCCGCGACGAGATGAACAAACTTTCCGGCGCGGATACGGACCTCATCTGCCAGCTTGCCGAATCCCTGCTGCTGACGCAGGCAAAAGACGTGCGCATCGCCACTTACTACATCTGGGCGCGACTGCACCGCGACGGTGAGCGCGGACTGGCTGAGGGGCTGGCGCTGCTGGCCGGACTGGTGGAACGCTTCGGTACGCAACTGCTGCCCTCGCGACCGGCCAGCCGGAAAATGGCGCTGGAGTGGCTGGCAGGGGAAAAGATGCTCGACAGCCTT‑GCCCGCTACCCGGAAGTGGCAAAAGAGGATTTT  >  CP006584/3028541‑3028965                                                                                                                                                                                                                                                                                            |                                                                                                                                               gggATGCACTGGAGGGGGCGCGAACACAGGCAGCGCTGTGGCAGACATGGCTGCTGCCGGTGACGGCAAATACGCCGGTCGGGGAAGACCCCGGCTACCACGACGATTTCCTGCGTATCCGCGACGAGATGAACAAACTTTCCGGCGCGGATACGGACCTCATCTGCCAGCTTGCCGAATCCCTGCTGCTGACGCAGGCAAAAGACGTGCGCATCGCCACTTACTACATCTGGGCGCGACTGCACCGCGACGGTGAGCGCGGACTGGCTGAGGGGCTGGCGCTACTGACCGGACtggt                                                                                                                                  <  1:431443/298‑1 (MQ=255)           ggATGTGGCGCGAACACAGGCAGCGCTGTGGCAGACATGGCTGCTGCCGGTGACGGCAAATACGCCGGTCGGGGAAGACCCCGGCTACCACGACGATTTCCTGCGTATCCGCGACGAGATGAACAAACTTTCCGGCGCGGATACGGACCTCATCTGCCAGCTTGCCGAATCCCTGCTGCTGACGCAGGCAAAAGACGTGCGCATCGCCACTTACTACATCTGGGCGCGACTGCACCGCGACGGTGAGCGCGGACTGGCTGAGGGGCTGGCGCTACTGACCGGACTGGTGGAACGCTTc                                                                                                                        <  1:332378/298‑1 (MQ=255)                  gcgcGAACACAGGCAGCGCTGTGGCAGACATGGCTGCTGCCGGTGACGGCAAATACGCCGGTCGGGGAAGACCCCGGCTACCACGACGATTTCCTGCGTATCCGCGACGAGATGAACAAACTTTCCGGCGCGGATACGGACCTCATCTGCCAGCTTGCCGAATCCCTGCTGCTGACGCAGGCAAAAGACGTGCGCATCGCCACTTACTACCTCTGGGCGCGACTGCCCCGCGACGGTGCGCGCGGCCTGGCCGGGGGGCTGGCGCTACTGCCCGGACTGGTGGACGCCGTCGGTACGc                                                                                                                 >  2:116893/1‑298 (MQ=25)                      gAACACAGGCAGCGCTGTGGCAGACATGGCTGCTGCCGGTGACGGCAAATACGCCGGTCGGGGAAGACCCCGGCTACCACGACGATTTCCTGCGTATCCGCGACGAGATGAACAAACTTTCCGGCGCGGATACGGACCTCATCTGCCAGCTTGCCGAATCCCTGCTGCTGACGCAGGCAAAAGACGTGCGCATCGCCACTTACTACATCTGGGCGCGACTGCACCGCGACGGTGAGCGCGGACTGGCTGAGGGGCTGGCGCTACTGACCGGACTGGTGGAACGCTTCGGTACGCAAct                                                                                                             <  1:559766/298‑1 (MQ=255)                      gAACACAGGCAGCGCTGTGGCAGACATGGCTGCTGCCGGTGACGGCAAATACGCCGGTCGGGGAAGACCCCGGCTACCACGACGATTTCCTGCGTATCCGCGACGAGATGAACAAACTTTCCGGCGCGGATACGGACCTCATCTGCCAGCTTGCCGAATCCCTGCTGCTGACGCAGGCAAAAGACGTGCGCATCGCCACTTACTACATCTGGGCGCGACTGCACCGCGACGGTGAGCGCGGACTGGCTGAGGGGCTGGCGCTACTGACCGGACTGGTGGAACGCTTCGGTACGCAAct                                                                                                             <  1:266674/298‑1 (MQ=255)                          acaGGCAGCGCTGTGGCAGACATGGCTGCTGCCGGTGACGGCAAATACGCCGGTCGGGGAAGACCCCGGCTACCACGACGATTTCCTGCGTATCCGCGACGAGATGAACAAACTTTCCGGCGCGGATACGGACCTCATCTGCCAGCTTGCCGAATCCCTGCTGCTGACGCAGGCAAAAGACGTGCGCATCGCCACTTACTACATCTGGGCGCGACTGCACCGCGACGGTGAGCGCGGACTGGCTGAGGGGCTGGCGCTACTGACCGGACTGGTGGAACGCTTCGGTACGCAActgctg                                                                                                         >  1:226700/1‑298 (MQ=255)                               cAGCGCTGTGGCAGACATGGCTGCTGCCGGTGACGGCAAATACGCCGGTCGGGGAAGACCCCGGCTACCACGACGATTTCCTGCGTATCCGCGACGAGATGAACAAACTTTCCGGCGCGGATACGGACCTCATCTGCCAGCTTGCCGAATCCCTGCTGCTGACGCAGGCAAAAGACGTGCGCATCGCCACTTACTACATCTGGGCGCGACTGCACCGCGACGGTGAGCGCGGACTGGCTGAGGGGCTGGCGCTACTGACCGGACTGGTGGAACGCTTCGGTACGCAACTGCTGCCCTc                                                                                                    <  1:469889/298‑1 (MQ=255)                                  cgcTGTGGCAGACATGGCTGCTGCCGGTGACGGCAAATACGCCGGTCGGGGAAGACCCCGGCTACCACGACGATTTCCTGCGTATCCGCGACGAGATGAACAAACTTTCCGGCGCGGATACGGACCTCATCTGCCAGCTTGCCGAATCCCTGCTGCTGACGCAGGCAAAAGACGTGCGCATCGCCACTTACTACATCTGGGCGCGACTGCACCGCGACGGTGAGCGCGGACTGGCTGAGGGGCTGGCGCTACTGACCGGACTGGTGGAACGCTTCGGTACGCAACTGCTGCCCTcgcg                                                                                                 >  1:303476/1‑298 (MQ=255)                                               aTGGCTGCTGCCGGTGACGGCAAATACGCCGGTCGGGGAAGACCCCGGCTACCACGACGATTTCCTGCGTATCCGCGACGAGATGAACAAACTTTCCGGCGCGGATACGGACCTCATCTGCCAGCTTGCCGAATCCCTGCTGCTGACGCAGGCAAAAGACGTGCGCATCGCCACTTACTACATCTGGGCGCGACTGCACCGCGACGGTGAGCGCGGACTGGCTGAGGGGCTGGCGCTACTGACCGGACTGGTGGAACGCTTCGGTACGCAACTGCTGCCCTCGCGACCGGCCAGCCgg                                                                                    >  1:443433/1‑298 (MQ=255)                                                  gctgctGCCGGTGACGGCAAATACGCCGGTCGGGGAAGACCCCGGCTACCACGACGATTTCCTGCGTATCCGCGACGAGATGAACAAACTTTCCGGCGCGGATACGGACCTCATCTGCCAGCTTGCCGAATCCCTGCTGCTGACGCAGGCAAAAGACGTGCGCATCGCCACTTACTACATCTGGGCGCGACTGCACCGCGCCGGTGAGCGCGGACTGGCTGAGGGGCTGGCGCCACTGACCGGACTGGTGGACCGCTTCGGTACGCAACTCCTGCCCCCGCGAccgccccgcccgcaa                                                                                 >  2:480514/1‑293 (MQ=18)                                                         ccGGGGACGGCAAATACGCCGGGCGGGGAAGCCCCCGGCTACCACGGCGATTTGCTGCGTATGCGGGACGAGAGGAACAAACTTTCCGGGGGGGGTACGGACCTCAGCTGCCAGCTTGGCGAATCCCTGCTGCTGACGCAGGCAAAAGACGTGCGCATCGCCACTTACTACATCGGGGCGCGACTGCACCGCGACGGTGAGCGCGGACTGGCTGAGGGGCTGGCGCTACTGACCGGACTGGTGGAACGCTTCGGTACGCAACTGCTGCCCTCGCGACCGGCCAGCCGGAAAATGgcgc                                                                          <  2:498989/298‑1 (MQ=17)                                                          