Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	CP006584	1,645,301	T→G	intergenic (+1095/+165)	LY180_07765 → / ← LY180_07770	transposase/sulfatase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP006584	1,645,301	0	T	G	80.0%	68.8 / 5.8	30	intergenic (+1095/+165)	LY180_07765/LY180_07770	transposase/sulfatase
Reads supporting (aligned to +/- strand):  ref base T (6/0);  new base G (11/13);  total (17/13)
Fisher's exact test for biased strand distribution p-value = 2.37e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.83e-01

GGTATACAGCGAGTCGCTCTTTGTGGAGGTGACGATTACCTAACAATCGGTCGATTCGTTTGATGTTATGTTTTGTTCTCGCTTTGGTTGGCAGGTTACGGCCAAGTTCGGTAAGAGTGAGAGTTTTACAGTCAAGTAATGCGTGGCAAGCCAACGTTAAGCTGTTGAGTCGTTTTAAGTGTAATTCGGGGCAGAATTGGTAAAGAGAGTCGTGTAAAATATCGAGTTCGCACATCTTGTTGTCTGATTATTGATTTTTCGCGAAACCATTTGATCATATGACAAGATGTG‑TATCTACCTTAACTTAATGATTTTGATAAAAATCATTAGGGGATTCATCAGGGTAAAGCATAAAAGGCTGGTCAAGTGTTTTGGCACGATCAACAACGCCAATTGCCTCATCGGTTAACTGATCGCTGATATAACCTTTTGCG  >  CP006584/1645162‑1645595                                                                                                                                            |                                                                                                                                                                                                                                                                                                        ggTATACAGCGAGTCGCTCTTTGTGGAGGTGACGATTACCTAACAATCGGTCGATTCGTTTGATGTTATGTTTTGTTCTCGCTTTGGTTGGCAGGTTACGGCCAAGTTCGGTAAGAGTGAGAGTTTTACAGTCAAGTAATGCGTGGCAAGCCAACGTTAAGCTGTTGAGTCGTTTTAAGTGTAATTCGGGGCAGAATTGGTAAAGGGAGTCGTGTAAAATATCGAGTTCGCATATCTTGTTGTCTGATTATCGATTTTTCGCTAAACCATTTTATCATATGAAAAGATGTG‑TATCTAc                                                                                                                                          >  2:62620/1‑298 (MQ=9)   tataCAGCGAGTCGCTCTTTGTGGAGGTGACGATTACCTAACAATCGGTCGATTCGTTTGATGTTATGTTTTGTTCTCGCTTTGGTTGGCAGGTTACGGCCAAGTTCGGTAAGAGTGAGAGTTTTACAGTCAAGTAATGCGTGGCAAGCCAACGTTAAGCTGTTGAGTCGTTTTAAGTGTAATTCGGGGCAGAATTGGTAAAGAGAGTCGTGTAAAATATCGAGTTCGCCAATCTTGTTGTCTGATTATTGATTTTTCGCGAAACCATTTGATCATATTACAAGATTTG‑TATCTCCct                                                                                                                                        >  2:976811/1‑298 (MQ=2)     taCAGCGAGTCGCTCTTTGTGGAGGTGACGATTACCTAACAATCGGTCGATTCGTTTGATGTTATGTTTTGTTCTCGCTTTGGTTGGCAGGTTACGGCCAAGTTCGGTAAGAGTGAGAGTTTTACAGTCAAGTAATGCGTGGCAAGCCAACGTTAAGCTGTTGAGTCGTTTTAAGTGTAATTCGGGGCAGAATTGGTAAAGAGAGTCGTGTAAAATATCGAGTTCGCACATCTTGTTGTCTGATTATTCATTTTTAGCGAAACCATTTGATCATATTACAAGAtgattttccatctta                                                                                                                                       >  2:265314/1‑285 (MQ=0)         gCGAGTCGCTCTTTGTGGAGGTGACGATTACCTAACAATCGTTCGATTCGTTTGATGTTATGTTTTGTTCTCGCTTTGGTTGTCAGGTTACTGCCTAGTTCGGTAATAGTGAGAGTTTTACAGTCAAGTAATGCGTGGCAAGCCAACGTTAACCTGTTGAGTCGTTTTAAGTGTAATTCGGGGCAGAATTGACAAAGAGACTCGTGTAAAATATTGAGTTCGACCCTATTGTTGTCTGAATATTTATTTTTCTCCAAACCCTTTACTCATATGCCAAGATGTT‑Tagcctacttacctt                                                                                                                                  >  2:773443/1‑285 (MQ=1)         gCGAGTCGCTCTTTGTGGAGGTGACGATTACCTAACAATCGGTCGATTCGTTTGATGTTATGTTTTGTTCTCGCTTTGGTTGGCAGGTTACGGCCAAGTTCGGTAAGAGTGAGAGTTTTACAGTCAAGTAATGCGTGGCAAGCCAACGTTAAGCTGTTGAGTCGTTTTAAGTGTAATTCGGGGCAGAATTGGTAAAGAGAGTCGTGTAAAATATCGAGTTCGCACATCTTGTTGTCTGCTTATTGATTTTTCGCGAAACGCTTTGATCATAGGACAAGATGTT‑TATCTACcttaactt                                                                                                                                  >  2:3519/1‑298 (MQ=9)                gCTCTTTGTGGAGGTGACGATTACCTAACAATCGGTCGATTCGTTTGATGTTATGTTTTGTTCTCGCTTTGGTTGGCAGGTTACGGCCAAGTTCGGTAAGAGTGAGAGTTTTACAGTCAAGTAATGCGTGGCAAGCCAACGTTAAGCTGTTGAGTCGTTTTAAGTGTAATTCGGGGCAGAATTGGTAAAGAGAGTCGTGTAAAATATCGAGTTCGCACATCTTGTTGTTTGATTATTTATTTTTCGCGAAACCATTTGATTATATGACAAGATGTGTTACCTA‑CTTAAATTAattatt                                                                                                                           >  2:212881/1‑298 (MQ=0)                                                          gTTTGATGTTATGTTTTGTTCTCGCTTTGGTTGGCAGGTCACGGCCAAGTTCGGTAAGAGTGAGAGTTTTACAGTCAAGTAAGGCGTGGCAAGCCAACGTTAAGCTGTTGAGTCGTTTTAAGTGTAATTCGGGGCAGAATTGGTAAAGAGAGTCGTGTAAAATATCGAGTTCGCACATTTTGTTGTCTGATTATTGATTTTTGGCGAAACCATTTGATCATATGACAAGATGTG‑TATCTACCTTAACTTAATGATTTTGATAAAAATCATTAGGGGATTCATCAGGGTAAAGCATaaa                                                                                 >  1:505868/1‑298 (MQ=25)                                                                 gttatgttTTGTTCTCGCTTTGGTTGGCAGGTTACGGCCAAGTTCGGTAAGAGTGAGAGTTTTACAGTCAAGTAAGGCGTGGCAAGCCAACGTTAAGCTGTTGAGTCGTTTTAAGTGTAATTCGGGGCAGAATTGGTAAAGAGAGTCGTGTAAAATATCGAGTTCGCACATTTTGTTGTCTGATTATTGATTTTTGGCGAAACCATTTGATCATATGACAAGATGTG‑TATCTACCTTAACTTAATGATTTTGATAAAAATCATTAGGGGATTCATCAGGGTAAAGCATAAAAGGCTgg                                                                          >  1:57620/1‑298 (MQ=255)                                                                  ttattgtttgtttgCGCTTTGGTTGGCAGGTTACGGCCAAGTTCGGTAAGAGTGAGAGTTTTACAGTCAAGTAAGGCGTGGCAAGCCAACGTTAAGCTGTTGAGTCGTGTTAAGTGTAATTCGGGGCAGAATTGGTAAAGAGAGTCGTGTAAAATATCGAGTTCGCACATTTTGTTGTCTGATTATTGATTTTTGGCGAAACCATTTGATCATATGACAAGATGTG‑TATCTACCTTAACTTAATGATTTTGATAAAAATCATTAGGGGATTCATCAGGGTAAAGCATAAAAGGCTGGt                                                                         <  2:730896/292‑1 (MQ=255)                                                                    atgttTTGTTCTCGCTTTGGTTGGCAGGTTACGGCCAAGTTCGGTAAGAGTGAGAGTTTTACAGTCAAGTAAGGCGTGGCAAGCCAACGTTAAGCTGTTGAGTCGTTTTAAGTGTAATTCGGGGCAGAATTGGTAAAGAGAGTCGTGTAAAATATCGAGTTCGCACATTTTGTTGTCTGATTATTGATTTTTGGCGAAACCATTTGATCATATGACAAGATGTG‑TATCTACCTTAACTTAATGATTTTGATAAAAATCATTAGGGGATTCATCAGGGTAAAGCATAAAAGGCTGGTCa                                                                       <  1:916389/298‑1 (MQ=255)                                                                                cgttttGGTTGGAAGGTTACGGCCAAGTTCGGTAAAGGTGAGAGTTTTACAGTCAAGTAAGGCGTGGCAAGCCAACGTTAAGCTGTTGAGTCGTTTTAAGTGTAATTCGGGGCAGAATTGGTAAAGAGAGTCGTGTAAAATATCGAGTTCGCACATTTTGTTGTCTGATTATTGATTTTTGGCGAAACCATTTGATCATATGACAAGATGTG‑TATCTACCTTAACTTAATGATTTTGATAAAAATCATTAGGGGATTCATCAGGGTAAAGCATAAAAGGCTGGTCAAGTGTTTTGGCa                                                           <  2:70849/295‑1 (MQ=255)                                                                                        ttggCAGGTTACGGCCAAGTTCGGTAAGAGTGAGAGTTTTACAGTCAAGTAAGGCGTGGCAAGCCAACGTTAAGCTGTTGAGTCGTTTTAAGTGTAATTCGGGGCAGAATTGGTAAAGAGAGTCGTGTAAAATATCGAGTTCGCACATTTTGTTGTCTGATTATTGATTTTTGGCGAAACCATTTGATCATATGACAAGATGTG‑TATCTACCTTAACTTAATGATTTTGATAAAAATCATTAGGGGATTCATCAGGGTAAAGCATAAAAGGCTGGTCAAGTGTTTTGGCACGATcaac                                                   <  1:413444/298‑1 (MQ=255)                                                                                         tggCGGGGTAGGGCCAAGTTAGGTAAGGGTGAGAGTTTTACAGTGAAGTAAGGCGTGGCAAGCCAACGTTAAGTTGTTGAGTCGTTTTAAGTGTAATTCGGGGCAGAATTGGTAAAGAGAGTCGTGTAAAATATCGAGTTCGCACATTTTGTTGTCTGATTATTGATTTTTGGCGAAACCATTTGATCATATGACAAGATGTG‑TATCTACCTTAACTTAATGATTTTGATAAAAATCATTAGGGGATTCATCAGGGTAAAGCATAAAAGGCTGGTCAAGTGTTTTGGCACGATcaaca                                                  <  2:457987/298‑1 (MQ=17)                                                                                         tggCAGGTTACGGCCAAGTTCGGTAAGAGTGAGAGTTTTACAGTCAAGTAAGGCGTGGCAAGCCAACGTTAAGCTGTTGAGTCGTTTTACGTGTAATTCGGGGCAGCATTGGTAAAGAGAGTCGTGTAAAATATCGAGTTCGCACATTTTGTAGTCTGATTATTGATTTTTGGCGAAACCATTTGATCATATGACAAGATGTG‑TATATACTTTACTTTAATGATTTTGATAAAAATCATTAGTGGCTTCATCAGGGTAAAGCATAACAGGCTGGACACCTGtttggcaaagatcacaa                                                  >  2:90235/1‑284 (MQ=11)                                                                                          