Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	CP006584	1,563,748	A→G	E343E (GAA→GAG)	LY180_07445 →	transposase IS609

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP006584	1,563,748	0	A	G	95.7%	38.3 / ‑4.9	23	E343E (GAA→GAG)	LY180_07445	transposase IS609
Reads supporting (aligned to +/- strand):  ref base A (1/0);  new base G (8/14);  total (9/14)
Fisher's exact test for biased strand distribution p-value = 3.91e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.96e-01

GGGCAAAATCAGGTTTAAACCGTTCGATACTGGATCAGGGCTGGTATGAAATGCGCCGCCAGCTTGAGTACAAGCAGCTCTGGCGTGGCGGTCAGGTGCTTGCTGTTCCGCCAGCGTACACAAGCCAGCGTTGCGCGTGCTGTGGTCATACAGCGAAAGAAAATCGCCTGTCACAAAGTAAATTCAGATGCCAGGTATGTGGATATACAGCGAACGCCGATGTAAATGGCGCTCGTAACATTTTAGCGGCGGGGCACGCCGTTCTTGCCTGTGGAGAGATGGTGCAGTCAGGCCGCCCGTTGAAGCAG‑GAACCCACCGAAATGATTCAGGCGACAGCCTGAACGTAGCAGGGATCCACGTCCTTCAGGGCGTGGAGGATGTCAATATCGGTTTCTGTCAGCGATTAAATTCAACACCACGTAACAAACGCCTCCGGCAATTAATCCC  >  CP006584/1563588‑1564034                                                                                                                                                                 |                                                                                                                                                                                                                                                                                                gggCAAAATCAGGTTTAAACCGTTCGATACTGGATCAGGGCTGGTATGAAATGCACCGCCAGCTTGAGTACAAGCAGCTCTGGCGTGGCGGTCAGGTGCTTGCTGTTCCGCCAGCGTATACAAGCCAGCGTTGCGCGTACTGTGGTCATACAGCGAAAGAGAACCGCCTGTCACAAAGTAAATTCAGATGCCAGGTATGTGGATATACAGCGAACGCCGATGTAAATGGCGCTCGTAACATTTTAGCGGCGGGGCACGCCGTTCTTGCCTGTGGAGAGATGGTGCAGTCAGGCCGCCCg                                                                                                                                                       <  1:492565/299‑1 (MQ=9)     aaaaTCAGGTTTAAACCGTTCGATACTGGATCAGGGCTGGTATGAAATGCACCGCCAGCTTGAGTACAAGCAGCTCTGGCGTGGCGGTCAGGTGCTTGCTGTTCCGCCAGCGTATACAAGCCAGCGTTGCGCGTACTGTGGTCATACAGCGAAAGAGAACCGCCTGTCACAAAGTAAATTCAGATGCCAGGTATGTGGATATACAGCGAACGCCGATGTAAATGGCGCTCGTAACATTTTAGCGGCGGGGCACGCCGTTCTTGCCTGTGGAGAGGTGGTGCAGGCAGGCCGCCCGTTGa                                                                                                                                                   >  1:113794/1‑299 (MQ=9)         tCAGGTTTAAACCGTTCGATACTGGATCAGGGCTGGTATGAAATGCACCGCCAGCTTGAGTACAAGCAGCTCTGGCGTGGCGGTCAGGTGCTTGCTGTTCCGCCAGCGTATACAAGCCAGCGTTGCGCGTACTGTGGTCATACAGCGAAAGAGAACCGCCTGTCACAAAGTAAATTCAGATGCCAGGTATGTGGATATACAGCGAACGCCGATGTAAATGGCGCTCGTAACATTTTAGCGGCGGGGCACGCCGTTCTTGCCTGTGGAGAGATGGTGCAGTCAGGCCGCCCGTTGAAGCa                                                                                                                                               <  1:241476/299‑1 (MQ=9)                   aCCGTTCGATACTGGATCAGGGCTGGTATGAAATGCACCGCCAGCTTGAGTACAAGCAGCTCTGGCGTGGCGGTCAGGTGCTTGCTGTTCCGCCAGCGTATACAAGCCAGCGTTGCGCGTACTGTGGTCATACAGCGAAAGAGAACCGCCTGTCACAAAGTAAATTCAGCTGCCAGGTATGTGGATATACAGCGAACGCCGATATAAATGGCCCTCGTAACATTTTAGCGGCGGGGCACGCCGTTTCTGCCGTGGGAGCAACGGTGTACGCAGGCCGCCCCTTGagcgaggcaccacac                                                                                                                                     >  2:24188/1‑285 (MQ=11)                        tcgagcggggtgcAGGGCTGGTTAGAAATGGACCGCCAGCTTGGGTAAAAGCAGTGCGGCCGGGGCGGACGGGGGCTTGCTGTGCCGCCAGCGTATACAAGCCAGCGTTGCGCGTACTGTGGTCATACAGCGAAAGAGAACCGCCTGTCACAAAGTAAATTCAGATGCCAGGTATGTGGATATACAGCGAACGCCGATGTAAATGGCGCTCGTAACATTTTAGCGGCGGGGCACGCCGTTCTTGCCTGTGGAGAGATGGTGCAGTCAGGCCGCCCGTTGAAGCAG‑GAACCCACCGAAAt                                                                                                                               <  2:355925/287‑1 (MQ=11)                         caagaCTGGGTCAGGGTGGGTAGGGAGTGGACCGCCGGCGTGAGTACACGCAGAGCTGTCGGGGCGGGCCGGGGCTGGCTGTTCCGCCAGCGTAAACGAGCCAGCGTTGCGCGGACTGTGGTCAGACAGCGAAAGAGAACCGCCGGTCACAAAGTAAAGTCGGATGCCAGGTATGTGGATATACAGCGAACGCCGATGTAAATGGCGCTCGGAACATTTTAGCGGCGGGGCACGCCGTTCTTGCCTGTGGAGAGATGGTGCAGTCAGGCCGCCCGTTGAAGCAG‑GAACCCACCGAAATg                                                                                                                              <  2:635718/295‑1 (MQ=11)                          gATACTGGATCAGGGCTGGTATGAAATGCACCGCCAGCTTGAGTACAAGCAGCTCTGGCGTGGCGGTCAGGTGCTTGCTGTTCCGCCAGCGTATACAAGCCAGCGTTGCGCGTACTGTGGTCATACAGCGAAAGAGAACCGCCTGTCACAAAGTAAATTCAGATGCCAGGTATGTGGATATACAGCGAACGCCGATGTAAATGGCGCTCGTAACATTTTAGCGGCGGGGCACGCCGTTCTTGCCTGTGGAGAGATGGTGCAGTCAGGCCGCCCGTTGAAGCAG‑GAACCCACCGAAATGa                                                                                                                             >  1:605349/1‑299 (MQ=9)                                 gATCAGGGCTGGTATGAAATGCACCGCCAGCTTGAGTACAAGCAGCTCTGGCGTGGCGGTCAGGTGCTTGCTGTTCCGCCAGCGTATACAAGCCAGCGTTGCGCGTACTGTGGTCATACAGCGAAAGAGAACCGCCTGTCACAAAGTAAATTCAGATGCCAGGTATGTGGATATACAGCGAACGCCGATGTAAATGGCGCTCGTAACATTTTAGCGGCGGGGCACGCCGTTCTTGCCTGTGGAGAGATGGTGCAGTCAGGCCGCCCGTTGAAGCAG‑GAACCCACCGAAATGATTCAGGc                                                                                                                      >  1:324899/1‑299 (MQ=9)                                        