Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	CP006584	1,563,751	T→C	N344N (AAT→AAC)	LY180_07445 →	transposase IS609

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP006584	1,563,751	0	T	C	96.2%	49.7 / ‑4.7	26	N344N (AAT→AAC)	LY180_07445	transposase IS609
Reads supporting (aligned to +/- strand):  ref base T (1/0);  new base C (13/12);  total (14/12)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.97e-01

GGCAAAATCAGGTTTAAACCGTTCGATACTGGATCAGGGCTGGTATGAAATGCGCCGCCAGCTTGAGTACAAGCAGCTCTGGCGTGGCGGTCAGGTGCTTGCTGTTCCGCCAGCGTACAC‑AAGCCAGCGTTGCGCGTGCTGTGGTCATACAGCGAAAGAAAATCGCCTGTCACAAAGTAAATTCAGATGCCAGGTATGTGGATATACAGCGAACGCCGATGTAAATGGCGCTCGTAACATTTTAGCGGCGGGGCACGCCGTTCTTGCCTGTGGAGAGATGGTGCAGTCAGGCCGCCCGTTGAAGCAGGAACCCACCGAAATGATTCAGGCGACAGCCTGAACGTAGCAGGGATCCACGTCCTTCAGGGCGTGGAGGATGTCAATATCGGTTTCTGTCA‑GCGATTAAATTCAACACCACGTAACAAACGCCTCCGGCAATTAATCCCCAGAAC  >  CP006584/1563589‑1564040                                                                                                                                                                    |                                                                                                                                                                                                                                                                                                   ggCAAAATCAGGTTTAAACCGTTCGATACTGGATCAGGGCTGGTATGAAATGCGCCGCCAGCTTGAGTACAAGCAGCTCTGGCGTGGCGGTCAGGTGCTTGCTGTTCCGCCAGCGTACAC‑AAGCCAGCGTTGCGCGTGCTGTGGTCATACAGCGAAAGAAAATCGCCTGTCACAAAGTAAATTCAGATCCCAGGGATGTGGCTATACAGCGAACGCCGCTGTACATGGCGCTCGTAACATTTTAGCGGCCGGGCCGCCCGTTCTTTCCTGTTGGGGGATGGTGACGTCCGggcgccgg                                                                                                                                                             >  2:638184/1‑296 (MQ=11)   cAAAATCAGGTTTAAACCGTTCGATACTGGATCAGGGCTGGTATGAAATGCACCGCCAGCTTGAGTACAAGCAGCTCTGGCGTGGCGGTCAGGTGCTTGCTGTTCCGCCAGCGTATAC‑AAGCCAGCGTTGCGCGTACTGTGGTCATACAGCGAAAGAGAACCGCCTGTCACAAAGTAAATTCAGATGCCAGGTATGTGGATATACAGCGAACGCCGATGTAAATGGCGCTCGTAACATTTTAGCGGCGGGGCACGCCGTTCTTGCCTGTGGAGAGATGGTGCAGTCAGGCCGCCCGtt                                                                                                                                                           >  1:166164/1‑298 (MQ=9)    aaaaTCAGGTTTAAACCGTTCGATACTGGATCAGGGCTGGTATGAAATGCACCGCCAGCTTGAGTACAAGCAGCTCTGGCGTGGCGGTCAGGTGCTTGCTGTTCCGCCAGCGTATAC‑AAGCCAGCGTTGCGCGTACTGTGGTCATACAGCGAAAGAGAACCGCCTGTCACAAAGTAAATTCAGATGCCAGGTATGTGGATATACAGCGAACGCCGATGTAAATGGCGCTCGTAACATTTTAGCGGCGGGGCACGCCGTTCTTGCCTGTGGAGAGATGGTGCAGTCAGGCCGCCCGTTg                                                                                                                                                          <  1:601822/298‑1 (MQ=9)          