ggCAGGTTACGGCCAAGTTCGGTAAGAGTGAGAGTTTTACAGTCAAGTAAGGCGTGGCAAGCCAACGTTAAGCTGTTGAGTCGTTTTAAGTGTAATTCGGGGCAGAATTGGTAAAGAGAGTCGTGTAAAATATCGAGTTCGCACATTTTGTTGTCTGATTATTGATTTTTGGCGAAACCATTTGATCATATGACAAGATGTG‑TATCTACCTTAACTTAATGATTTTGATAAAAATCATTAGGGGATTCATCAGGGTAAAGCATAAAAGGCTGGTCAAGTGTTTTGGCACGATcaacaa                                                 >  1:723043/1‑298 (MQ=255)                                                                                                   cGGCCAAGTTCGGTAAGAGTGAGAGTTTTACAGTCAAGTAAGGCGTGGCAAGCCAACGTTAAGCTGTTGAGTCGTTTTAAGTGTAATTCGGGGCAGAATTGGTAAAGAGAGTCGTGTAAAATATCGAGTTCGCACATTTTGTTGTCTGATTATTGATTTTTGGCGAAACCATTTGATCATATGACAAGATGTG‑TATCTACCTTAACTTAATGATTTTGATAAAAATCATTAGGGGATTCATCAGGGTAAAGCATAAAAGGCTGGTCAAGTGTTTTGGCACGATCAACAACGCCAATTg                                        >  2:110454/1‑298 (MQ=255)                                                                                                    ggCCAAGTTCGGTAAGAGTGAGAGTTTTACAGTCAAGTAAGGCGTGGCAAGCCAACGTTAAGCTGTTGAGTCGTTTTAAGTGTAATTCGGGGCAGAATTGGTAAAGAGAGTCGTGTAAAATATCGAGTTCGCACATTTTGTTGTCTGATTATTGATTTTTGGCGAAACCATTTGATCATATGACAAGATGTG‑TATCTACCTTAACTTAATGATTTTGATAAAAATCATTAGGGGATTCATCAGGGTAAAGCATAAAAGGCTGGTCAAGTGTTTTGGCACGATCAACAACGCCAATTGc                                       <  1:17312/298‑1 (MQ=255)                                                                                                       cAAGTTGGGTAAGAGTGAGAGTTTTACGGTCAAGTAAGGCGTGGCAAGACAAAGTTAAGCTGTTGAGGTGTTTTAAGTGTAATTCGGGGCAGAATTGGTAAAGAGAGTCGTGTAAAATATCGAGTTCGCACATTTTGTTGTCTGATTATTGATTTTTGGCGAAACCATTTGATCATATGACAAGATGTG‑TATCTACCTTAACTTAATGATTGTGATAAAAATCATTAGGGGATTCATCAGGGTAAAGCATAAAAGGCTGGTCAAGTGTTTTGGCACGATCAACAACGCCAATTGCCTc                                    <  2:671217/298‑1 (MQ=17)                                                                                                        aaGTTCGGTAAGAGTGAGAGTTTTACAGTCAAGTAAGGCGTGGCAAGCCAACGTTAAGCTGTTGAGTCGTTTTAAGTGTAATTCGGGGCAGAATTGGTAAAGAGAGTCGTGTAAAATATCGAGTTCGCACATTTTGTTGTCTGATTATTGATTTTTGGCGAAACCATTTGATCATATGACAAGATGTG‑TATCTACCTTAACTTAATGATTTTGATAAAAATCATTAGGGGATTCATCAGGGTAAAGCATAAAAGGCTGGTCAAGTGTTTTGGCACGATCAACAACGCCAATTGCCTCa                                   >  1:638754/1‑298 (MQ=255)                                                                                                        aaGATCGGTAAGAGTGAGAGGTTTACAGTCAAGTAAGGCGTGGCAAGCAAACGTTAAGCTGTTGAGTCGTTTTAAGTGTAATTCGGTGCAGAATTGGTAAAGAGAGTCGTGTAAAATATCGAGTTCGCACATTTTGTTGTCTGATTATTGATTTTTGGCGAAACCATTTGATCATATGACAAGATGTG‑TATCTACCTTAACTTAATGATTTTGATAAAAATCATTAGGGGATTCATCAGGGTAAAGCATAAAAGGCTGGTCAAGTGTTTTGGCACGATCAACAACGCCAATTGCCTCa                                   <  2:505181/298‑1 (MQ=255)                                                                                                              