Spreadsheet: 244b7bc9-0699-4ef2-8369-57b09322bdc5
Sheet: Table S1

Table S1. The rate of spontaneous and DSB-associated Lys+ mutations.
Position | Construct | HO site | Relevant Genotype | Rate of Lys+ (x10-10)a |  |  |  | Fold overc | Fold over  wt                           (p-value)d | % BIRe
 |  |  |  | Before galactose (0h) |  | After galactose  (frequency (7h -0h)) |  | "No-DSB"
 |  |  |  | Median | CI or rangeb [# of repeats] | Median | CI or rangeb  [# of repeats] | control
MAT | A4 | DSB | WT | 42.10284907004502 | (25 - 81) [9] | 22999.053030303 | (18,058 - 30,416) [9] | 1533 | NA | 96.3 (2.1)
MAT | A4 | DSB | msh2D | 352.8633779696218 | (243 - 1,346) [12] | 43278.5285652706 | (35,579 - 54,757) [12] | 163 | 1.9 (0.0095) | 79.1 (6.6)
MAT | A4 | DSB | mlh1D | 769.6493997245545 | (551 - 1,261) [7] | 78052.47005247005 | (47,071 - 164,969) [7] | 121 | 3.4 (0.0007) | 84.3 (10.5)
MAT | A4 | DSB | pol3-5DV | 255.7155118561941 | (99 - 822) [9] | 74124.45032813551 | (52,370 - 91,275) [9] | 988 | 3.2 (0.0005) | 90.5 (4.4)
MAT | A4 | DSB | rev3D | 21.19777531005302 | (13 - 33) [6] | 7692.055260321922 | (2,745 - 12,153) [6] | 2564 | 0.3 (0.0004) | 96.5 (0)
MAT | A4 | DSB | rad30D | 57.36094159492833 | (38 - 65) [6] | 30619.7194450609 | (16,447 - 35,988) [6] | 2784 | NS | 93.0 (4.0)
MAT | A4 | DSB | dun1D | 25.93123408471576 | (15 - 147) [7] | 5695.146958304853 | (3,031 - 9,959) [7] | 475 | 0.2 (0.0002) | 86.4 (11.4)
MAT | A4 | DSB | sml1D | 43.93890427549553 | (33 - 131) [6] | 32652.29219043257 | (28,439 - 41,467) [6] | 3628 | 1.4 (0.0176) | 91.3 (5.2)
MAT | A4 | DSB | msh3D | 52.19120458861089 | (36 - 68) [10] | 19161.01054108512 | (4,243 - 31,481) [10] | 1916 | NS | 86.5 (11.2)
MAT | A4 | DSB | pol3-5DV msh3D | 595.5422875072493 | (474 - 1,004) [6] | 121012.088841627 | (107,698 - 141,069) [6] | 349 | 5.3 (0.0004, 0.0002†, 0.0004‡) | 85.0 (15.0)
MAT | A4 | No | WT | 14.59700830983351 | (4 - 16) [7] | 0 | (0 - 12) [7] | NA | NA | 4.0 (4.0)
MAT | A4 | No | msh2D | 264.7302903257993 | (114 - 3,418) [6] | 0 | (0 - 102) [6] | NA | 17.7 (0.0034) | 0 (0)
MAT | A4 | No | mlh1D | 644.8939794504141 | (215 - 1,404) [6] | 0 | (0 - 272) [6] | NA | 43.0 (0.0034) | 4.5 (1.8)
MAT | A4 | No | pol3-5DV | 74.83999854845604 | (40 - 105) [9] | 61.18779283272129 | (0 - 205) [9] | NA | 5.0 (0.0010) | 0 (0)
MAT | A4 | No | rev3D | 3.155888095295162 | (1 - 5) [4] | 0.7003741906449701 | ( 0 - 1) [4] | NA | 0.2 (0.0179) | 0 (0)
MAT | A4 | No | rad30D | 11.21294449500497 | (8 - 15) [10] | 5.529659305592915 | (0 - 27)[10] | NA | NS | 0 (0)
MAT | A4 | No | dun1D | 11.61245911238817 | (9 - 24)[6] | 1.809229186820012 | (0 - 19) [6] | NA | NS | ND
