Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	CP006584	1,563,706	C→T	Y329Y (TAC→TAT)	LY180_07445 →	transposase IS609

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP006584	1,563,706	0	C	T	90.5%	27.0 / ‑5.7	22	Y329Y (TAC→TAT)	LY180_07445	transposase IS609
Reads supporting (aligned to +/- strand):  ref base C (1/0);  major base T (7/12);  minor base A (0/2);  total (8/14)
Fisher's exact test for biased strand distribution p-value = 5.33e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CGACTGCATTCCTGTATCGCAAATATCCGCAGGGACTACCTTCACAAAGTCACAACGACCGTCAGCAAAAACCACGCAATGATAGTCATTGAGGATTTGAAGGTCAGCAACATGTCAAAGTCAGCAGCGGGTACGGTCAGCCAGCCGGGGCGCAATGTCCGGGCAAAATCAGGTTTAAACCGTTCGATACTGGATCAGGGCTGGTATGAAATGCGCCGCCAGCTTGAGTACAAGCAGCTCTGGCGTGGCGGTCAGGTGCTTGCTGTTCCGCCAGCGTACACAAGCCAGCGTTGCGCGTGCTGTGGTCATACAGCGAAAGAAAATCGCCTGTCACAAAGTAAATTCAGATGCCAGGTATGTGGATATACAGCGAACGCCGATGTAAATGGCGCTCGTAACATTTTAGCGGCGGGGCACGCCGTTCTTGCCTGTGGAGAGATGGTGCAGTCAGGCCGCCCGTTGAAGCAG‑GAACCCACCGAAATGATTCAGGCGACAGCCTGAACGTAGCAGGGATCCACGTCCTTCAGGGCGTGGAGGATGTCAATATCGGTTTCTGTCAGCGATTA  >  CP006584/1563428‑1563993                                                                                                                                                                                                                                                                                       |                                                                                                                                                                                                                                                                                                 cGACTGCATTCCTGTATCGCAAATATCCGCAGGGACTACCTTCACAAAGTCACAACGGCCGTCAGCAAAAACCACGCAATGATAGTCATTGAGGATTTGAAGGTCAGCAACATGTCAAAGTCAGCAGCGGGTACGGTCAGCCAGCCGGGGCGCAATGTCCGGGCAAAATCAGGTTTAAACCGTTCGATACTGGATCAGGGCTGGTATGAAATGCACCGCCAGCTTGAGTACAAGCAGCTCTGGCGTGGCGGTCAGGTGCTTGCTGTTCCGCCAGCGTATACAAGCCAGCGTTGCGCGta                                                                                                                                                                                                                                                                              <  1:466014/299‑2 (MQ=14)  gACTGCATTCCTGTATCGCAAATATCCGCAGGGACTACCTTCACAAAGTCACAACGGCCGTCAGCAAAAACCACGCAATGATAGTCATTGAGGATTTGAAGGTCAGCAACATGTCAAAGTCAGCAGCGGGTACGGTCAGCCAGCCGGGGCGCAATGTCCGGGCAAAATCAGGTTTAAACCGTTCGATACTGGATCAGGGCTGGTATGAAATGCACCGCCAGCTTGAGTACAAGCAGCTCTGGCGTGGCGGTCAGGTGCTTGCTGTTCCGCCAGCGTATACAAGCCAGCGTTGCGCGtac                                                                                                                                                                                                                                                                             <  1:242514/299‑3 (MQ=14)                                                                                                                                                                 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)                                                                                                                                                                                                                                                                                       |                                                                                                                                                                                                                                                                                                 CGACTGCATTCCTGTATCGCAAATATCCGCAGGGACTACCTTCACAAAGTCACAACGACCGTCAGCAAAAACCACGCAATGATAGTCATTGAGGATTTGAAGGTCAGCAACATGTCAAAGTCAGCAGCGGGTACGGTCAGCCAGCCGGGGCGCAATGTCCGGGCAAAATCAGGTTTAAACCGTTCGATACTGGATCAGGGCTGGTATGAAATGCGCCGCCAGCTTGAGTACAAGCAGCTCTGGCGTGGCGGTCAGGTGCTTGCTGTTCCGCCAGCGTACACAAGCCAGCGTTGCGCGTGCTGTGGTCATACAGCGAAAGAAAATCGCCTGTCACAAAGTAAATTCAGATGCCAGGTATGTGGATATACAGCGAACGCCGATGTAAATGGCGCTCGTAACATTTTAGCGGCGGGGCACGCCGTTCTTGCCTGTGGAGAGATGGTGCAGTCAGGCCGCCCGTTGAAGCAG‑GAACCCACCGAAATGATTCAGGCGACAGCCTGAACGTAGCAGGGATCCACGTCCTTCAGGGCGTGGAGGATGTCAATATCGGTTTCTGTCAGCGATTA  >  CP006584/1563428‑1563993

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 9 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