ggTAAGAGTGAGAGTTTTACAGTCAAGTAAGGCGTGGCAAGCCAACGTTAAGCTGTTGAGTCGTTTTAAGTGTAATTCGGGGCAGAATTGGTAAAGAGAGTCGTGTAAAATATCGAGTTCGCACATTTTGTTGTCTGATTATTGATTTTTGGCGAAACCATTTGATCATATGACAAGATGTG‑TATCTACCTTAACTTAATGATTTTGATAAAAATCATTAGGGTATTCACAAGGGTAAAGCCTAAAAGGCTGGTAAAGTGTTTTGGCACGATCAACAACGCCAATACCCTCATCGGtt                             >  2:464699/1‑298 (MQ=17)                                                                                                                         gagTTTTACAGTCAAGTAAGGCGTGGCAAGCCAACGTTAAGCTGTTGAGTCGTTTTAAGTGTAATTCGGGGCAGAATTGGTAAAGAGAGTCGTGTAAAATATCGAGTTCGCACATTTTGTTGTCTGATTATTGATTTTTGGCGAAACCATTTGATCATATGACAAGATGTG‑TATCTACCTTAACTTAATGATTTTGATAAAAATCATTAGGGGATTCATCAGGGTAAAGCATAAAAGGCTGGTCAAGTGTTTTGGCACGATCAACAACGCCAATTGCCTCATCGGTTAACTGATCGCt                  >  1:997062/1‑298 (MQ=255)                                                                                                                            ttttACAGTCAAGTAAGGCGTGGCAAGCCAACGTTAAGCTGTTGAGTCGTTTTAAGTGTAATTCGGGGCAGAATTGGTAAAGAGAGTCGTGTAAAATATCGAGTTCGCACATTTTGTTGTCTGATTATTGATTTTTGGCGAAACCATTTGATCATATGACAAGATGTG‑TATCTACCTTAACTTAATGATTTTGATAAAAATCATTAGGGGATTCATCAGGGTAAAGCATAAAAGGCTGGTCAAGTGTTTTGGCACGATCAACAACGCCAATTGCCTCATCGGTTAACTGATCGCTGat               <  1:31955/298‑1 (MQ=255)                                                                                                                                  aGTCAAGTAAGGCGTGGCAAGCCAACGTTAAGCTGTTGAGTAGTTTTAAGTGTAATTCGGGGCAGAATTGGTAAAGAGAGTCGTGTAAAATATCGAGTTAGCACATTTTGTTGTCTGATTATTGATTTTTGGCGAAACCATTTGATCATATGACAAGATGTG‑TATCTACCTTAACTTAATGATTTTGATCACAATTCTTAGGGGATTCAACAGGGTAAAGCATAAAAGGCTGGTCAAGTGTTTTGGCACGATACACGAAGCAAATTCCCTTCTCGGTTAACTAATCGCAtatatacac         >  2:256235/1‑295 (MQ=14)                                                                                                                                      aaGTAAGGCGTGGCAAGCCAACGTTAAGCTGTTGAGTCGTTTTAAGTGTAATTCGGGGCAGAATTGGTAAAGAGAGTCGTGTAAAATATCGAGTTCGCACATTTTGTTGTCTGATTATTGATTTTTGGCGAAACCATTTGATCATATGACAAGATGTG‑TATCTACCTTAACTTAATGATTTTGATAAAAATCATTAGGGGATTCATCAGGGTAAAGCATAAAAGGCTGGTCAAGTGTTTTGGCACGATca                                                     <  2:303529/250‑1 (MQ=255)                                                                                                                                      aaGTAAGGCGTGGCAAGCCAACGTTAAGCTGTTGAGTCGTTTTAAGTGTAATTCGGGGCAGAATTGGTAAAGAGAGTCGTGTAAAATATCGAGTTCGCACATTTTGTTGTCTGATTATTGATTTTTGGCGAAACCATTTGATCATATGACAAGATGTG‑TATCTACCTTAACTTAATGATTTTGATAAAAATCATTAGGGGATTCATCAGGGTAAAGCATAAAAGGCTGGTCAAGTGTTTTGGCACGATca                                                     >  1:303529/1‑250 (MQ=255)                                                                                                                                      