Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	CP006584	1,563,726	G→A	C336Y (TGC→TAC)	LY180_07445 →	transposase IS609

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP006584	1,563,726	0	G	A	95.2%	31.1 / ‑4.5	21	C336Y (TGC→TAC)	LY180_07445	transposase IS609
Reads supporting (aligned to +/- strand):  ref base G (1/0);  new base A (8/12);  total (9/12)
Fisher's exact test for biased strand distribution p-value = 4.29e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.81e-01

GGGCAAAATCAGGTTTAAACCGTTCGATACTGGATCAGGGCTGGTATGAAATGCGCCGCCAGCTTGAGTACAAGCAGCTCTGGCGTGGCGGTCAGGTGCTTGCTGTTCCGCCAGCGTACACAAGCCAGCGTTGCGCGTGCTGTGGTCATACAGCGAAAGAAAATCGCCTGTCACAAAGTAAATTCAGATGCCAGGTATGTGGATATACAGCGAACGCCGATGTAAATGGCGCTCGTAACATTTTAGCGGCGGGGCACGCCGTTCTTGCCTGTGGAGAGATGGTGCAGTCAGGCCGCCCGTTGAAGCAG‑GAACCCACCGAAATGATTCAGGCGACAGCCTGAACGTAGCAGGGATCCACGTCCTTCAGGGCGTGGAGGATGTCAATATCGGTTTCTGTCAGCGATTAAATTCAACACCACGTAAC  >  CP006584/1563588‑1564011                                                                                                                                           |                                                                                                                                                                                                                                                                                               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)                                                                                                                                           |                                                                                                                                                                                                                                                                                               GGGCAAAATCAGGTTTAAACCGTTCGATACTGGATCAGGGCTGGTATGAAATGCGCCGCCAGCTTGAGTACAAGCAGCTCTGGCGTGGCGGTCAGGTGCTTGCTGTTCCGCCAGCGTACACAAGCCAGCGTTGCGCGTGCTGTGGTCATACAGCGAAAGAAAATCGCCTGTCACAAAGTAAATTCAGATGCCAGGTATGTGGATATACAGCGAACGCCGATGTAAATGGCGCTCGTAACATTTTAGCGGCGGGGCACGCCGTTCTTGCCTGTGGAGAGATGGTGCAGTCAGGCCGCCCGTTGAAGCAG‑GAACCCACCGAAATGATTCAGGCGACAGCCTGAACGTAGCAGGGATCCACGTCCTTCAGGGCGTGGAGGATGTCAATATCGGTTTCTGTCAGCGATTAAATTCAACACCACGTAAC  >  CP006584/1563588‑1564011

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 9 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