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	96.0%	37.2 / ‑4.7	25	C336Y (TGC→TAC)	LY180_07445	transposase IS609
Reads supporting (aligned to +/- strand):  ref base G (1/0);  new base A (11/13);  total (12/13)
Fisher's exact test for biased strand distribution p-value = 4.80e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.70e-01

ATTCCTGTATCGCAAATATCCGCAGGGACTACCTTCACAAAGTCACAACGACCGTCAGCAAAAACCACGCAATGATAGTCATTGAGGATTTGAAGGTCAGCAACATGTCAAAGTCAGCAGCGGGTACGGTCAGCCAGCCGGGGCGCAATGTCCGGGCAAAATCAGGTTTAAACCGTTCGATACTGGATCAGGGCTGGTATGAAATGCGCCGCCAGCTTGAGTACAAGCAGCTCTGGCGTGGCGGTCAGGTGCTTGCTGTTCCGCCAGCGTACAC‑AAGCCAGCGTTGCGCGTGCTGTGGTCATACAGCGAAAGAAAATCGCCTGTCACAAAGTAAATTCAGATGCCAGGTATGTGGATATACAGCGAACGCCGATGTAAATGGCGCTCGTAACATTTTAGCGGCGGGGCACGCCGTTCTTGCCTGTGGAGAGATGGTGCAGTCAGGCCGCCCGTTGAAGCAGGAACCCACCGAAATGATTCAGGCGACAGCCTGAACGTAGCAGGGATCCACGTCCTTCAGGGCGTGGAGGATGTCAATATCGGTTTCTGTCAGCGATTAAATTCAACAC  >  CP006584/1563435‑1564003                                                                                                                                                                                                                                                                                                     |                                                                                                                                                                                                                                                                                      aTTCCTGTATCGCAAATATCCGCAGGGACTACCTTCACAAAGTCACAACGGCCGTCAGCAAAAACCACGCAATGATAGTCATTGAGGATTTGAAGGTCAGCAACATGTCAAAGTCAGCAGCGGGTACGGTCAGCCAGCCGGGGCGCAATGTCCGGGCAAAATCAGGTTTAAACCGTTCGATACTGGATCAGGGCTGGTATGAAATGCACCGCCAGCTTGAGTACAAGCAGCTCTGGCGTGGCGGTCAGGTGCTTGCTGTTCCGCCAGCGTATAC‑AAGCCAGCGTTGCGCGTACTGTgg                                                                                                                                                                                                                                                                                 <  1:606959/298‑1 (MQ=14) aTTCCTGTATCGCAAATATCCGCAGGGACTACCTTCACAAAGTCACAACGGCCGTCAGCAAAAACCACGCAATGATAGTCATTGAGGATTTGAAGGTCAGCAACATGTCAAAGTCAGCAGCGGGTACGGTCAGCCAGCCGGGGCGCAATGTCCGGGCAAAATCAGGTTTAAACCGTTCGATACTGGATCAGGGCTGGTATGAAATGCACCGCCAGCTTGAGTACAAGCAGCTCTGGCGTGGCGGTCAGGTGCTTACTGTTCCGCCAGCGTATAC‑AAGCCAGCGTTGCGCGTACTGTgg                                                                                                                                                                                                                                                                                 >  1:544434/1‑298 (MQ=9)     cTGTATCGCAAATATCCGCAGGGACTACCTTCACAAAGTCACAACGGCCGTCAGCAAAAACCACGCAATGATAGTCATTGAGGATTTGAAGGTCAGCAACATGTCAAAGTCAGCAGCGGGTACGGTCAGCCAGCCGGGGCGCAATGTCCGGGCAAAATCAGGTTTAAACCGTTCGATACTGGATCAGGGCTGGTATGAAATGCACCGCCAGCTTGAGTACAAGCAGCTCTGGCGTGGCGGTCAGGTGCTTGCTGTTCCGCCAGCGTATAC‑AAGCCAGCGTTGCGCGTACTGTGGTCAt                                                                                                                                                                                                                                                                             >  1:387187/1‑298 (MQ=11)      