aaGTAAGGCGTGGCAAGCCAACGTTAAGCTGTTGAGTCGTTTTAAGTGTAATTCGGGGCAGAATTGGTAAAGAGAGTCGTGTAAAATATCGAGTTCGCACATTTTGTTGTCTGATTATTGATTTTTGGCGAAACCATTTGATCATATGACAAGATGTG‑TATCTACCTTAACTTAATGATTTTGATAAAAATCATTAGGGGATTCATCAGGGTAAAGCATAAAAGGCTGGTCAAGTGTTTTGGCACGATca                                                     <  2:507785/250‑1 (MQ=255)                                                                                                                                      aaGTAAGGCGTGGCAAGCCAACGTTAAGCTGTTGAGTCGTTTTAAGTGTAATTCGGGGCAGAATTGGTAAAGAGAGTCGTGTAAAATATCGAGTTCGCACATTTTGTTGTCTGATTATTGATTTTTGGCGAAACCATTTGATCATATGACAAGATGTG‑TATCTACCTTAACTTAATGATTTTGATAAAAATCATTAGGGGATTCATCAGGGTAAAGCATAAAAGGCTGGTCAAGTGTTTTGGCACGATca                                                     >  1:507785/1‑250 (MQ=255)                                                                                                                                       aGTAAGGCGTGGCAAGCCAACGTTAAGCTGTTGAGTCGTTTTAAGTGTAATTCGGGGCAGAATTGGTAAAGAGAGTCGTGTAAAATATCGAGTTCGCACATTTTGTTGTCTGATTATTGATTTTTGGCGAAACCATTTGATCATATGACAAGATGTG‑TATCTACCTTAACTTAATGATTTTGATAAAAATCATTAGGGGATTCATCAGGGTAAAGCATAAAAGGCTGGTCAAGTGTTTTGGCACGATCAACAACGCTAATTGCCTCATCGGTTAACTGATCGCTGATATAACCTTTTg    <  1:228911/298‑1 (MQ=255)                                                                                                                                         tAAGGCGTGGCAAGCCAACGTTAAGCTGTTGAGTCGTTTTAAGTGTAATTCGGGGCAGAATTGGTAAAGAGAGTCGTGTAAAATATCGAGTTCGCACATTTTGTTGTCTGATTATTGATTTTTGGCGAAACCATTTGATCATATGACAAGATGTG‑TATCTACCTTATCTTAATGATTTTGATAAAAATCATTAGGGGATTCATCAGGGTAAAGCATAAAAGGCTGGTCAAGTGTTTTGGCACGATCAACAACGCCAATTGCCTCATCGGTTAACTGATCGCTGATATAACCTTTTGCg  <  2:360936/298‑1 (MQ=255)                                                                                                                                            |                                                                                                                                                                                                                                                                                                        GGTATACAGCGAGTCGCTCTTTGTGGAGGTGACGATTACCTAACAATCGGTCGATTCGTTTGATGTTATGTTTTGTTCTCGCTTTGGTTGGCAGGTTACGGCCAAGTTCGGTAAGAGTGAGAGTTTTACAGTCAAGTAATGCGTGGCAAGCCAACGTTAAGCTGTTGAGTCGTTTTAAGTGTAATTCGGGGCAGAATTGGTAAAGAGAGTCGTGTAAAATATCGAGTTCGCACATCTTGTTGTCTGATTATTGATTTTTCGCGAAACCATTTGATCATATGACAAGATGTG‑TATCTACCTTAACTTAATGATTTTGATAAAAATCATTAGGGGATTCATCAGGGTAAAGCATAAAAGGCTGGTCAAGTGTTTTGGCACGATCAACAACGCCAATTGCCTCATCGGTTAACTGATCGCTGATATAACCTTTTGCG  >  CP006584/1645162‑1645595

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 10 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