MAT | A4 | No | sml1D | 8.75260309691535 | (6 - 12) [6] | 13.66138225731261 | (0 - 32)[6] | NA | NS | 0 (0)
MAT | A4 | No | msh3D | 9.988971821884181 | (7 - 39) [6] | 12.94133276940719 | (0 - 30) [6] | NA | NS | 0 (0)
MAT | A4 | No | pol3-5DV msh3D | 347 | (33 - 896) [11] | 162.019 | (0 - 3778) [11] | NA | 23.1 (0.0006, 0.0030†, 0.0030‡) | 0 (0)
MAT | A7 | DSB | WT | 55.15930808370662 | (31 - 80) [9] | 27769.2827794248 | (21,700 - 30,220) [9] | 2777 | NA | 91.4 (4.8)
MAT | A7 | DSB | msh2D | 121230.9547844537 | (70,337 - 467,001) [ 7] | 1834678.203383239 | (1,351,974 - 5,649,194) [7] | 7 | 66.1 (0.0002) | 88.9 (6.7)
MAT | A7 | DSB | pol3-5DV | 135.7147183076547 | (93 - 162) [10] | 90216.36689745265 | (68,881 - 161,880) [10] | 1432 | 3.2 ( <0.0001) | 86.7 (4.4)
MAT | A7 | DSB | rev3D | 20.10131492312321 | (15 - 150) [7] | 13282.05128205128 | (6,638 - 39,278) [7] | 1476 | 0.48 (0.0115) | 98.0 (0.7)
MAT | A7 | DSB | rad30D | 53.20271388706284 | (26 - 73) [6] | 24482.5611577737 | (11,015 - 54,849) [6] | 1883 | NS | 89.4 (1.8)
MAT | A7 | DSB | msh3D | 52.0235 | (33 - 87) [10] | 101201 | (23,881 - 187,343) [10] | 7785 | 3.6 (0.0440) | 88.6 (3.6)
MAT | A7 | DSB | pol3-5DV msh3D | 2109.99 | (1,061 - 9,328) [9] | 413703 | (242,689 - 1,321,030) [9] | 345 | 14.9 (<0.0001 <0.0001†, <0.0001‡) | 90.0 (4.0)
MAT | A7 | No | WT | 9.949864292620486 | (5 - 28) [6] | 0 | - [6] | NA | NA | 0 (0)
MAT | A7 | No | msh2D | 263768.506974377 | (72,228 - 489,915) [6] | 0 | - [6] | NA | 26377.0 (0.0022) | 0 (1.7)
MAT | A7 | No | pol3-5DV | 63.066881566066 | (33 - 107) [6] | 0 | (0 - 286) [6] | NA | 6.3   (0.0022) | 0 (0.9)
MAT | A7 | No | rev3D | 8.864517540222641 | (3 - 33) [8] | 0 | (0 - 17) [8] | NA | NS | 7.1 (0)
MAT | A7 | No | rad30D | 13.24056504273857 | (4 - 224) [6] | 3 | (0 - 11)[6] | NA | NS | ND
MAT | A7 | No | msh3D | 13.45839823915581 | (9 - 168) [8] | 0 | (0 - 29) [8] | NA | NS | 0 (0)
MAT | A7 | No | pol3-5DV msh3D | 1200.28 | (624 - 2,322) [6] | 0 | (0 - 542) [6] | NA | 120.0 (0.0022, 0.0007†, 0.0022‡) | ND
MAT | A14 | DSB | WT | 10824.12947954584 | (3,156 - 24,267) [9] | 5012906.405915002 | (3,208,725 - 6,143,645) [9] | 310 | NA | 93.2 (6.1)
MAT | A14 | No | WT | 16187.8818079603 | (4,868 - 28,917) [6] | 0 | (0 - 12,250) [6] | NA | NA | 4.2 (4.2)
16 kb | A4 | DSB | WT | 366.5931792821627 | (166 - 615) [10] | 49131.74409063394 | (24,012 - 83,090) [10] | 1170 | NA | 91.2 (7.1)
16 kb | A4 | DSB | msh2D | 12295.74533266168 | (5,470 - 20,584) [7] | 370114.9425287356 | (275,661 - 479,013) [7] | 60 | 7.5 (0.0001) | 73.9 (16.6)
16 kb | A4 | DSB | pol3-5DV | 712.5538859708518 | (328 - 1,174) [7] | 194586.9919657414 | (159,505 - 254,883) [7] | 432 | 4.0 (0.0001) | 94.8 (3.3)
