Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	W3110S.gb	4,501,608	A→G	K59K (AAA→AAG)	intB →	predicted integrase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	4,501,608	0	A	G	85.3%	87.2 / 7.4	34	K59K (AAA→AAG)	intB	predicted integrase
Reads supporting (aligned to +/- strand):  ref base A (0/5);  new base G (8/21);  total (8/26)
Fisher's exact test for biased strand distribution p-value = 3.09e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.13e-01

TGCCAGAGTACGTCGTGACGAGGCGCGTAAGCTGCTTGCGAATGGCGTCGATCCGGGAGACAAAAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAAAGAAGTCGCGA  >  W3110S.gb/4501545‑4501663                                                                |                                                        tGCCAGAGTACGTCGTGACGAGGCGCGTAAGCTGCTTGCGAATGGCGTCGATCCGGGAGACAAGAAGaaaa                                                  <  1:3010650/71‑1 (MQ=255)    cAGAGTACGTCGTGACGAGGCGCGTAAGCTGCTTGCGAATGGCGTCGATCCGGGAGACAAGAAGAAAAATg                                               <  1:3721038/71‑1 (MQ=255)                  aCGAGGCGCGTAAGCTGCTTGCGAATGGCGTCGATCCGGGAGACAAAAAGAAAAATGATAAGGTTGAACa                                  <  1:2257073/70‑1 (MQ=255)                  aCGAGGCGCGTAAGCTGCTTGCGAATGGCGTCGATCCGGGAGACAAAAAGAAAAATGATAAGGTTGAACa                                  <  1:2842395/70‑1 (MQ=255)                  aCGAGGCGCGTAAGCTGCTTGCGAATGGCGTCGATCCGGGAGACAAAAAGAAAAATGATAAGGTTGAACa                                  <  1:2589795/70‑1 (MQ=255)                  aCGAGGCGCGTAAGCTGCTTGCGAATGGCGTCGATCCGGGAGACAAAAAGAAAAATGATAAGGTTGAACa                                  <  1:3987907/70‑1 (MQ=255)                  aCGAGGCGCGTAAGCTGCTTGCGAATGGCGTCGATCCGGGAGACAAAAAGAAAAATGATAAGGTTGAACa                                  <  1:812129/70‑1 (MQ=255)                     aGGCGCGTAAGCTGCTTGCGAATGGCGTCGATCCGGGAGACAAGAAGAAAAATGATAAGGTTGAACagag                               >  1:4048462/1‑70 (MQ=255)                     aGGCGCGTAAGCTGCTTGCGAATGGCGTCGATCCGGGAGACAAGAAGAAAAATGATAAGGTTGAACagag                               >  1:2581621/1‑70 (MQ=255)                     aGGCGCGTAAGCTGCTTGCGAATGGCGTCGATCCGGGAGACAAGAAGAAAAATGATAAGGTTGAACagag                               >  1:2142193/1‑70 (MQ=255)                              aGCTGCTTGCGAATGGCGTCGATCCGGGAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGa                     <  1:726961/71‑1 (MQ=255)                              aGCTGCTTGCGAATGGCGTCGATCCGGGAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGa                     <  1:3854754/71‑1 (MQ=255)                              aGCTGCTTGCGAATGGCGTCGATCCGGGAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGa                     <  1:3537415/71‑1 (MQ=255)                              aGCTGCTTGCGAATGGCGTCGATCCGGGAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGa                     <  1:1513914/71‑1 (MQ=255)                              aGCTGCTTGCGAATGGCGTCGATCCGGGAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGa                     <  1:3463630/71‑1 (MQ=255)                              aGCTGCTTGCGAATGGCGTCGATCCGGGAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGa                     <  1:997590/71‑1 (MQ=255)                               gctgctTGCGAATGGCGTCGATCCGGGAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGa                     <  1:3050075/70‑1 (MQ=255)                                ctgctTGCGAATGGCGTCGATCCGGGAGACAAGATGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAAc                   <  1:4081996/71‑1 (MQ=255)                                ctgctTGCGAATGGCGTCGATCCGGGAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAAc                   <  1:2956729/71‑1 (MQ=255)                                ctgctTGCGAATGGCGTCGATCCGGGAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAAc                   <  1:2112693/71‑1 (MQ=255)                                ctgctTGCGAATGGCGTCGATCCGGGAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAAc                   <  1:3568314/71‑1 (MQ=255)                                ctgctTGCGAATGGCGTCGATCCGGGAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAAc                   <  1:2143522/71‑1 (MQ=255)                                ctgctTGCGAATGGCGTCGATCCGGGAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAAc                   <  1:2329414/71‑1 (MQ=255)                                             gCGTCGATCCGGGAGAGAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGc                         <  1:3099350/52‑1 (MQ=39)                                             gCGTCGATCCGGGAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGc                         <  1:1337889/52‑1 (MQ=255)                                             gCGTCGATCCGGGAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGc                         <  1:1305282/52‑1 (MQ=255)                                             gCGTCGATCCGGGAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGc                         <  1:997286/52‑1 (MQ=255)                                             gCGTCGATCCGGGAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGc                         <  1:2157083/52‑1 (MQ=255)                                                     ccGGGAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAAAGAAGTCGCGa  >  1:2143756/1‑67 (MQ=255)                                                     ccGGGAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAAAGAAGTCGCGa  >  1:620183/1‑67 (MQ=255)                                                     ccGGGAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAAAGAAGTCGCGa  >  1:2708290/1‑67 (MQ=255)                                                     ccGGGAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAAAGAAGTCGCGa  >  1:2809720/1‑67 (MQ=255)                                                     ccGGGAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAAAGAAGTCGCGa  >  1:3335380/1‑67 (MQ=255)                                                        ggAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGa                     <  1:3075333/45‑1 (MQ=255)                                                                |                                                        TGCCAGAGTACGTCGTGACGAGGCGCGTAAGCTGCTTGCGAATGGCGTCGATCCGGGAGACAAAAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAAAGAAGTCGCGA  >  W3110S.gb/4501545‑4501663

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