cGGTGACGGCAAATACGCCGGTCGGGGAAGACCCCGGCTACCACGACGATTTCCTGCGTATCCGCGACGAGATGAACAAACTTTCCGGCGCGGATACGGACCTCATCTGCCAGCTTGCCGAATCCCTGCTGCTGACGCAGGCAAAAGACGTGCGCATCGCCACTTACTACATCTGGGCGCGACTGCACCGCGACGGTGAGCGCGGACTGGCTGAGGGGCTGGCGCTACTGACCGGACTGGTGGAACGCTTCGGTACGCAACTGCTGCCCTCGCGACCGGCCAGCCGGAAAATGGCGCt                                                                         <  1:522059/298‑1 (MQ=255)                                                               ccggaaaatcgcccggccggGAAAGCCCCCGCGCACCACGACGCTTTCCGGCGTATCCCGGACGAGAGGAACAAACTTTCCGGGGCGGATACGGACCTCAGCTGCCAGCTTGCCGAATCCCTGCTGCTGACGCAGGCAAAAGACGTGCGCATCGCCACTTACTACATCTGGGCGCGACTGCACCGCGACGGTGAGCGCGGACTGGCTGAGGGGCTGGCGCTACTGACCGGACTGGTGGAACGCTTCGGTACGCAACTGCTGCCCTCGCGACCGGCCAGCCGGAAAATGGCGCTGGAGt                                                                    <  2:244634/286‑1 (MQ=14)                                                                cGGCAAATACGCCGGTCGGGGAAGACCCCGGCTACCACGACGATTTCCTGCGTATCCGGGACGAGATGAACAAACTTTCCGGCGCGGATACGGACCTCATCTGCCAGCTTGCCGAATCCCTGCTGCTGACGCAGGCAAAAGACGTGCGCATCGCCACTTACTACATCTGGGCGCGACTGCACCGCGACGGTGAGCGCGGACTGGCTGAGGGGCTGGCGCTACTGACCGGACTGGTGGAACGCTTCGGTACGCAACTGCTGCCCTCGCGACCGGCCAGCCGGAAAATGGCGCTGGAGtg                                                                   <  1:253290/298‑1 (MQ=255)                                                                cGGCAAATACGCCGGTCGGGGAAGACCCCGGCTACCACGACGATTTCCTGCGTATCCGCGACGAGATGAACAAACTTTCCGGCGCGGATACGGACCTCATCTGCCAGCTTGCCGAATCCCTGCTGCTGACGCAGGCAAAAGACGTGCGCATCGCCACTTACTACATCTGGGCGCGACTGCACCGCGACGGTGAGCGCGGACTGGCTGAGGGGCTGGCGCTACTGACCGGACTGGTGGAACGCTTCGGTACGCAACTGCTGCCCTCGCGACCGGCCAGCCGGAAAATGGCGCTGGAGtg                                                                   <  1:586511/298‑1 (MQ=255)                                                                  gCAAATACGCCGGTCGGGGAAGACCCCGGCTACCACGACGATTTCCTGCGTATCCGCGACGAGATGAACAAACTTTCCGGCGCGGATACGGACCTCATCTGCCAGCTTGCCGAATCCCTGCTGCTGACGCAGGCAAAAGACGTGCGCATCGCCACTTACTACATCTGGGCGCGACTGCACCGCGACGGTGAGCGCGGACTGGCTGAGGGGCTGGCGCTCCTGACCGGACTGTTGGAACGCTTCGGTACGCAATTGCTGCCCTCGCGACCGGCCAGCCGGAAATAGGCCCCGGGGtggc                                                                 >  1:292749/1‑298 (MQ=255)                                                                       tACGCCGGTCGGGGAAGACCCCGGCTACCACGACGATTTCCTGCGTATCCGCGACGAGATGAACAAACTTTCCGGCGCGGATACGGACCTCATCTGCCAGCTTGCCGAATCCCTGCTGCTGACGCAGGCAAAAGACGTGCGCATCGCCACTTACTACATCTGGGCGCGACTGCACCGCGACGGTGAGCGCGGACTGGCTGAGGGGCTGGCGCTACTGACCGGACTGGTGGAACGCTTCGGTACGCAACTGCTGCCCTCGCGACCGGCCAGCCGGAAAATGGCGCTGGAGTGGCTGGCa                                                            >  1:320339/1‑298 (MQ=255)                                                                                                  