16 kb | A4 | DSB | rev3D | 243.5860229889969 | (82 - 550) [7] | 18048.75098288272 | (5,327 - 24,374) [7] | 668 | 0.4 (0.0004) | 94.1 (4.9)
16 kb | A4 | DSB | rad30D | 196.6033431579171 | (161 - 306) [5] | 62359.70081861021 | (31,104 - 73,402) [5] | 904 | NS | 97.6 (0)
16 kb | A4 | DSB | dun1D | 196.4656580253545 | (36 - 352) [6] | 20329.6632977157 | (10,599 - 51,278) [6] | 239 | 0.4 (0.031) | 84.0 (12.3)
16 kb | A4 | DSB | sml1D | 644.7725751513319 | (231 - 930) [6] | 90507.32937535133 | (61,618 - 209,507) [6] | 526 | 1.8 (0.011) | 96.4 (1.8)
16 kb | A4 | DSB | msh3D | 361.9594303628447 | (238- 589) [7] | 109715.5000581689 | (96,350 - 150,870) [7] | 459 | 2.2 (0.0012) | 88.1 (8.4)
16 kb | A4 | DSB | pol3-5DV msh3D | 4716.965438521017 | (2,377 - 15,538) [6] | 371069.586382831 | (282,924 - 557,955) [6] | 78 | 7.6 (0.0002, 0.0012†, 0.0012‡) | 71.3 (18.1)
16 kb | A4 | No | WT | 42 | (38 - 99) [6] | 4.897375455751086 | (0 - 52) [6] | NA | NA | 8.0 (0)
16 kb | A4 | No | msh2D | 6163 | (4,677- 8147) [9] | 13971.61754318372 | (0 - 94,394) [9] | NA | 146.7 (0.0004) | 1.2 (1.2)
16 kb | A4 | No | pol3-5DV | 450 | (208 - 765) [5] | 1918.494317737725 | (0 - 7,850) [5] | NA | 10.7 (0.0043) | 4.9 (0)
16 kb | A4 | No | rev3D | 27 | (16 - 81) [6] | 9.090458238994543 | (0 - 67) [6] | NA | 0.6 (0.0410) | 19.5 (0)
16 kb | A4 | No | rad30D | 69 | (51 - 132) [7] | 0 | (0 - 74) [7] | NA | NS | 16.7 (0)
16 kb | A4 | No | dun1D | 85 | (32 - 110) [9] | 51.97132616487456 | (0 - 99) [9] | NA | NS | 0 (0)
16 kb | A4 | No | sml1D | 172 | (57- 254) [4] | 0 | (0 - 17)[4] | NA | NS | 0 (0)
16 kb | A4 | No | msh3D | 239 | (195 - 280) [6] | 0 | - [6] | NA | 5.7 (0.0012) | 0 (0)
16 kb | A4 | No | pol3-5DV msh3D | 4771 | (2,490- 11,007) [6] | 5699.422520232822 | (0 - 16,834)  [6] | NA | 113.6 (0.0022, 0.0022†, 0.0043‡) | 0 (0)
16 kb | A7 | DSB | WT | 2735.94004525911 | (975 - 10,447) [8] | 266765.2746537559 | (161,398 - 323,714) [8] | 1947 | NA | 92.6 (6.6)
16 kb | A7 | DSB | msh2D | 2276297.777106783 | (882,761 - 3,976,321) [10] | 9567051.800389512 | (2,465,474 - 47,976,249) [10] | 3 | 35.9 (<0.0001) | 84.0 (6.0)
16 kb | A7 | DSB | pol3-5DV | 4745.30373433045 | (3,963 - 13,357) [9] | 585822.5187391762 | (415,737 - 771,709) [9] | 347 | 2.2 (0.0055) | 93.0 (1.2)
16 kb | A7 | DSB | rev3D | 1248.611192367513 | (1,019 - 1,779) [9] | 200141.6077529708 | (125,984 - 392,259) [9] | 590 | NS | 99.1 (0.2)
16 kb | A7 | DSB | rad30D | 2150.998868165244 | (869 - 8,129) [6] | 206091.4224281649 | (136,858 - 306,281) [6] | 517 | NS | 96.5 (1.9)
16 kb | A7 | DSB | msh3D | 14461.27390737181 | (10,380 - 29,155) [7] | 630666.6666666665 | (162,052 - 1,960,118)[7] | 252 | NS | 82.1 (12.2)
