Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	W3110S.gb	4,501,500	A→G	35.1%	Q23Q (CAA→CAG)	intB →	predicted integrase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	4,501,500	0	A	G	35.1%	35.2 / 34.8	37	Q23Q (CAA→CAG)	intB	predicted integrase
Reads supporting (aligned to +/- strand):  ref base A (17/7);  new base G (4/9);  total (21/16)
Fisher's exact test for biased strand distribution p-value = 3.57e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.99e-01

TGCTTGTCCATCCAAATGGTTCTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAAAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAGCGGATGCCAGAG  >  W3110S.gb/4501439‑4501552                                                              |                                                     tGCTTGTCCATCCAAATGGTTCTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAGAAAATGCTg                                             >  1:1903472/1‑71 (MQ=255) tGCTTGTCCATCCAAATGGTTCTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAAAAAATGCTg                                             >  1:1938347/1‑71 (MQ=255)             caAATGGTTCTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAGAAAATGCTgg                                            >  1:1681022/1‑60 (MQ=255)             caAATGGTTCTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAAAAAATGCTGGCACTTGGGGtt                                 >  1:490557/1‑71 (MQ=255)             caAATGGTTCTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAAAAAATGCTGGCACTTGGGGtt                                 >  1:232197/1‑71 (MQ=255)             caAATGGTTCTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAAAAAATGCTGGCACTTGGGGtt                                 >  1:1842379/1‑71 (MQ=255)                      cTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAGAAAATGCTGGCACTTGGGGTTTATCCTGa                         <  1:911365/70‑1 (MQ=255)                      cTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAGAAAATGCTGGCACTTGGGGTTTATCCTGa                         <  1:454726/70‑1 (MQ=255)                      cTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAAAAAATGCTGGCACTTGGGGTTTATCCTGa                         <  1:294403/70‑1 (MQ=255)                       tAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAGAAAATGCTGGCACTTGGGGTTTATCCTGa                         <  1:724263/69‑1 (MQ=255)                         aGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAGAAAATGCTGGCACTTGGGGTTTATCCTGaa                        <  1:451596/68‑1 (MQ=255)                         aGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAGAAAATGCTGGCACTTGGGGTTTATCCTGaa                        <  1:1412944/68‑1 (MQ=255)                         aGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAGAAAATGCTGGCACTTGGGGTTTATCCTGaa                        <  1:1628814/68‑1 (MQ=255)                         aGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAAAAAATGCTGGCACTTGGGGTTTATCCTGAAAt                      <  1:1069769/70‑1 (MQ=255)                         aGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAAAAAATGCTGGCACTTGGGGTTTATCCTGAAAt                      <  1:304501/70‑1 (MQ=255)                         aGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAAAAAATGCTGGCACTTGGGGTTTATCCTGAAAt                      <  1:1631427/70‑1 (MQ=255)                         aGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAAAAAATGCTGGCACTTGGGGTTTATCCTGAAAt                      <  1:1629285/70‑1 (MQ=255)                         aGTACTGCCGTTTGCAGTACCGTTATGAGGGAAAGCAGAAAATGCTGGCACTTGGGGTTTATCCTGaa                        <  1:96936/68‑1 (MQ=255)                                  gTTTGCAGTACCGTTATGAGGGAAAGCAGAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAGCg            <  1:1732554/71‑1 (MQ=255)                                  gTTTGCAGTACCGTTATGAGGGAAAGCAAAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAGCg            <  1:320443/71‑1 (MQ=255)                                  gTTTGCAGTACCGTTATGAGGGAAAGCAAAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAGCg            <  1:1088092/71‑1 (MQ=255)                                           aCCGTTATGAGGGAAAGCAGAAAATGCTGGCACTTGGGGTTTATCCTGa                         <  1:1501284/49‑1 (MQ=255)                                            ccGTTATGAGGGAAAGCAGAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAGCGGATGCCagag  >  1:974629/1‑71 (MQ=255)                                            ccGTTATGAGGGAAAGCAGAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAGCGGATGCCagag  >  1:905772/1‑71 (MQ=255)                                            ccGTTATGAGGGAAAGCAAAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAGCGGATGCCagag  >  1:1735961/1‑71 (MQ=255)                                            ccGTTATGAGGGAAAGCAAAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAGCGGATGCCagag  >  1:984116/1‑71 (MQ=255)                                            ccGTTATGAGGGAAAGCAAAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAGCGGATGCCagag  >  1:941265/1‑71 (MQ=255)                                            ccGTTATGAGGGAAAGCAAAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAGCGGATGCCagag  >  1:403932/1‑71 (MQ=255)                                            ccGTTATGAGGGAAAGCAAAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAGCGGATGCCagag  >  1:1648620/1‑71 (MQ=255)                                            ccGTTATGAGGGAAAGCAAAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAGCGGATGCCaga   >  1:1262263/1‑70 (MQ=255)                                                 aTGAGGGAAAGCAAAAAATGCTGGCACTTGGGGTTTATCCTGAAATcaca                  >  1:1210563/1‑50 (MQ=255)                                                 aTGAGGGAAAGCAAAAAATGCTGGCACTTGGGGTTTATCCTGAAATcaca                  >  1:1279248/1‑50 (MQ=255)                                                 aTGAGGGAAAGCAAAAAATGCTGGCACTTGGGGTTTATCCTGAAATcaca                  >  1:842172/1‑50 (MQ=255)                                                 aTGAGGGAAAGCAAAAAATGCTGGCACTTGGGGTTTATCCTGAAATcaca                  >  1:1006365/1‑50 (MQ=255)                                                 aTGAGGGAAAGCAAAAAATGCTGGCACTTGGGGTTTATCCTGAAATcaca                  >  1:1506542/1‑50 (MQ=255)                                                 aTGAGGGAAAGCAAAAAATGCTGGCACTTGGGGTTTATCCTGAAATcaca                  >  1:1516885/1‑50 (MQ=255)                                                 aTGAGGGAAAGCAAAAAATGCTGGCACTTGGGGTTTATCCTGAAATcaca                  >  1:1769114/1‑50 (MQ=255)                                                              |                                                     TGCTTGTCCATCCAAATGGTTCTAAGTACTGGCGTTTGCAGTACCGTTATGAGGGAAAGCAAAAAATGCTGGCACTTGGGGTTTATCCTGAAATCACACTAGCGGATGCCAGAG  >  W3110S.gb/4501439‑4501552

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: ‑