tGTATCGCAAATATCCGCAGGGACTACCTTCAAAAAGTCACAACGGCCGTCAGCAAAAACCACGCAATGATAGTCATTGAGGATTTGAAGGTCAGCAACATGTCAAAGTCAGCAGCGGGTACGGTCAGCCAGCCGGGGCGCAATGTCCGGGCAAAATCAGGTTTAAACCGTTCGATACTGGATCAGGGCTGGTATGAAATGCACCGCCAGCTTGAGTACAAGCAGCTCTGGCGTGGCGGTCAGGTGCTTGCTGTTCCGCCAGCGTATAC‑AAGCCAGCGTTGCGCGTACTGTGGTCATa                                                                                                                                                                                                                                                                            <  1:9279/298‑1 (MQ=2)                                                                                                                                                           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‑AAGCCAGCGTTGCGCGTACTGTGGTCATACAGCGAAAGAGAACCGCCTGTCACAAAGTAAATTCAGATGCCAGGTATGTGGATATACAGCGAACGCCGATGTAAATGGCGCTCGTAACATTTTAGCGGCGGGGCACGCCGTTCTTGCCTGTGGAGAGATGGTGCAGTCAGGCCGCCCGTTGAAGCAGGAACCCACCGAAATGATTCAGGCGACAGCCTGAACGTAGCAGGGATCCACGTCCTTCAGGGCGTGGAGGATGTCAATATCGGTTTCTGTCAg                  <  1:400592/298‑1 (MQ=255)                                                                                                                                                                                                                                                                               atac‑aAGCCAGCGTTGCGCGTACTGTGGTCATACAGCGAAAGAGAACCGCCTGTCACAAAGTAAATTCAGATGCCAGGTATGTGGATATACAGCGAACGCCGATGTAAATGGCGCTCGTAACATTTTAGCGGCGGGGCACGCCGTTCTTGCCTGTGGAGAGATGGTGCAGTCAGGCCGCCCGTTGAAGCAGGAACCCACCGAAATGATTCAGGCGACAGCCTGAACGTAGCAGGGATCCACGTCCTTCAGGGCGTGGAGGATGTCAATATCGGTTTCTGTCAGCGATTAAATTCAaca   <  1:232598/296‑1 (MQ=255)                                                                                                                                                                                                                                                                                tac‑aAGCCAGCGTTGCGCGTACTGTGGTCATACAGCGAAAGAGAACCGCCTGTCACAAAGTAAATTCAGATGCCAGGTATGTGGATATACAGCGAACGCCGATGTAAATGGCGCTCGTAACATTTTAGCGGCGGGGCACGCCGTTCTTGCCTGTGGAGAGATGGTGCAGTCAGGCCGCCCGTTGAAGCAGGAACCCACCGAAATGATTCAGGCGACAGCCTGAACGTAGCAGGGATCCACGTCCTTCAGGGCGTGGAGGATGTCAATATCGGTTTCTGTCAGCGATTAAATTCAacac  >  1:371074/2‑298 (MQ=255)                                                                                                                                                                                                                                                                                                     |                                                                                                                                                                                                                                                                                      ATTCCTGTATCGCAAATATCCGCAGGGACTACCTTCACAAAGTCACAACGACCGTCAGCAAAAACCACGCAATGATAGTCATTGAGGATTTGAAGGTCAGCAACATGTCAAAGTCAGCAGCGGGTACGGTCAGCCAGCCGGGGCGCAATGTCCGGGCAAAATCAGGTTTAAACCGTTCGATACTGGATCAGGGCTGGTATGAAATGCGCCGCCAGCTTGAGTACAAGCAGCTCTGGCGTGGCGGTCAGGTGCTTGCTGTTCCGCCAGCGTACAC‑AAGCCAGCGTTGCGCGTGCTGTGGTCATACAGCGAAAGAAAATCGCCTGTCACAAAGTAAATTCAGATGCCAGGTATGTGGATATACAGCGAACGCCGATGTAAATGGCGCTCGTAACATTTTAGCGGCGGGGCACGCCGTTCTTGCCTGTGGAGAGATGGTGCAGTCAGGCCGCCCGTTGAAGCAGGAACCCACCGAAATGATTCAGGCGACAGCCTGAACGTAGCAGGGATCCACGTCCTTCAGGGCGTGGAGGATGTCAATATCGGTTTCTGTCAGCGATTAAATTCAACAC  >  CP006584/1563435‑1564003

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 9 ≤ ATCG/ATCG < 23 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