16 kb | A7 | DSB | pol3-5DV msh3D | 93738.071927872 | (34,515 - 134,072) [6] | 1871657.563087409 | (1,347,373 - 4,292,566) [6] | 30 | 7.0 (0.0007, 0.0140†, 0.0004‡) | 73.5 (12.6)
16 kb | A7 | No | WT | 137.1839748194512 | (120 - 339) [6] | 157.1237904571238 | (0 - 1,491) [6] | NA | NA | 0 (0)
16 kb | A7 | No | msh2D | 2884398.848134245 | (1,633,488 - 3,366,307) [12] | 0 | - [12] | NA | 21054.0 (0.0009) | 0 (0)
16 kb | A7 | No | pol3-5DV | 1690.264001073778 | (746 - 2,655) [6] | 1035.486849269667 | (0 - 4,684) [6] | NA | 12.3 (0.0022) | 0.6 (0)
16 kb | A7 | No | rev3D | 339.354 | (237 - 654) [10] | 884.688 | (0 - 2,185) [10] | NA | 2.5 (0.0047) | 0.1 (0)
16 kb | A7 | No | rad30D | 398.6413067394838 | (90 - 645) [8] | 119.5551436515291 | (0 - 517) [8] | NA | NS | 8.7 (0)
16 kb | A7 | No | msh3D | 2504.966013921643 | (1,198 - 3,379) [6] | 2756.900782582457 | (1,398 - 7,138) [6] | NA | 18.3 (0.0022) | 0 (1.7)
16 kb | A7 | No | pol3-5DV msh3D | 61820.7742625026 | (41,789 - 209,839) [6] | 37204.77716084259 | (0 - 1,286,693) [6] | NA | 451.2 (0.0022, 0.0022†, 0.0022‡) | 0 (1.5)
16 kb | A14 | DSB | WT | 147325.2968634152 | (47,905 - 668,125) [6] | 2370464.968704891 | (1,275,755 - 4,181,943) [6] | 26 | NA | 90.2 (6.8)
16 kb | A14 | No | WT | 90599.41662452227 | (73,797 - 338,588) [8] | 0 | (0 - 498,176) [8] | NA | NA | 0 (0)
36 kb | A4 | DSB | WT | 50.76731174694117 | (37 - 71) [9] | 12015.0389530575 | (5,158 - 14,123) [9] | 2003 | NA | 95.2 (3.1)
36 kb | A4 | DSB | msh2D | 2580.831356036614 | (1,233 - 5,824) [11] | 131303.8241493526 | (93,629 - 175,262) [11] | 61 | 10.9 (0.0002) | 92.2 (2.9)
36 kb | A4 | DSB | mlh1D | 1263.25200553367 | (809 - 7,104) [6] | 55700.78802607388 | (25,767 - 64,380) [6] | 32 | 4.6 (0.0004) | 85.3 (5.9)
36 kb | A4 | DSB | pol3-5DV | 224.0411859319355 | (119 - 262) [13] | 66896.01706970128 | (58,853 - 92,282) [13] | 1487 | 5.6 (0.0001) | 92.7 (5.9)
36 kb | A4 | DSB | rev3D | 29.57287374180977 | (22 - 61) [9] | 8591.691600008142 | (6,080 - 11,757) [9] | 2148 | NS | 93.2 (2.7)
36 kb | A4 | DSB | rad30D | 63.16289891257517 | (34 - 157) [7] | 10739.04068002429 | (9,662 - 21,157) [7] | 1790 | NS | 92.3 (7.3)
36 kb | A4 | DSB | dun1D | 17.3447338607227 | (12 - 51) [10] | 2208.024461021466 | (954 - 3,499) [10] | 116 | 0.2 (0.0021) | 98.0 (2.0)
36 kb | A4 | DSB | sml1D | 22.90232201726266 | (21 - 37) [9] | 10040.23387601485 | (4,595 - 246,470) [9] | 558 | NS | 92.5 (2.5)
36 kb | A4 | DSB | msh3D | 113.7686851972566 | (26 - 161) [6] | 28269.41690244929 | (14,056 - 37,574)[6] | 1488 | 2.4 (0.0016) | 91.7 (6.2)
36 kb | A4 | DSB | pol3-5DV msh3D | 521.3043595070717 | (224 - 5,197) [8] | 229357.6366636302 | (140,694 - 340,488) [8] | 717 | 19.1 (0.0006, 0.0024†, 0.0003‡) | 78.7 (15.7)
36 kb | A4 | No | WT | 6.281190261694419 | (5 - 12) [9] | 1.877306128421955 | (0 - 10) [9] | NA | NA | ND