aGGTTTAAACCGTTCGATACTGGATCAGGGCTGGTATGAAATGCACCGCCAGCTTGAGTACAAGCAGCTCTGGCGTGGCGGTCAGGTGCTTGCTGTTCCGCCAGCGTATAC‑AAGCCAGCGTTGCGCGTACTGTGGTCATACAGCGAAAGAGAACCGCCTGTCACAAAGTAAATTCAGATGCCAGGTATGTGGATATACAGCGAACGCCGATGTAAATGGCGCTCGTAACATTTTAGCGGCGGGGCACGCCGTTCTTGCCTGTGGAGAGATGGTGCAGTCAGGCCGCCCGTTGAAGCAg                                                                                                                                                    >  1:340710/1‑298 (MQ=9)                 aaCAGTTCGTTAATGGCTCAGGGGGGTTTTGCACTGCGCCGGCAGCAGGGGCACAGGCAGCTCGGGGGTAGCGGGCAGGTGCTTGCGGTT‑CGGCTGCCTAATCGAATCCAGCGTGGCGCGGACTGTGGGCATACAGCGGAAGGGAACCGGCTGTCACAAAGTAAGTTCAGATGCCAGGTATGTGGATAGACAGCGAACGCCGAGGTAAATGGCGCTCGTAACTGTGTAGCGGCGGGGCACGCCGTTCTTGCCTGTGGAGAGAGGGTGCAGTCAGGCCGCCCGTTGAAGCAGGAACCCa                                                                                                                                             <  2:324316/298‑1 (MQ=2)                  aCCGTTCGATACTGGATCAGGGCTGGTATGAAATGCACCGCCAGCTTGAGTACAAGCAGCTCTGGCGTGGCGGTCAGGTGCTTGCTGTTCCGCCAGCGTATAC‑AAGCCAGCGTTGCGCGTACTGTGGTCATACAGCGAAAGAGAACCGCCTGTCACAAAGTAAATTCAGATGCCAGGTATGTGGATATACAGCGAACGCCGATGTAAATGGCGCTCGTAACATTTTAGCGGCGGGGCACGCCGTTCTTGCCTGTGGAGAGATGGTGCAGTCAGGCCGCCCGTTGAAGCAGGAACCCAc                                                                                                                                            >  1:287437/1‑298 (MQ=9)                          aTACTGGATCAGGGCTGGTATGAAATGCACCGCCAGCTTGAGTACAAGCAGCTCTGGCGTGGCGGTCAGGTGCTTGCTGTTCCGCCAGCGTATAC‑AAGCCAGCGTTGCGCGTACTGTGGTCATACAGCGAAAGAGAACCGCCTGTCACAAAGTAAATTCAGATGCCAGGTATGTGGATATACAGCGAACGCCGATGTAAATGGCGCTCGTAACATTTTAGCGGCGGGGCACGCCGTTCTTGCCTGTGGAGAGATGGTGCAGTCAGGCCGCCCGTTGAAGCAGGAACCCACCGAAATGa                                                                                                                                    <  1:506507/298‑1 (MQ=9)                                    aGGGCTGGTATGAAATGCACCGCCAGCTTGAGTACAAGCAGCTCTGGCGTGGCGGTCAGGTGCTTGCTGTTCCGCCAGCGTATAC‑AAGCCAGCGTTGCGCGTACTGTGGTCATACAGCGAAAGAGAACCGCCTGTCACAAAGTAAATTCAGATGCCAGGTATGTGGATATACAGCGAACGCCGATGTAAATGGCGCTCGTAACATTTTAGCGGCGGGGCACGCCGTTCTTGCCTGTGGAGAGATGGTGCAGTCAGGCCGCCCGTTGAAGCAGGAACCCACCGAAATGATTCAGGCGAc                                                                                                                          >  1:379086/1‑298 (MQ=9)                                     gggCTGGTATGAAATGCACCGCCAGCTTGAGTACAAGCAGCTCTGGCGTGGCGGTCAGGTGCTTGCTGTTCCGCCAGCGTATAC‑AAGCCAGCGTTGCGCGTACTGTGGTCATACAGCGAAAGAGAACCGCCTGTCACAAAGTAAATTCAGATGCCAGGTATGTGGATATACAGCGAACGCCGATGTAAATGGCGCTCGTAACATTTTAGCGGCGGGGCACGCCGTTCTTGCCTGTGGAGAGATGGTGCAGTCAGGCCGCCCGTTGAAGCAGGAACCCACCGAAATGATTCAGGCGACa                                                                                                                         <  1:312606/298‑1 (MQ=9)                                         tGGTATGAAAGGCACCGCCAGCTTGAGTACAAGCAGCTCTGGCGTGGCGGTCAGGTGCTTGCTGTTCCGCCAGCGTATAC‑AAGCCAGCGTTGCGCGTACTGTGGTCATACAGCGAAAGAGAACCGCCTGTCACAAAGTAAATTCAGATGCCAGGTATGTGGATATACAGCGAACGCCGATGTAAATGGCGCTCGTAACATTTTAGCGGCGGGGCACGCCGTTCTTGCCTGTGGAGAGATGGTGCAGTCAGGCCGCCCGTTGAAGCAGGAACCCACCGAAATGATTCAGGCGACAGCCt                                                                                                                     <  1:1091/298‑1 (MQ=9)                                            tATGAAATGCACCGCCAGCTTGAGTACAAGCAGCTCTGGCGTGGCGGTCAGGTGCTTGCTGTTCCGCCAGCGTATAC‑AAGCCAGCGTTGCGCGTACTGTGGTCATACAGCGAAAGAGAACCGCCTGTCACAAAGTAAATTCAGATGCCAGGTATGTGGATATACAGCGAACGCCGATGTAAATGGCGCTCGTAACATTTTAGCGGCGGGGCACGCCGTTCTTGCCTGTGGAGAGATGGTGCAGTCAGGCCGCCCGTTGAAGCAGGAACCCACCGAAATGATTCAGGCGACAGCCTGaa                                                                                                                  >  1:620482/1‑298 (MQ=9)                                                      accgccAGCTTGAGTACAAGCAGCTCTGGCGTGGCGGTCAGGTGCTTGCTGTTCCGCCAGCGTATAC‑AAGCCAGCGTTGCGCGTACTGTGGTCATACAGCGAAAGAGAACCGCCTGTCACCAAGTAAATTCAGCTGCCAGGTATGTGGATATACAGCGAACGCCGATGTAACTGGCGACCGTAACATTTTAGCGGCGGGGCACGCCGTTCTAGCCCGAGGCGAGACTGTGACGCCCGGACGCCCGCTACAGCAGCAACCCCACGAAAAGATTCCGGCGACAGCCttcacggcacaggg                                                                                                        >  2:409512/2‑285 (MQ=11)                                                            aGCTTGAGTACAAGCAGCTCTGGCGTGGCGGTCAGGTGCTTGCTGTTCCGCCAGCGTATAC‑AAGCCAGCGTTGCGCGTACTGTGGTCATACAGCGAAAGAGAACCGCCTGTCACAAAGTAAATTCAGATGCCAGGTATGTGGATATACAGCGAACGCCGATGTAAATGGCGCTCGTAACATTTTAGCGGCGGGGCACGCCGTTCTTGCCTGTGGAGAGATGGTGCAGTCAGGCCGCCCGTTGAAGCAGGAACCCACCGAAATGATTCAGGCGACAGCCTGAACGTAGCAGGGATCCAc                                                                                                  >  1:652952/1‑298 (MQ=17)                                                                                 ggagcggcgGTCGGGTGCTTGCGGTTCCGCCAGCGTATAC‑AAGCCAGCGTTGCGCTTACTGTGGGCATACAGCGAAAGAGAACCGCCTGTCACAAAGTAAATTCAGAGGCCAGGTATGTGGATATACAGCGAACGCCGATGTAAAGGGCGCTCGTAACAGTGTAGCGGCGGGGCACGCCGTTCTTGCCTGTGGAGAGATGGTGCAGTCAGGCCGCCCGTTGAAGCAGGAACCCACCGAAATGATTCAGGCGACAGCCTGAACGTAGCAGGGATCCACGTCCTTCAGGGCGTGGAGGAt                                                                             <  2:116205/293‑1 (MQ=11)                                                                                     ccggtctcgggggcttggtGTTCCGCCAGCGTATAC‑AAGCCAGCGTTGCCCGTACTGTGGTCATACAGCGAAAGAGAACCGCCTGTCACAAAGTAAATTCAGATGCCAGGTATGTGGTTATACAGCGAACGCCGATGTAAATGGCGCTCGTAACATTTTAGCGGCGGGGCACGCCGTTCTTGCCTGTGGAGAGATGGTGCAGTCAGGCCGCCCGTTGAAGCAGGAACCCACCGAAATGATTCAGGCGACAGCCTGAACGTAGCAGGGATCCACGTCCTTCAGGGCGTGGAGGATGTCa                                                                         <  2:82109/286‑1 (MQ=11)                                                                                             aGGTGCTTGCTGTTCCGCCAGCGTATAC‑AAGCCAGCGTTGCGCGTACTGTGGTCATACAGCGAAAGAGAACCGCCTGTCACAAAGTAAATTCAGATGCCAGGTATGTGGATATACAGCGAACGCCGATGTAAATGGCGCTCGTAACATTTTAGCGGCGGGGCACGCCGTTCTTGCCTGTGGAGAGATGGTGCAGTCAGGCCGCCCGTTGAAGCAGGAACCCACCGAAATGATTCAGGCGACAGCCTGAACGTAGCAGGGATCCACGTCCTTCAGGGCGTGGAGGATGTCaaagatcgg                                                                 >  1:82109/1‑291 (MQ=12)                                                                                                 gcttgctGTTCCGCCAGCGTATAC‑AAGCCAGCGTTGCGCGTACTGTGGTCATACAGCGAAAGAGAACCGCCTGTCACAAAGTAAATTCAGATGCCAGGTATGTGGATATACAGCGAACGCCGATGTAAATGGCGCTCGTAACATTTTAGCGGCGGGGCACGCAGTTCTTGCCTGTGGAGAGATGGTGCAGTCAGGCCGCCCGTTGAAGCAGGAACCCACCGAAATGATTCAGGCGACAGCCTGAACGTAGCAGGGATCCACGTCCTTCAGGGCGTGGAGGATGTCAATATCGGTTTCt                                                             <  1:545431/298‑1 (MQ=255)                                                                                                 gcgtgctGGTCCGCAAGGGTATAC‑AGGGCAGGTTTGGGCGTACTGGGGTCATACAGCGAAAGAGAACCGGCTGTCACAAAGGAAATACAGATGCCAGGTATGTGGATATACAGCGAACGCCGGTGTAAATGGCGCTCGTAACAGTTTAGCGGCGGGGCACGCCGGTCTTGCCTGTGGAGAGATGGTGCAGTCAGGCCGCCCGTTGAAGCAGGAACCCACCGAAATGATTCAGGCGACAGCCTGAACGTAGCAGGGATCCACGTCCTTCAGGGCGTGGAGGATGTCAATATCGGTTTCt                                                             <  2:351334/295‑1 (MQ=11)                                                                                                      ctGTTCCGCCAGCGTATAC‑AAGCCAGCGTTGCGCGTACTGTGGTCATACAGCGAAAGAGAACCGCCTGTCACAAAGTAAATTCAGATGCCAGGTATGTGGATATACAGCGAACGCCGATGTAAATGGCGCTCGTAACATTTTAGCGGCGGGGCACGCCGTTCTTGCCTGTGGAGAGATGGTGCAGTCAGGCCGCCCGTTGAAGCAGGAACCCACCGAAATGATTCAGGCGACAGCCTGAACGTAGCAGGGATCCACGTCCTTCAGGGCGTGGAGGATGTCAATATCGGTTTCTGTCA‑g                                                       <  1:400592/298‑1 (MQ=255)                                                                                                                     atac‑aAGCCAGCGTTGCGCGTACTGTGGTCATACAGCGAAAGAGAACCGCCTGTCACAAAGTAAATTCAGATGCCAGGTATGTGGATATACAGCGAACGCCGATGTAAATGGCGCTCGTAACATTTTAGCGGCGGGGCACGCCGTTCTTGCCTGTGGAGAGATGGTGCAGTCAGGCCGCCCGTTGAAGCAGGAACCCACCGAAATGATTCAGGCGACAGCCTGAACGTAGCAGGGATCCACGTCCTTCAGGGCGTGGAGGATGTCAATATCGGTTTCTGTCA‑GCGATTAAATTCAaca                                        <  1:232598/296‑1 (MQ=255)                                                                                                                      tac‑aAGCCAGCGTTGCGCGTACTGTGGTCATACAGCGAAAGAGAACCGCCTGTCACAAAGTAAATTCAGATGCCAGGTATGTGGATATACAGCGAACGCCGATGTAAATGGCGCTCGTAACATTTTAGCGGCGGGGCACGCCGTTCTTGCCTGTGGAGAGATGGTGCAGTCAGGCCGCCCGTTGAAGCAGGAACCCACCGAAATGATTCAGGCGACAGCCTGAACGTAGCAGGGATCCACGTCCTTCAGGGCGTGGAGGATGTCAATATCGGTTTCTGTCA‑GCGATTAAATTCAacac                                       >  1:371074/2‑298 (MQ=255)                                                                                                                                           acTGTGGTCATACAGCGAAAGAGAACCGCCTGTCACAAAGTAAATTCAGATGCCAGGTATGTGGATATACAGCGAACGCCGATGTAAATGGCGCTCGTAACATTTTAGCGGCGGGGCACGCCGTTCTTGCCTGTGGATAGATGGTGCAGTCACGCCGCCCGTTGAAGCAGGAACCCACCGAAATGATTCAGGCGACAGCCTGAACGTAGCAGGGCTCCACGTCCTTCAGGGCGTGGAGGATGTCCATATCGGTTTCTGTCA‑ACGATTAAATTCAACACCACGTCACAAACGCCTCCgg                   >  1:234634/2‑298 (MQ=255)                                                                                                                                                     tACAGCGAAAGAGAACCGCCTGTCACAAAGTAAATTCAGATGCCAGGTATGTGGATATACAGCGAACGCCGATGTAAATGGCGCTCGTAACATTTTAGCGGCGGGGCACGCCGTTCTTGCCTGTGGAGAGATGGTGCAGTCAGGCCGCCCGTTGAAGCAGGAACCCACCGAAATGATTCAGGCGACAGCCTGAACGTAGCAGGGATCCACGTCCTTCAGGGCGTGGAGGATGTCAATATCGGTTTCTGTCA‑GCGATTAAATTCAACACCACGTAACAAACGCCTCCGGCAATTAATcc         <  1:42657/298‑1 (MQ=255)                                                                                                                                                     tACAGCGAAAGAGAACCGCCTGTCACAAAGTAAATTCAGATGCCAGGTATGTGGATATACAGCGAACGCCGATGTAAATGGCGCTCGTAACATTTTAGCGGCGGGGCACGCCGTTCTTGCCTGTGGAGAGATGGTGCAGTCAGGCCGCCCGTTGAAGCAGGAACCCACCGAAATGATTCAGGCGACAGCCTGAACGTAGCAGGGATCCACGTCCTTCAGGGCGTGGAGGATGTCAATATCGGTTTCTGTCA‑GCGATTAAATTCAACACCACGTAACAAACGCCTCCGGCAATTAATcc         >  1:367822/1‑298 (MQ=255)                                                                                                                                                           gaaagagaACCGCCTGTCACAAAGTAAATTCAGATGCCAGGTATGTGGATATACAGCGAACGCCGATGTAAATGGCGCTCGTAACATTTTAGCGGCGGGGCACGCCGTTCTTGCCTGTGGAGAGATGGTGCAGTCAGGCCGCCCGTTGAAGCAGGAACCCACCGAAATGATTCAGGCGACAGCCTGAACGTAGCAGGGATCCACGTCCTTCAGGGCGTGGAGGATGTCAATATCGGTTTCTGTCA‑GCGATTAAATTCAACACCACGTAACAAACGCCTCCGGCAATTAATCCCCAGaa   >  1:192385/1‑298 (MQ=255)                                                                                                                                                            aaagagaACCGCCTGTCACAAAGTAAATTCAGATGCCAGGTATGTGGATATACAGCGAACGCCGATGTAAATGGCGCTCGTAACATTTTAGCGGCGGGGCACGCCGGTCTTGCCTGTGGAGAGACGGTGCAGTCAGGCCGCCCGTTGCAGCAGGAACCCAACGAAATGATTCAGGCTACAGCCTGAACGCCACAGGGATCCACGTCCTTCCGGGCGCGGAGGATGGCCAAATCGGTTTC‑CTCACGCGATTAAATTCCACAACCCCGAACAAACCCCCACACCACATAATCCCCAGAAc  >  2:406900/1‑298 (MQ=11)                                                                                                                                                                    |                                                                                                                                                                                                                                                                                                   GGCAAAATCAGGTTTAAACCGTTCGATACTGGATCAGGGCTGGTATGAAATGCGCCGCCAGCTTGAGTACAAGCAGCTCTGGCGTGGCGGTCAGGTGCTTGCTGTTCCGCCAGCGTACAC‑AAGCCAGCGTTGCGCGTGCTGTGGTCATACAGCGAAAGAAAATCGCCTGTCACAAAGTAAATTCAGATGCCAGGTATGTGGATATACAGCGAACGCCGATGTAAATGGCGCTCGTAACATTTTAGCGGCGGGGCACGCCGTTCTTGCCTGTGGAGAGATGGTGCAGTCAGGCCGCCCGTTGAAGCAGGAACCCACCGAAATGATTCAGGCGACAGCCTGAACGTAGCAGGGATCCACGTCCTTCAGGGCGTGGAGGATGTCAATATCGGTTTCTGTCA‑GCGATTAAATTCAACACCACGTAACAAACGCCTCCGGCAATTAATCCCCAGAAC  >  CP006584/1563589‑1564040

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 9 ≤ ATCG/ATCG < 19 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