gCTGGTATGAAATGCACCGCCAGCTTGAGTACAAGCAGCTCTGGCGTGGCGGTCAGGTGCTTGCTGTTCCGCCAGCGTATACAAGCCAGCGTTGCGCGTACTGTGGTCATACAGCGAAAGAGAACCGCCTGTCACAAAGTAAATTCAGATGCCAGGTATGTGGATATACAGCGAACGCCGATGTAAATGGCGCTCGTAACATTTTAGCGGCGGGGCACGCCGTTCTTGCCTGTGGAGAGATGGTGCAGTCAGGCCGCCCGTTGAAGCAG‑GAACCCACCGAAATGATTCAGGCGACAGcc                                                                                                               <  1:277383/299‑1 (MQ=9)                                         cTGGTATGAAATGCACCGCCAGCTTGAGTACAAGCAGCTCTGGCGTGGCGGTCAGGTGCTTGCTGTTCCGCCAGCGTATACAAGCCAGCGTTGCGCGTACTGTGGTCATACAGCGAAAGAGAACCGCCTGTCACAAAGTAAATTCAGATGCCAGGTATGTGGATATACAGCGAACGCCGATGTAAATGGCGCTCGTAACATTTTAGCGGCGGGGCACGCCGTTCTTGCCTGTGGAGAGATGGTGCAGTCAGGCCGCCCGTTGAAGCAG‑GAACCCACCGAAATGATTCAGGCGACAGCCt                                                                                                              >  1:517078/1‑299 (MQ=9)                                          tGGTATGAAATGCACCGCCAGCTTGAGTACAAGCAGCTCTGGCGTGGCGGTCAGGTGCTTGCTGTTCCGCCAGCGTATACAAGCCAGCGTTGCGCGTACTGTGGTCATACAGCGAAAGAGAACCGCCTGTCACAAAGTAAATTCAGATGCCAGGTATGTGGATATACAGCGAACGCCGATGTAAATGGCGCTCGTAACATTTTAGCGGCGGGGCACGCCGTTCTTGCCTGTGGAGAGATGGTGCAGTCAGGCCGCCCGTTGAAGCAG‑GAACCCACCGAAATGATTCAGGCGACAGCCTg                                                                                                             >  1:420871/1‑299 (MQ=9)                                                      caccgccAGCTTGAGTACAAGCAGCTCTGGCGTGGCGGTCAGGTGCTTGCTGTTCCGCCAGCGTATACAAGCCAGCGTTGCGCGTACTGTGGTCATACAGCGAAAGAGAACCGCCTGTCACAAAGTAAATTCAGATGCCAGGTATGTGGATATACAGCGAACGCCGATGTAAATGGCGCTCGTAACATTTTAGCGGCGGGGCACGCCGTTCTTGCCTGTGGAGAGATGGTGCAGTCAGGCCGCCCGTTGAAGCAG‑GAACCCACCGAAATGATTCAGGCGACAGCCTGAACGTAGCAggg                                                                                                 <  1:400945/297‑1 (MQ=17)                                                          gccAGCTTGAGTACAAGCAGCTCTGGCGTGGCGGTCAGGTGCTTGCTGTTCCGCAAGCGTACACAAGCCAGCGTTGCGCGTGCTGTGGTCATAAAGCGAAAGAAAATCGCCTGTCACAAAGTAAATTCAGATGCCCGGTATGAGGATATACAGCGACCGCCGAAGTAAATGGCGCTCGTAACATTTTAGCGGAGGGGCACGCCTTCATTTCCCGGGGAGAGCTCGTTCAGTCAGGCCGCCCCTGGAA‑CAGAGAACCCACCCAAATGACTCGCGCACAAGCCCGAACCCAGCAGGGAAcc                                                                                             >  2:13248/1‑299 (MQ=11)                                                                ttGAGTACAAGCAGCTCTGGCGTGGCGGTCAGGTGCTTGCTGTTCCGCCAGCGTATACAAGCCAGCGTTGCGCGTACTGTGGTCATACAGCGAAAGAGAACCGCCTGTCACAAAGTAAATTCAGATGCCAGGTATGTGGATATACAGCGAACGCCGATGTAAATGGCGCTCGTAACATTTTAGCGGCGGGGCACGCCGTTCTTGCCTGTGGAGAGATGGTGCAGTCAGGCCGCCCGTTGAAGCAG‑GAACCCACCGAAATGATTCAGGCGACAGCCTGAACGTAGCAGGGATCCACGTcc                                                                                       <  1:55653/299‑1 (MQ=17)                                                                    gTACAAGCAGCTCTGGCGTGGCGGTCAGGTGCTTGCTGTTCCGCCAGCGTATACAAGCCAGCGTTGCGCGTACTGTGGTCATACAGCGAAAGAGAACCGCCTGTCACAAAGTAAATTCAGATGCCAGGTATGTGGATATACAGCGAACGCCGATGTAAATGGCGCTCGTAACATTTTAGCGGCGGGGCACGCCGTTCTTGCCTGTGGAGAGATGGTGCAGTCAGGCCGCCCGTTGAAGCAG‑GAACCCACCGAAATGATTCAGGCGACAGCCTGAACGTAGCAGGGATCCACGTCCTTCa                                                                                   <  1:70731/299‑1 (MQ=17)                                                                        aaGCAGCTCTGGCGTGGCGGTCAGGTGCTTGCTGTTCCGCCAGCGTATACAAGCCAGCGTTGCGCGTACTGTGGTCATACAGCGAAAGAGAACCGCCTGTCACAAAGTAAATTCAGATGCCAGGTATGTGGATATACAGCGAACGCCGATGTAAATGGCGCTCGTAACATTTTAGCGGCGGGGCACGCCGTTCTTGCCTGTGGAGAGATGGTGCAGTCAGGCCGCCCGTTGAAGCAG‑GAACCCACCGAAATGATTCAGGCGACAGCCTGAACGTAGCAGGGATCCACGTCCTTCAGGGc                                                                               >  1:77320/1‑299 (MQ=17)                                                                        aaGCAGCTCTGGCGTGGCGGTCAGGTGCTTGCTGTTCCGCCAGCGTATACAAGCCAGCGTTGCGCGTACTGTGGTCATACAGCGAAAGAGAACCGCCTGTCACAAAGTAAATTCAGATGCCAGGTATGTGGATATACAGCGAACGCCGATGTAAATGGCGCTCGTAACATTTTAGCGGCGGGGCACGCCGTTCTTGCCTGTGGAGAGATGGTGCAGTCAGGCCGCCCGTTGAAGCAG‑GAACCCACCGAAATGATTCAGGCGACAGCCTGAACGTAGCAGGGATCCACGTCCTTCAGGGc                                                                               <  1:98370/299‑1 (MQ=17)                                                                             gcTCTGGCGTGGCGGTCAGGTGCTTGCTGTTCCGCCAGCGTATACAAGCCAGCGTTGCGCGTACTGTGGTCATACAGCGAAAGAGAACCGCCTGTCACAAAGTAAATTCAGATGCCAGGTATGTGGATATACAGCGAACGCCGATGTAAATGGCGCTCGTAACATTTTAGCGGCGGGGCACGCCGTTCTTGCCTGTGGAGAGATGGTGCAGTCAGGCCGCCCGTTGAAGCAG‑GAACCCACCGAAATGATTCAGGCGACAGCCTGAACGTAGCAGGGATCCACGTCCTTCAGGGCGTgga                                                                          <  1:606665/299‑1 (MQ=17)                                                                                          ggTCAGGTGCTTGCTGTTCCGCCAGCGTATACAAGCCAGCGTTGCGCGTACTGTGGTCATACAGCGAAAGAGAACCGCCTGTCACAAAGTAAATTCAGATGCCAGGTATGTGGATATACAGCGAACGCCGATGTAAATGGCGCTCGTAACATTTTAGCGGCGGGGCACGCCGTTCTTGCCTGTGGAGAGATGGTGCAGTCAGGCCGCCCGTTGAAGCAG‑GAACCCACCGAAATGATTCAGGCGACAGCCTGAACGTAGCAGGGATCCACGTCCTTCAGGGCGTGGAGGATGTCAATATc                                                             <  1:66760/299‑1 (MQ=18)                                                                                                            