36 kb | A4 | No | msh2D | 2142.980730784007 | (1,034 - 4,230) [6] | 0 | (0 - 7,770) [6] | NA | 357.2 (0.0011) | 0 (7.0)
36 kb | A4 | No | mlh1D | 1731.391767985169 | (1,087 - 2,003) [6] | 85.07487486907789 | (0 - 3,971) [6] | NA | 288.5 (0.0011) | 2.5 (1.3)
36 kb | A4 | No | pol3-5DV | 44.5610160660318 | (15 - 295) [6] | 45.3578769125461 | (23 - 365) [6] | NA | 7.5 (0.0042) | 4.2 (2.1)
36 kb | A4 | No | rev3D | 3.755639717285427 | (2 - 7) [6] | 7.966163365209434 | (0 - 21) [6] | NA | NS | 10 (0)
36 kb | A4 | No | rad30D | 6.016908116052459 | (4 - 17) [6] | 7.86161512419643 | (0 - 21) [6] | NA | NS | 4 (0)
36 kb | A4 | No | dun1D | 19.02937980994797 | (9 - 116) [7] | 14.46737649492859 | (0 - 21) [7] | NA | 3.2 (0.0066) | 0 (0)
36 kb | A4 | No | sml1D | 18.13540840233501 | (14 - 26) [6] | 0 | (0 - 55)[6] | NA | 3.0 (0.0140) | 0 (0)
36 kb | A4 | No | msh3D | 19.04882702420987 | (4 - 75) [6] | 23.81349829798377 | (0 - 193) [6] | NA | NS | 1.2 (0)
36 kb | A4 | No | pol3-5DV msh3D | 320.1073183258099 | (254 - 611) [6] | 0 | (0 - 504)[6] | NA | 53.3 (0.0011, 0.0022†, 0.0152‡) | 0 (0)
36 kb | A7 | DSB | WT | 38.52855028789951 | (16 - 119) [8] | 8586.12 | (6,217 - 22,002) [8] | 781 | NA | 96.9 (1.3)
36 kb | A7 | DSB | msh2D | 1103095.063602928 | (804,278 - 1,583,201) [13] | 10605324.37322305 | (4,291,667 - 15,077,381) [13] | 14 | 1235.2 (0.0002) | 98.1 (1.9)
36 kb | A7 | DSB | pol3-5DV | 215.204849869161 | (137 - 409) [12] | 77636.37953079445 | (72,667 - 132,734) [12] | 3697 | 9.0 (0.0002) | 97.1 (2.2)
36 kb | A7 | DSB | rev3D | 37.36789817408525 | (12 - 67) [8] | 8417.104358297698 | (3,659 - 12,472) [8] | 842 | NS | 97.3 (0)
36 kb | A7 | DSB | rad30 D | 73.88726116612905 | (23 - 121) [6] | 10965.12305004174 | (6,818 - 22,531) [6] | 1371 | NS | 99.1 (0)
36 kb | A7 | DSB | msh3D | 43.85299603832114 | (28 - 93) [6] | 31310.68759664861 | (21,560 - 186,879) [6] | 3479 | 3.6 (0.0013) | 95.6 (1.1)
36 kb | A7 | DSB | pol3-5DV msh3D | 483.3199812426308 | (146 - 2,890) [7] | 291652.1473174461 | (42,813 - 474,104) [7] | 704 | 34.0 (0.0003, 0.0047†, 0.0127‡) | 92.4 (3.8)
36 kb | A7 | No | WT | 10.69554598837284 | (2 - 14) [8] | 7.417224481640445 | (0 - 22) [8] | NA | NA | 4.8 (0)
36 kb | A7 | No | msh2D | 745078.3739471674 | (289,360 - 918,023) [6] | 0 | - [6] | NA | 67734.4 (0.0007) | 0 (0)
36 kb | A7 | No | pol3-5DV | 20.78661335712956 | (4 - 35) [6] | 41.16030069176183 | (15 - 126) [6] | NA | 1.9 (0.0293) | 5.3 (0)
36 kb | A7 | No | rev3D | 10.22449303745043 | (4 - 17) [6] | 0 | (0 -25) [6] | NA | NS | ND
36 kb | A7 | No | rad30D | 7.88507946757695 | (6 - 19) [11] | 15.91133004926109 | (0 - 21) [11] | NA | NS | 0 (0)
