Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	CP006584	1,645,421	C→G	intergenic (+1215/+45)	LY180_07765 → / ← LY180_07770	transposase/sulfatase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP006584	1,645,421	0	C	G	92.3%	64.0 / ‑4.1	28	intergenic (+1215/+45)	LY180_07765/LY180_07770	transposase/sulfatase
Reads supporting (aligned to +/- strand):  ref base C (2/0);  new base G (11/13);  total (14/14)
Fisher's exact test for biased strand distribution p-value = 4.80e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.03e-01

CAGCGAGTCGCTCTTTGTGGAGGTGACGATTACCTAACAATCGGTCGATTCGTTTGATGTTATGTTTTGTTCTCGCTTTGGTTGGCAGGTTACGGCCAAGTTCGGTAAGAGTGAGAGTTTTACAGTCAAGTAATGCGTGGCAAGCCAACGTTAAGCTGTTGAGTCGTTTTAAGTGTAATTCGGGGCAGAATTGGTAAAGAGAGTCGTGTAAAATATCGAGTTCGCACATCTTGTTGTCTGATTATTGATTTTTCGCGAAACCATTTGATCATATGACAAGA‑TGTGTATCTACCTTAACTTAATGATTTTGATAAAAATCATTAGGGGATTCATCAGGGTAAAGCATAAAAGGCTGGTCAAGTGTTTTGGCACGATCAACAACGCCAATTGCCTCATCGGTTAACTGATCGCTGATATAACCTTTTGCGGGGACACGTTCACGATTTTTGAACAGTGAAGGGGAGTTGTAATATGCCGTTCCTGCAGCGTGGAATCCCATAAAGTAATCAAAGCCACGGTTTTGAGGTTGCCATTCTTCCGCA  >  CP006584/1645168‑1645709                                                                                                                                                                                                                                                              |                                                                                                                                                                                                                                                                                                  cAGCGAGTCGCTCTTTGTGGAGGTGACGATTACCTAACAATCGGTCGATTCGTTTGATGTTATGTTTTGTTCTCGCTTTGGTTGGCAGGTTACGGCCAAGTTCGGTAAGAGTGAGAGTTTTACAGTCAAGTAATGCGTGGCAAGCCAACGTTAAGCTGTTGAGTCGTTTTAAGTGTAATTCGGGGCAGAATTGGTAAAGAGAGTCGTGTAAAATATCGAGTTCGCACATCTTGTTGTCTGATTATTGATTTTTCGCGAAACCATTTGATTATATGACAAGA‑TGTTTactcactttaac                                                                                                                                                                                                                                                      >  1:179595/1‑287 (MQ=0)           ctctTTGTGGAGGTGACGATTACCTAACAATCGGTCGATTCGTTTGATGTTATGTTTTGTTCTCGCTTTGGTTGGCAGGTTACGGCCAAGTTCGGTACGAGTGAGAGTTTTACAGTCAAGTAATGCGTGGCAAGCCAACGTTAAGCTGTTGAGTCGTTTTAAGTGTAATTCGGGGCAGAATTTGTAAATAGAGGCGTGTAAAATATCGAGTTCGCACCTCTTGATGTCTGATTATTGATTTTTCGCGAAACCATTCGATCATATGACCAGA‑TGTTTATCTCCTTTAACTTAATTAttt                                                                                                                                                                                                                                            >  2:391907/1‑298 (MQ=11)           ctctTTGTGGAGGTGACGATTACCTAACAATCGGTCGATTCGTTTGATGTTATGTTTTGTTCTCGCTTTGGTTGGCAGGTTACGGCCAAGTTCGGTAAGAGTGAGCGTTTTACAGTCAAGTAATGCGTGGCAAGCCACCGTTAAGCTGTTGAGTCGTTTTACGTGTAATTCGGGGCAGAATTGGTAAAGAGAGTAGTGTAAAATCTCGAGTTGGCACATATTGTTGTATGCTTTTTGATTTTTAGGCAAACCATTTGTTTATTTGACAAAATTTTTTATC‑ACTTTAACTTTATTAttt                                                                                                                                                                                                                                            >  2:191398/1‑298 (MQ=1)                                      cAATCGGTCGATTCGTTTGATGTTATGTTTTGTCCTCGCTTTGGTTGGCAGGTTACGGCCAAGTTCGGTAAGAGCGAGAGTTTTACAGTCAAGTAAGGCGTGGCAAGCCACCGTTCAGCTGTTGAGTCGTTTTACGTGTAATTCGGGGCAGCCTTGGTACACAGAGTCGTGTAAAATATCGAGTTCGCAAATCTTGTTGTCTGATTATTGATTTTTGGCCACAACATTTCAACATATGCCACGA‑TTTTTAACTCTCTTAACTTATTGATTTTTATACAAAGTATTAggggcatcaatc                                                                                                                                                                                                                 >  2:24594/1‑290 (MQ=11)                                                                                     gCAGGTTACGGCCAAGTTCGGTAAGAGTGAGAGTTTTACAGTCAAGTAAGGCGTGGCAAGCCAACGTTAAGCTGTTGAGTCGTTTTAAGTGTAATTCGGGGCAGAATTGGTAAAGAGAGTCGTGTAAAATATCGAGTTCGCACATTTTGTTGTCTGATTATTGATTTTTGGCGAAACCATTTGATCATATGACAAGA‑TGTGTATCTACCTTAACTTAATGATTTTGATAAAAATCATTAGGGGATTCATCAGGGTAAAGCATAAAAGGCTGGTCAAGTGTTTTGGCACGATCaacaac                                                                                                                                                                  <  1:312846/298‑1 (MQ=255)                                                                                                    gTTCGGTAAGAGTGAGAGTTTTACAGTCAAGTAAGGCGTGGCAAGCCAACGTTAAGCTGTTGAGTCGTTTTAAGTGTAATTCGGGGCAGAATTGGTAAAGAGAGTCGTGTAAAATATCGAGTTCGCACATTTTGTTGTCTGATTATTGATTTTTGGCGAAACCATTTGATCATATGACAAGA‑TGTGTATCTACCTTAACTTAATGATTTTGATAAAAATCATTAGGGGATTCATCAGGGTAAAGCATAAAAGGCTGGTCAAGTGTTTTGGCACGATCAACAACGCCAATTGCCTCATc                                                                                                                                                   <  1:292982/298‑1 (MQ=255)                                                                                                           aaGAGTGAGAGTTTTACAGTCAAGTAAGGCGTGGCAAGCCAACGTTAAGCTGTTGAGTCGTTTTAAGTGTAATTCGGGGCAGAATTGGTAAAGAGAGTCGTGTAAAATATCGAGTTCGCACATTTTGTTGTCTGATTATTGATTTTTGTCGAAACCATTTGATCATATGACAAGA‑TGTGTATCTACCTTAACTTAATGATTTTGATAAAAATCATTAGGGGATTCATCAGGGTAAAGCATAAAAGGCTGGTCAAGTGTTTTGGTACGATCAACAACGCAAATTGCCTCATCGGTTAAc                                                                                                                                            >  2:53210/1‑298 (MQ=255)                                                                                                                         tACAGTCAAGTAAGGCGTGGCAAGCCAACGTTAAGCTGTTGAGTCGTTTTAAGTGTAATTCGGGGCAGAATTGGTAAAGAGAGACGTGTAAAATATCGAGTTCGCACATTTTGTTGTCTGATTATTGATTTTTGGCGAAACCATTTGATCATATGACAAGA‑TGTGTATCTACCTTAACTTAATGATTTTGATAAAAATCATTAGGGGATTCATCAGGGTAAAGCATACAAGGCTGGTCAAGTGTTTTGGCACGATCAACAACGCCAATTGCCTCATCGGTTAACTGATCGCTGAtata                                                                                                                              <  1:187047/298‑1 (MQ=255)                                                                                                                                               