Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	W3110S.gb	4,501,608	A→G	51.2%	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	51.2%	2.5 / 120.9	84	K59K (AAA→AAG)	intB	predicted integrase
Reads supporting (aligned to +/- strand):  ref base A (20/21);  new base G (20/23);  total (40/44)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.42e-01

GTGACGAGGCGCGTAAGCTGCTTGCGAATGGCGTCGATCCGGGAGACAAAAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAAAGAAGTCGCGATTGAG  >  W3110S.gb/4501559‑4501668                                                  |                                                             gtGACGAGGCGCGTAAGCTGCTTGCGAATGGCGTCGATCCGGGAGACAAAAAGAAAAATGATAAGGTTGaa                                         >  1:2098515/1‑71 (MQ=255) gtGACGAGGCGCGTAAGCTGCTTGCGAATGGCGTCGATCCGGGAGACAAAAAGAAAAATGATAAGGTTGaa                                         >  1:1048575/1‑71 (MQ=255) gtGACGAGGCGCGTAAGCTGCTTGCGAATGGCGTCGATCCGGGAGACAAAAAGAAAAATGATAAGGTTGaa                                         >  1:1821486/1‑71 (MQ=255) gtGACGAGGCGCGTAAGCTGCTTGCGAATGGCGTCGATCCGGGAGACAAAAAGAAAAATGATAAGGTTGaa                                         >  1:2281141/1‑71 (MQ=255) gtGACGAGGCGCGTAAGCTGCTTGCGAATGGCGTCGATCCGGGAGACAAAAAGAAAAATGATAAGGTTGaa                                         >  1:2456009/1‑71 (MQ=255) gtGACGAGGCGCGTAAGCTGCTTGCGAATGGCGTCGATCCGGGAGACAAAAAGAAAAATGATAAGGTTGaa                                         >  1:441054/1‑71 (MQ=255) gtGACGAGGCGCGTAAGCTGCTTGCGAATGGCGTCGATCCGGGAGACAAAAAGAAAAATGATAAGGTTGaa                                         >  1:417385/1‑71 (MQ=255) gtGACGAGGCGCGTAAGCTGCTTGCGAATGGCGTCGATCCGGGAGACAAAAAGAAAAATGATAAGGTTGaa                                         >  1:1423427/1‑71 (MQ=255)                  ctgctTGCGAATGGCGTCGATCCGGGAGACAAGAAGAAAAATGATAAGGTTGAACaga                                     >  1:999671/1‑58 (MQ=255)                  ctgctTGCGAATGGCGTCGATCCGGGAGACAAGAAGAAAAATGATAAGGTTGAACaga                                     >  1:3013792/1‑58 (MQ=255)                  ctgctTGCGAATGGCGTCGATCCGGGAGACAAGAAGAAAAATGATAAGGTTGAACaga                                     >  1:586917/1‑58 (MQ=255)                   tgctTGCGAATGGCGTCGATCCGGGAGACAAAAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAAcc                       >  1:2547051/1‑71 (MQ=255)                   tgctTGCGAATGGCGTCGATCCGGGAGACAAAAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAAcc                       >  1:1697704/1‑71 (MQ=255)                            aTGGCGTCGATCCGGGAGACAAAAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAaag                >  1:2371507/1‑69 (MQ=255)                             tGGCGTCGATCCGGGAGACAAAAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGaa                         >  1:1471288/1‑59 (MQ=255)                             tGGCGTCGATCCGGGAGACAAAAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAaagaag             >  1:3037316/1‑71 (MQ=255)                             tGGCGTCGATCCGGGAGACAAAAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAaagaag             >  1:290981/1‑71 (MQ=255)                             tGGCGTCGATCCGGGAGACAAAAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAaagaag             >  1:2603943/1‑71 (MQ=255)                             tGGCGTCGATCCGGGAGACAAAAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAaagaag             >  1:469806/1‑71 (MQ=255)                             tGGCGTCGATCCGGGAGACAAAAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAaagaag             >  1:2238817/1‑71 (MQ=255)                             tGGCGTCGATCCGGGAGACAAAAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAaagaag             >  1:774258/1‑71 (MQ=255)                             tGGCGTCGATCCGGGAGACAAAAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAaagaag             >  1:1015765/1‑71 (MQ=255)                             tGGCGTCGATCCGGGAGACAAAAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAaagaag             >  1:1234694/1‑71 (MQ=255)                                  tCGATCCGGGAGACAAAAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAAAGAAGTcgcg        <  1:1886563/71‑1 (MQ=255)                                  tCGATCCGGGAGACAAAAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAAAGAAGTcgcg        <  1:2810130/71‑1 (MQ=255)                                  tCGATCCGGGAGACAAAAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAAAGAAGTcgcg        <  1:291242/71‑1 (MQ=255)                                  tCGATCCGGGAGACAAAAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAAAGAAGTcgcg        <  1:164875/71‑1 (MQ=255)                                  tCGATCCGGGAGACAAAAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAAAGAAGTcgcg        <  1:1423208/71‑1 (MQ=255)                                  tCGATCCGGGAGACAAAAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAAAGAAGTcgcg        <  1:3216627/71‑1 (MQ=255)                                  tCGATCCGGGAGACAAAAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAAAGAAGTcgcg        <  1:3269608/71‑1 (MQ=255)                                  tCGATCCGGGAGACAAAAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAAAGAAGTcgcg        <  1:2132845/71‑1 (MQ=255)                                  tCGATCCGGGAGACAAAAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAAAGAAGTcgcg        <  1:3329904/71‑1 (MQ=255)                                  tCGATCCGGGAGACAAAAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAAAGAAGTcgcg        <  1:591614/71‑1 (MQ=255)                                  tCGATCCGGGAGACAAAAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAAAGAAGTcgcg        <  1:1089947/71‑1 (MQ=255)                                      tCCGGGAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAAAGAAGTCGCGATTg    <  1:1173333/71‑1 (MQ=255)                                      tCCGGGAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAAAGAAGTCGCGATTg    <  1:503523/71‑1 (MQ=255)                                      tCCGGGAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAAAGAAGTCGCGATTg    <  1:3196409/71‑1 (MQ=255)                                      tCCGGGAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAAAGAAGTCGCGATTg    <  1:3145633/71‑1 (MQ=255)                                      tCCGGGAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAAAGAAGTCGCGATTg    <  1:803125/71‑1 (MQ=255)                                      tCCGGGAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAAAGAAGTCGCGATTg    <  1:853101/71‑1 (MQ=255)                                      tCCGGGAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAAAGAAGTCGCGATTg    <  1:2888709/71‑1 (MQ=255)                                      tCCGGGAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAAAGAAGTCGCGATTg    <  1:2948392/71‑1 (MQ=255)                                      tCCGGGAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAAAGAAGTCGCGATTg    <  1:1554524/71‑1 (MQ=255)                                      tCCGGGAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAAAGAAGTCGCGATTg    <  1:2595776/71‑1 (MQ=255)                                      tCCGGGAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAAAGAAGTCGCGATTg    <  1:2535702/71‑1 (MQ=255)                                      tCCGGGAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAAAGAAGTCGCGATTg    <  1:1784965/71‑1 (MQ=255)                                      tCCGGGAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAAAGAAGTCGCGATTg    <  1:2326090/71‑1 (MQ=255)                                      tCCGGGAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAAAGAAGTCGCGATTg    <  1:2358217/71‑1 (MQ=255)                                      tCCGGGAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAAAGAAGTAGCGATTg    <  1:1910746/71‑1 (MQ=255)                                      tCCGGGAGACAAAAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACTAACCTTTAAAGAAGTCGCGATTg    <  1:1158984/71‑1 (MQ=255)                                      tCCGGGAGACAAAAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAAAGAAGTCGCGATTg    <  1:1207659/71‑1 (MQ=255)                                      tCCGGGAGACAAAAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAAAGAAGTCGCGATTg    <  1:1975101/71‑1 (MQ=255)                                      tCCGGGAGACAAAAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAAAGAAGTCGCGATTg    <  1:625631/71‑1 (MQ=255)                                      tCCGGGAGACAAAAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAAAGAAGTCGCGATTg    <  1:193136/71‑1 (MQ=255)                                      tCCGGGAGACAAAAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAAAGAAGTCGCGATTg    <  1:241922/71‑1 (MQ=255)                                      tCCGGGAGACAAAAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAAAGAAGTCGCGATTg    <  1:2431912/71‑1 (MQ=255)                                      tCCGGGAGACAAAAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAAAGAAGTCGCGATTg    <  1:3330989/71‑1 (MQ=255)                                      tCCGGGAGACAAAAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAAAGAAGTCGCGATTg    <  1:2454911/71‑1 (MQ=255)                                      tCCGGGAGACAAAAAGAAAAATGATAAGGTTGAACAGAGAAAAGCACGAACCTTTAAAGAAGTCGCGATTg    <  1:1860152/71‑1 (MQ=255)                                       ccGGGAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAAAGAAGTCGCGATTg    <  1:3081166/70‑1 (MQ=255)                                        cGGGAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAAAGAAGTCGCGATTg    <  1:2089826/69‑1 (MQ=255)                                        cGGGAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAAAGAAGTCGCGATTg    <  1:757713/69‑1 (MQ=255)                                        cGGGAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAAAGAAGTCGCGATTg    <  1:3206847/69‑1 (MQ=255)                                        cGGGAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAAAGAAGTCGCGATTg    <  1:171149/69‑1 (MQ=255)                                        cGGGAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAAAGAAGTCGCGATTg    <  1:1886850/69‑1 (MQ=255)                                        cGGGAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAAAGAAGTCGCGATTg    <  1:10130/69‑1 (MQ=255)                                        cGGGAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAAAGAAGTCGCGATTGAg  >  1:157659/1‑71 (MQ=255)                                        cGGGAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAAAGAAGTCGCGATTGAg  >  1:549501/1‑71 (MQ=255)                                        cGGGAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAAAGAAGTCGCGATTGAg  >  1:1998661/1‑71 (MQ=255)                                        cGGGAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAAAGAAGTCGCGATTGAg  >  1:763406/1‑71 (MQ=255)                                        cGGGAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAAAGAAGTCGCGATTGAg  >  1:1226853/1‑71 (MQ=255)                                        cGGGAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAAAGAAGTCGCGATTGAg  >  1:386785/1‑71 (MQ=255)                                        cGGGAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAAAGAAGTCGCGATTGAg  >  1:1829063/1‑71 (MQ=255)                                        cGGGAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAAAGAAGTCGCGATTGAg  >  1:3286070/1‑71 (MQ=255)                                        cGGGAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAAAGAAGTCGCGATTGAg  >  1:2219490/1‑71 (MQ=255)                                        cGGGAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAAAGAAGTCGCGATTGAg  >  1:3188042/1‑71 (MQ=255)                                        cGGGAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAAAGAAGTCGCGATTGAg  >  1:3140010/1‑71 (MQ=255)                                        cGGGAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAAAGAAGTCGCGATTGAg  >  1:2364242/1‑71 (MQ=255)                                        cGGGAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAAAGAAGTCGCGATTGAg  >  1:1530289/1‑71 (MQ=255)                                        cGGGAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAAAGAAGTCGCGATTGAg  >  1:2433364/1‑71 (MQ=255)                                        cGGGAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAAAGAAGTCGCGATTGAg  >  1:1632292/1‑71 (MQ=255)                                         gggAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAAAGAAGTCGCGATTg    <  1:2385488/68‑1 (MQ=255)                                          ggAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAAAGAAGTCGCGATTGAg  >  1:3255523/1‑69 (MQ=255)                                          ggAGACAAGAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAAAGAAGTCGCGATTGAg  >  1:3175739/1‑69 (MQ=255)                                                  |                                                             GTGACGAGGCGCGTAAGCTGCTTGCGAATGGCGTCGATCCGGGAGACAAAAAGAAAAATGATAAGGTTGAACAGAGTAAAGCACGAACCTTTAAAGAAGTCGCGATTGAG  >  W3110S.gb/4501559‑4501668

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: ‑