ccgccgGCGTAAACATGGGAGCGTTGCGGGTAGTGTGGTCATACAGCGAAAGAGAACCGCCCGGCACATAGTAAATTAAGATGCCAGGTATGTGGATAGACAGCGAACGCCGATGTAAATGGCTCGCGTAACATTTTAGCGGCGGGGCACGCCGTTCTGGCCTGTGGAGGGATGGTGCAGTCAGGCCGCCCGTTGAAGCAG‑GAACCCACCGAAATGATTCAGGCGACAGCCTGAACGTAGCAGGGATCCACGTCCTTCAGGGCGTGGAGGATGTCAATATCGGTTTCTGTCAGCGATTa                                           <  2:313584/299‑1 (MQ=14)                                                                                                                              cAGCGTTGCGCGTACTGTGGTCATACAGCGAAAGAGAACCGCCTGTCACAAAGTAAATTCAGATGCCAGGTATGTGGATATACAGCGAACGCCGATGTAAATGGCGCTCGTAACATTTTAGCGGCGGGGCACGCCGTTCTTGCCTGTGGAGAGACGGTGCAGTCAGGCCGCCCGTTGAAGCAG‑GAACCCACCGAAATGATTCAGGCGACAGCCTGAACGTAGCAGGGATCCACGTCCTTCAGGGCGTGGAGGATGTCAATATCGGTTTCTGTCAGCGATTAAATTCAACACCACGTAAc                         >  1:221308/1‑299 (MQ=255)                                                                                                                                         gtacTGTGGTCATACAGCGAAAGAGAACCGCCTGTCACAAAGTAAATTCAGATGCCAGGTATGTGGATATACAGCGAACGCCGATGTAAATGGCGCTCGTAACATTTTAGCGGCGGGGCACGCCGTTCTTGCCTGTGGAGAGATGGTGCAGTCAGGCCGCCCGTTGAAGCAG‑GAACCCACCGAAATGATTCAGGCGACAGCCTGAACGTAGCAGGGATCCACGTCCTTCAGGGCGTGGAGGATGTCAATATCGGTTTCTGTCAGCGATTAAATTCAACACCACGTAACAAACGCCTCCg              <  1:660862/296‑1 (MQ=255)                                                                                                                                                     tACAGCGAAAGAGAACCGCCTGTCACAAAGTAAATTCAGATGCCAGGTATGTGGATATACAGCGAACGCCGATGTAAATGGCGCTCGTAACATTTTAGCGGCGGGGCACGCCGTTCTTGCCTGTGGAGAGATGGTGCAGTCAGGCCGCCCGTTGAAGCAG‑GAACCCACCGAAATGATTCAGGCGACAGCCTGAACGTAGCAGGGATCCACGTCCTTCAGGGCGTGGAGGATGTCAATATCGGTTTCTGTCAGCGATTAAATTCAACACCACGTAACAAACGCCTCCGGCAATTAATccc  <  1:24188/299‑1 (MQ=255)                                                                                                                                                                 |                                                                                                                                                                                                                                                                                                GGGCAAAATCAGGTTTAAACCGTTCGATACTGGATCAGGGCTGGTATGAAATGCGCCGCCAGCTTGAGTACAAGCAGCTCTGGCGTGGCGGTCAGGTGCTTGCTGTTCCGCCAGCGTACACAAGCCAGCGTTGCGCGTGCTGTGGTCATACAGCGAAAGAAAATCGCCTGTCACAAAGTAAATTCAGATGCCAGGTATGTGGATATACAGCGAACGCCGATGTAAATGGCGCTCGTAACATTTTAGCGGCGGGGCACGCCGTTCTTGCCTGTGGAGAGATGGTGCAGTCAGGCCGCCCGTTGAAGCAG‑GAACCCACCGAAATGATTCAGGCGACAGCCTGAACGTAGCAGGGATCCACGTCCTTCAGGGCGTGGAGGATGTCAATATCGGTTTCTGTCAGCGATTAAATTCAACACCACGTAACAAACGCCTCCGGCAATTAATCCC  >  CP006584/1563588‑1564034

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 9 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