aGCCAACGTTAAGCTGTTGAGTCGTTTTAAGTGTAATTCGGGGCAGAATTGGTAAAGAGAGTCGTGTAAAATATCGAGTTCGCACATTTTGTTGTCTGATTATTGATTTTTGGCGAAACCATTTGATCATATGACAAGA‑TGTGTATCTACCTTAACTTAATGATTTTGATAAAAATCATTAGGGGATTCATCAGGGTAAAGCATAAAAGGCTGGTCAAGTGTTTTGGCACGATCAACAACGCCAATTGCCTCATCGGTTAACTGATCGCTGATATAACCTTTTGCGGGGACACGTTCa                                                                                                        >  2:169449/1‑298 (MQ=255)                                                                                                                                               aGCCAACGTTAAGCTGTTGAGTCGTTTTAAGTGTAATTCGGGGCAGAATTGGTAAAGAGAGTCGTGTAAAATATCGAGTTCGCACATTTTGTTGTCTGATTATTGATTTTTGGCGAAACCATTTGATCATATGACAAGA‑TGTGTATCTACCTTAACTTAATGATTTTGATAAAAATCATTAGGGGATTCATCAGGGTAAAGCATAAAAGGCTGGTCAAGTGTTTTGGCACGATCAACAACGCCAATTGCCTCATCGGTTAACTGATCGCTGATATAACCTTTTGCGGGGACACGTTCa                                                                                                        <  1:172210/298‑1 (MQ=255)                                                                                                                                                   aaCGTTAAGCTGTTGAGTCGTTTTAAGTGTAATTCGGGGCAGAATTGGTAAAGAGAGTCGTGTAAAATATCGAGTTCGCACATTTTGTTGTCTGATTATTGATTTTTGGCGAAACCATTTGATCATATGACAAGA‑TGTGTATCTACCTTAACTTAATGATTTTGATAAAAATCATTAGGGGATTCATCAGGGTAAAGCATAAAAGGCTGGTCAAGTGTTTTGGCACGATCAACAACGCCAATTGCCTCATCGGTTAACTGATCGCTGATATAACCTTTTGCGGGGACACGTTCACGAt                                                                                                    >  1:131523/1‑298 (MQ=255)                                                                                                                                                              gTTGAGTCGTTTTAAGTGTAATTCGGGGCAGAATTGGTAAAGAGAGTCGTGTAAAATATCGAGTTCGCACATTTTGTTGTCTGATTATTGATTTTTGGCGAAACCATTTGATCATATGACAAGA‑TGTGTATCTACCTTAACTTAATGATTTTGATAAAAATCATTAGGGGATTCATCAGGGTAAAGCATAAAAGGCTGGTCAAGTGTTTTGGCACGATCAACAACGCCAATTGCCTCATCGGTTAACTGATCGCTGATATAACCTTTTGCGGGGACACGTTCACGATTTTTGAACAGt                                                                                         >  1:404488/1‑298 (MQ=255)                                                                                                                                                                 gAGTCGTTTTAAGTGTAATTCGGGGCAGAATTGGTAAAGAGAGTCGTGTAAAATATCGAGTTCGCACATTTTGTTGTCTGATTATTGATTTTTGGCGAAACCATTTGATCATATGACAAGA‑TGTGTATCTACCTTAACTTAATGATTTTGATAAAAATCATTAGGGGATTCATCAGGGTAAAGCATAAAAGGCTGGTCAAGTGTTTTGGCACGATCAACAACGCCAATTGCCTCATCGGTTAACTGATCGCTGATATAACCTTTTGCGGGGACACGTTCACGATTTTTGAACAGTGaa                                                                                      <  2:181396/298‑1 (MQ=255)                                                                                                                                                                                 