36 kb | A7 | No | msh3D | 9.075000000000001 | (5 - 44) [10] | 1.1395 | (0 - 94) [10] | NA | NS | ND
36 kb | A7 | No | pol3-5DV msh3D | 413.6353727550089 | (133 - 947) [7] | 313.3056452853408 | (0 - 1,443) [7] | NA | 37.6 (0.0003, 0.0001†, 0.0012‡) | 0 (12.9)
36 kb | A14 | DSB | WT | 13070.63910440121 | (4,184 - 56,583) [8] | 2224522.864982447 | (713,783 - 11,515,027) [8] | 149 | NA | 98.4 (1.6)
36 kb | A14 | No | WT | 14937.16830355583 | (5,862 - 78,194) [6] | 0 | (0 - 5,809) [6] | NA | NA | 1.1 (0)
Chr II, native | A4 | Yes | WT | 14.10296933119966 | (8 - 48) [6] | 30.67400623193773 | (0 - 69) [6] | NA | NA | ND
Chr II, native | A7 | Yes | WT | 36.53900224322985 | (8 - 170) [6] | 24.84475107666976 | (0 - 329) [6] | NA | NA | ND
Chr II, native | A14 | Yes | WT | 4756.504971564639 | (3,346 - 34,711) [6] | 2059.319177620491 | (0 - 7,860) [6] | NA | NA | ND
a Rates calculated at 0h based on 0h frequencies using the Drake equation (see Materials and methods for details). At 7 hrs, rates were calculated as (7h frequency - 0h frequency); differences  <0 are reported as "0".   b For strains with ≥6 experiments, the 95% CI of the median is given. For the strains with <6 experiments, the median range is given. A dash indicates cases where both the minimum and maximum values were 0. c Statistically significant elevation of 7h median rate in strains with a DSB over 0h median rate in isogenic no-DSB controls. Significance determined using the Mann-Whitney U test at the p≤0.05 level. dStatistically significant elevation of: 7h median rate of mutant compared to 7h median rate of WT in strains with a DSB; 0h median rate of mutant compared to 0h median of WT in no-DSB control strains;  parentheses = p-values  determined using the Mann-Whitney U test; †Significant difference of 7h pol3-5DVmsh3D median rate from 7h msh3D median rate in strains with a DSB and 0h pol3-5DVmsh3D median rate from 0h msh3D median rate  in no-DSB control strains ‡Significant difference of 7h pol3-5DVmsh3D median rate from the 7h pol3-5DV median rate in strains with a DSB and 0h pol3-5DVmsh3D median rate from 0h pol3-5DV median rate in no-DSB control strains. e [NAME] for 7h Lys+ colonies for strains with a DSB site and for 0h Lys+ colonies for no-DSB controls; parentheses = percent partial BIR (colonies containing ≥1 Ade+Leu- sector).  For strains with a DSB, 35 - 1000 colonies were analyzed from 2 - 5 independent experiments; for no-DSB controls, 6 - 200 colonies were analyzed from 2 - 5 independent experiments.  Lys+ BIR events observed in no-DSB control could result from extremely rare HO-induced DSBs at MATα-inc or from spontaneous BIR.  Abbreviations:  ND, not determined; NS, not significant; NA, not applicable.