ccACGACGATTTCCTGCGTATCCGCGACGAGATGAACAAACTTTCCGGCGCGGATACGGACCTCATCTGCCAGCTTGCCGAATCCCTGCTGCTGACGCAGGCAAAAGACGTGCGCATCGCCACTTACTACATCTGGGCGCGACTGCACCGCGACGGTGAGCGCGGACTGGCTGAGGGGCTGGCGCTACTGACCGGACTGGTGGAACGCTTCGGTACGCAACTGCTGCCCTCGCGACCGGCCAGCCGGAAAATGGCGCTGGAGTGGCTGGCAGGGGAAAAGATGCTCGACAGCCTT‑Gcc                                >  1:240578/1‑298 (MQ=255)                                                                                                   cACGACGATTTCCTGCGTATCCGCGACGAGATGAACAAACTTTCCGGCGCGGATACGGACCTCATCTGCCAGCTTGCCGAATCCCTGCTGCTGACGCAGGCAAAAGACGTGCGCATCGCCACTTACTACATCTGGGCGCGACTGCACCGCGACGGTGAGCGCGGACTGGCTGAGGGGCTGGCGCTACTGACCGGACTGGTGGAACGCTTCGGTACGCAACTGCTGCCCTCGCGACCGGCCAGCCGGAAAATGGCGCTGGAGTGGCTGGCAGGGGAAAAGATGCTCGACAGCCTT‑Gccc                               <  1:467051/298‑1 (MQ=255)                                                                                                       acgaTTTCCTGCGTATCCGCGACGAGATGAACAAACTTTCCGGCGCGGATACGGACCTCATCTGCCAGCTTGCCGAATCCCTGCTGCTGACGCAGGCAAAAGACGTGCGCATCGCCACTTACTACATCTGGGCGCGACTGCACCGCGACGGTGAGCGCGGACTGGCTGAGGGGCTGGCGCTACTGACCGGACTGGTGGAACGCTTCGGTACGCAACTGCTGCCCTCGCGACCGGCCAGCCGGAAAATGGCGCTGGAGTGGCTGGCAGGGGAAAAGATGCTCGACAGCCTT‑GCCCGCTa                           <  1:180892/298‑1 (MQ=255)                                                                                                        cgaTTTCCTGCGTATCCGCGACGAGATGAACAAACTTTCCGGCGCGGATACGGACCTCATCTGCCAGCTTGCCGAATCCCTGCTGCTGACGCAGGCAAAAGACGTGCGCATCGCCACTTACTACATCTGGGCGCGACTGCACCGCGACGGTGAGCGCGGACTGGCTGAGGGGCTGGCGCTACTGACCGGCCTGGTGGAACGCTTCGGTACGCAACTGCCGCCCTCGCGACCGGCCAGCCGGAAAATGGCCCCGGGAGGGCCGGCCGGGGGCAAGATTCTCCACAGCCTTGGCCCGcac                           >  2:130084/1‑296 (MQ=14)                                                                                                          aTTTCCTGCGTATCCGCGACGAGATGAACAAACTTTCCGGCGCGGATACGGACCTCATCTGCCAGCTTGCCGAATCCCTGCTGCTGACGCAGGCAAAAGACGTGCGCATCGCCACTTACTACATCTGGGCGCGACTGCACCGCGACGGTGAGCGCGGACTGGCTGAGGGGCTGGCGCTACTGACCGGACTGGTGGAACGCTTCGGTACGCAACTGCTGCCCTCGCGACCGGCCAGCCGGAAAATGGCGCTGGAGTGGCTGGCAGGGGAAAAGATGCTCGACAGCCTT‑GCCCGCTAccc                        >  1:360975/1‑298 (MQ=255)                                                                                                                tGCGTATCCGCGACGAGATGAACAAACTTTCCGGCGCGGATACGGACCTCATCTGCCAGCTTGCCGAATCCCTGCTGCTGACGCAGGCAAAAGACGTGCGCATCGCCACTTACTACATCTGGGCGCGACTGCACCGCGACGGTGAGCGCGGACTGGCTGAGGGGCTGGCGCTACTGACCGGACTGGTGGAACGCTTCGGTACGCAACTGCTGCCCTCGCGACCGGCCAGCCGGAAAATGGCGCTGGAGTGGCTGGCAGGGGAAAAGATGCTCGACAGCCTT‑GCCCGCTACCCGGAAGt                  <  1:568348/298‑1 (MQ=38)                                                                                                                      tCCGCGACGAGATGAACAAACTTTCCGGCGCGGATACGGACCTCATCTGCCAGCTTGCCGAATCCCTGCTGCTGACGCAGGCAAAAGACGTGCGCATCGCCACTTACTACATCTGGGCGCGACTGCACCGCGACGGTGAGCGCGGACTGGCTGAGGGGCTGGCGCTACTGACCGGACTGGTGGAACGCTTCGGTACGCAACTGCTGCCCTCGCGACCGGCCAGCCGGAAAATGGCGCTGGAGTGGCTGGCAGGGGAAAAGATGCTCGACAGCCTT‑GCCCGCTACCCGGAAGTGGCaaa            >  1:469744/1‑298 (MQ=25)                                                                                                                               agaTGAACAAACTTTCCGGCGCGGATACGGACCTCATCTGCCAGCTTGCCGAATCCCTGCTGCTGACGCAGGCAAAAGACGTGCGCATCGCCACTTACTACATCTGGGCGCGACTGCACCGCGACGGTGAGCGCGGACTGGCTGAGGGGCTGGCGCTACTGACCGGACTGGTGGAACGCTTCGGTACGCAACTGCTGCCCTCGCGACCGGCCAGCCGGAAAATGGCGCTGGAGtggc                                                                 >  1:243323/1‑237 (MQ=17)                                                                                                                               agaTGAACAAACTTTCCGGCGCGGATACGGACCTCATCTGCCAGCTTGCCGAATCCCTGCTGCTGACGCAGGCAAAAGACGTGCGCATCGCCACTTACTACATCTGGGCGCGACTGCACCGCGACGGTGAGCGCGGACTGGCTGAGGGGCTGGCGCTACTGACCGGACTGGTGGAACGCTTCGGTACGCAACTGCTGCCCTCGCGACCGGCCAGCCGGAAAATGGCGCTGGAGtggc                                                                 <  2:243323/237‑1 (MQ=17)                                                                                                                                gaTGAACAAACTTTCCGGCGCGGATACGGACCTCATCTGCCAGCTTGCCGAATCCCTGCTGCTGACGCAGGCAAAAGACGTGCGCATCGCCACTTACTACATCTGGGCGCGACTGCACCGCGACGGTGAGCGCGGACTGGCTGAGGGGCTGGCGCTACTGACCGGACTGGTGGAACGCTTCGGTACGCAACTGCTGCCCTCGCGACCGGCCAGCCGGAAAATGGCGCTGGAGTGGCTGGCAGGGGAAAAGATGCTCGACAGCCTT‑GCCCGCTACCCGGAAGTGGCAAAAGAGGAtttt  <  1:57379/298‑1 (MQ=14)                                                                                                                                gaTGAACAAACTTTCCGGCGCGGATACGGACCTCATCTGCCAGCTTGCCGAATCCCTGCTGCTGACGCAGGCAAAAGACGTGCGCATCGCCACTTACTACATCTGGGCGCGACTGCACCGCGACGGTGAGCGCGGACTGGCTGAGGGGCTGGCGCTACTGACCGGACTGGTGGAACGCTTCGGTACGCAACTGCTGCCCTCGCGACCGGCCAGCCGGAAAATGGCGCTGGAGTGGCTGGCAGGGGAAAAGATGCTCGACAGCCTT‑GCCCGCTACCCGGAAGTGGCAAAAGAGGAtttt  >  1:453668/1‑298 (MQ=14)                                                                                                                                                                                                                                                                                            |                                                                                                                                               GGGATGCACTGGATGTGGCGCGAACACAGGCAGCGCTGTGGCAGACATGGCTGCTGCCGGTGACGGCAAATACGCCGGTCGGGGAAGACCCCGGCTACCACGACGATTTCCTGCGTATCCGCGACGAGATGAACAAACTTTCCGGCGCGGATACGGACCTCATCTGCCAGCTTGCCGAATCCCTGCTGCTGACGCAGGCAAAAGACGTGCGCATCGCCACTTACTACATCTGGGCGCGACTGCACCGCGACGGTGAGCGCGGACTGGCTGAGGGGCTGGCGCTGCTGGCCGGACTGGTGGAACGCTTCGGTACGCAACTGCTGCCCTCGCGACCGGCCAGCCGGAAAATGGCGCTGGAGTGGCTGGCAGGGGAAAAGATGCTCGACAGCCTT‑GCCCGCTACCCGGAAGTGGCAAAAGAGGATTTT  >  CP006584/3028541‑3028965

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 10 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