aaTTCGGGGCAGAATTGGTAAAGAGAGTCGTGTAAAATATCGAGTTCGCACATTTTGTTGTCTGATTATTGATTTTTGGCGAAACCATTTGATCATATGACAAGA‑TGTGTATCTACCTTAACTTAATGATTTTGATAAAAATCATTAGGGGATTCATCAGGGTAAAGCATAAAAGGCTGGTCAAGTGTTTTGGCACGATCAACAACGCCAATTGCCTCATCGGTTAACTGATCGCTGATATAACCTTTTGCGGGGACACGTTCACGATTTTTGAACAGTGAAGGGGAGTTGTAATATg                                                                      <  1:102241/298‑1 (MQ=255)                                                                                                                                                                                        ggaaGAATTGGTAAAGTGAGTGGTTTAAAATATTGAGTTCGCACATTTTGTTGTCTGATTATTGATTTTTGGCGAAACCATGTTATCATATGACAAGA‑TGTGGATCTACCTTAACTTAATGATTTTGATAAAAATCATTAGGGGATTCATCAGGGTAAAGCATAAAAGGCTGGTCAAGTGTTTTGGCACGATCAACAACGCCAATTGCATCATCGGTTAACTGATCGCTGATATAACCTTTTGCGGGGACACGTTCACGATTTTTGAACAGTGAAGGGGAGTTGTAATATGCCGTTcc                                                               <  2:215759/295‑1 (MQ=37)                                                                                                                                                                                                  ttaaaggaagtgtggtAAAAATTCGTGTTCGTACATTTTTTTGTCTGATTTATTAGTTTTGTCGAAACCATTTGATAATATGACAAGA‑TGTGTAGTTACCTTAACTGAATGATTTTGATAAAAAGCATTAGTGGATTCATCAGGGTAAAGCATAAAAGGCTGGTCAAGTGTTTTGGCACGATCAACAACGCCAATTGCCTCATCGGTTAACTGATCGCTGATATAACCTTTTGCGGGGACACGTTCACGATTTTTGAACAGTGAAGGGGAGTTGTAATATGCCGTTCCTGCAGCGTgg                                                     <  2:3579/284‑1 (MQ=255)                                                                                                                                                                                                    aaggagtgTCGTGTAAAATATCGAGTTCGCTCATTTTGTTGGCTTGTTATTGATTTTTGGCGAAACCTTTTTATCATATGACAAGA‑TGTGTATCTACCTTACATTAATGATTTTGATATAAATCATTAGGGGATTCATCAGGGTAAAGCATAAAAGGCTGGTCAAGTGTTTTGGCACGATCAACAACGCCAATTGCCTCATCGGTTAACTGATCGCTGATATAACCTTTTGCGGGGACACGTTCACGATTTTTGAACAGTGAAGGGGAGTTGTAATATGCCGTTCCTGCAGCGTGGaa                                                   <  2:195085/295‑1 (MQ=255)                                                                                                                                                                                                           gTCGTGTAAAGTATCGAGTTCGCACATTTTGTTGTCTGATTATTGATTTTTGGCGAAACAATTTGATCATATGACAAGA‑GGTGTATCTACCTTAACTTAATGCTTTTGATAATAATCATTAGGGGATTCATCAGGGTAAAGCATAAAAGGCTGGACAAGTGTCTTGGCACGATCGACAACGACAATTGCCAAATCGGTTAACTGATCGATGATATAACATTTTGAGGTGACCCGTCTCGGAATTTTGTCCAGTGAAGAGGCAGTGAAATTCGCTGTCCCTGCAGctcgtaagaactta                                            >  2:42966/1‑285 (MQ=18)                                                                                                                                                                                                                       atCGAGTTCGCACATTTTGTTGTCTGATTATTGATTTTTGGCGAAACCATTTGATCATATGACAAGA‑TGTGTATCTACCTTAACTTAATGATTTTGATAAAAATCATTAGGGGATTCATCAGGGTAAAGCATAAAAGGCTGGTCAAGTGTTTTGGCACGATCAACAACGCCAATTGCCTCATCGGTTAACTGATCGCTGATATAACCTTTTGCGGGGACACGTTCACGATTTTTGAACAGTGAAGGGGAGTTGTAATATGCCGTTCCTGCAGCGTGGAATCCCATAAAGTAATCAAAg                                >  1:65588/1‑298 (MQ=255)                                                                                                                                                                                                                            gTTGGCACATTTTTTTTTTTGTTTTTTTGTTTTTGGCGAAACCAGTTGTTCAAATGACAAGT‑TGTGTAGTTACCTTAAATTAATGATTTGGAATAAAATCATTTGGGGGTTCAGCAGGGGAAAGCATAAAAGGCTGGTCAAGTGTTTTGGCACGGTCAACAACGCCAATTGCCTCATCGGTTAACTGGTCGCTGATATAACCTTTTGCGGGGACACGTTCACGATTTTTGAACAGTGAAGGGGAGTTGTAATATGCCGTGCCTGCAGCGTGGAATCCCATAAAGTAATCAAAGCCACg                           <  2:45683/298‑1 (MQ=255)                                                                                                                                                                                                                            gTTCGCACATTTTGTTGTCTGATTATTGATTTTTGGCGAAACCATTTGATCATATGACAAGA‑TGTGTATCTACCTTAACTTAATGATTTTGATAAAAATCATTAGGGGATTCATCAGGGTAAAGCATAAAAGGCTGGTCAAGTGTTTTGGCACGATCAACAACGCCAATTGCCTCATCGGTTAACTGATCGCTGATATAACCTTTTGCGGGGACACGTTCACGATTTTTGAACAGTGAAGGGGAGTTGTAATATGCCGTTCCTGCAGCGTGGAATCCCATAAAGTAATCAAAGCCACg                           >  1:295943/1‑298 (MQ=255)                                                                                                                                                                                                                                  acaTTTTGTTGTCTGATTATTGATTTTTGGCGAAACCATTTGATCATATGACAAGA‑TGTGTATCTACCTTAACTTAATGATTTTGATAAAAATCATTAGGTGATTCATCAGGGTAAAGCATAAAAGGCTGGTCAAGTGTTTTGGCACGATCAACAACGCCAATTGCCTCATCGGTTAACTGATCGCTGATATAACCTTTTGCGGGGACACGTTCACGATTTTTGAACAGTGAAGGGGAGTTGTAATATGCCGTTCCTGCAGCGTGGAATCCCATAAAGTAATCAAAGCCACGGTTTTg                     >  1:186341/1‑298 (MQ=255)                                                                                                                                                                                                                                   caTTTTGTTGTCTGATTATTGATTTTTGGCGAAACCATTTGATCATATGACAAGA‑TGTGTATCTACCTTAACTTAATGATTTTGATAAAAATCATTAGGGGATTCATCAGGGTAAAGCATAAAAGGCTGGTCAAGTGTTTTGGCACGATCAACAACGCCAATTGCCTCATCGGTTAACTGATCGCTGATATAACCTTTTGCGGGGACACGTTCACGATTTTTGAACAGTGAAGGGGAGTTGTAATATGCCGTTCCTGCAGCGTGGAATCCCATAAAGTAATCAAAGCCACGGTTTTGa                    >  1:404830/1‑298 (MQ=255)                                                                                                                                                                                                                                     tttggttgtCTGATTATTGATTTTTGGCAGAACCATTTGTTTATATGACAAGA‑TGTGTATCTACCTTAACTTAATGATTTTGATAAAAATCATTAGGTGATTCATCAGGGTAAAGCATAAAAGGCTGGTCAAGTGTTTTGGCACGATCAACAACGCCAATTGCCTCATCGGTTAACTGATCGCTGATATAACCTTTTGCGGGGACACGTTCACGATTTTTGAACAGTGAAGGGGAGTTGTAATATGCCGTTCCTGCAGCGTGGAATCCCATAAAGTAATCAAAGCCACGGTTTTGAgg                  <  2:186341/294‑1 (MQ=255)                                                                                                                                                                                                                                         tttgttttgttattGTTGTTTTGACAAACTATTTGCTCATATTAAAAGA‑TGGTTTTTTAACTTAACTTAATGATTTTTATAAAAATCATTAGGGAATTCATCCGGGTAAAGCATAAAAGGCTGGTCAAGTGTGTTGGCACGATCAACAACGCCAATTGCCTCATCGGTTAACTGATCGCTGATATAACCTTTTGCGGGGACACGTTCACGATTTTTGAACAGTGAAGGGGAGTTGTAATATGCCGTTCCTGCAGCGTGGAATCCCATAAAGTAATCAAAGCCACGGTTTTGAGGTTGc              <  2:236597/289‑1 (MQ=255)                                                                                                                                                                                                                                           tgtCTGATTATTGATTTTTGGCGAAACCATTTGATCATATGACAAGA‑TGTGTATCTACCTTAACTTAATGATTTTGATAAAAATCATTAGGGGATTCATCAGGGTAAAGCATAAAAGGCTGGTCAAGTGTTTTGGCACGATCAACAACGCCAATTGCCTCATCGGTTAACTGATCGCTGATATAACCTTTTGCGGGGACACGTTCACGATTTTTGAACAGTGAAGGGGAGTTGTAATATGCCGTTCCTGCAGCGTGGAATCCCATAAAGTAATCAAAGCCACGGTTTTGAGGTTGCCa            <  1:131798/298‑1 (MQ=255)                                                                                                                                                                                                                                                 attattGATTTTTGGCGAAACCATTTGATCATATGACAAGA‑TGTGTATCTACCTTAACTTAATGATTTTGATAAAAATCATTAGGGGATTCATCAGGGTAAAGCATAAAAGGCTGGTCAAGTGTTTTGGCACGATCAACAACGCCAATTGCCTCATCGGTTAACTGATCGCTGATATAACCTTTTGCGGGGACACGTTCACGATTTTTGAACAGTGAAGGGGAGTTGTAATATGCCGTTCCTGCAGCGTGGAATCCCATAAAGTAATCAAAGCCACGGTTTTGAGGTTGCCAttcttc      <  2:404830/298‑1 (MQ=255)                                                                                                                                                                                                                                                     ttGATTTTTGGCGAAACCATTTGATCATATGACAAGA‑TGTGTATCTACCTTAACTTAATGATTTTGATAAAAATCATTAGGGGATTCATCAGGGTAAAGCATAAAAGGCTGGTCAAGTGTTTTGGCACGATCAACAACGCCAATTGCCTCATCGGTTAACTGATCGCTGATATAACCTTTTGCGGGGACACGTTCACGATTTTTGAACAGTGAAGGGGAGTTGTAATATGCCGTTCCTGCAGCGTGGAATCCCATAAAGTAATCAAAGCCACGGTTTTGAGGTTGCCATTCTTCCGCa  >  1:10037/1‑298 (MQ=255)                                                                                                                                                                                                                                                              |                                                                                                                                                                                                                                                                                                  CAGCGAGTCGCTCTTTGTGGAGGTGACGATTACCTAACAATCGGTCGATTCGTTTGATGTTATGTTTTGTTCTCGCTTTGGTTGGCAGGTTACGGCCAAGTTCGGTAAGAGTGAGAGTTTTACAGTCAAGTAATGCGTGGCAAGCCAACGTTAAGCTGTTGAGTCGTTTTAAGTGTAATTCGGGGCAGAATTGGTAAAGAGAGTCGTGTAAAATATCGAGTTCGCACATCTTGTTGTCTGATTATTGATTTTTCGCGAAACCATTTGATCATATGACAAGA‑TGTGTATCTACCTTAACTTAATGATTTTGATAAAAATCATTAGGGGATTCATCAGGGTAAAGCATAAAAGGCTGGTCAAGTGTTTTGGCACGATCAACAACGCCAATTGCCTCATCGGTTAACTGATCGCTGATATAACCTTTTGCGGGGACACGTTCACGATTTTTGAACAGTGAAGGGGAGTTGTAATATGCCGTTCCTGCAGCGTGGAATCCCATAAAGTAATCAAAGCCACGGTTTTGAGGTTGCCATTCTTCCGCA  >  CP006584/1645168‑1645709

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 10 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