Martin Krzywinski | Genome Sciences Center
haploid statistics | diploid statistics | triploid statistics

Haploid Genome Coverage Tables

Given a location x defined in the context of h associated chromosomes, the probability that position x is covered at least φ times is Ph,φ and given by

For more details, see Wendl, M.C. and R.K. Wilson. 2008. Aspects of coverage in medical DNA sequencing. BMC Bioinformatics 9: 239.

For a given sequencing redundancy ρ (e.g. 1-fold, 2-fold, 3-fold, etc) of a haploid genome, the fraction of the genome represented by at least φ reads is reported (Ph,φ). Additionally, coverage by fewer than φ reads is reported (1-Ph,φ), as is the coverage by exactly φ reads (Ph,φ - Ph,φ+1).

Entries for which fractional coverage is <0.0001 are not shown.

A rudimentary Monte Carlo simulation of genome coverage is also available, and is a useful supplement to the exact probabilities shown here.

EXAMPLE 1

Suppose you carried out 3-fold redundant (ρ=3) sequencing of a haploid genome. 95.02% of the genome will be covered by at least one read (P1,1) while 22.40% will be covered by exactly 3 reads (Ph,3 - Ph,4).

ANALYTICAL vs STOCHASTIC

View plot that compares analytical vs stochastic results.

HAPLOID vs DIPLOID

View plot that compares 100x and 200x coverage of haploid and diploid genomes.

CODE

Download Perl scripts for analytical (to produce the tables below for any ρ) and stochastic coverage calculations.

View table for sequencing redundancy ρ = 1 2 3 4 5 6 7 8 9 10 15 20 25 30 40 50 100

sequencing redundancy 1-fold

φ Ph,φ - Ph,φ+1 1-Ph,φ Ph,φ
0 0.3679 0.0000 1.0000
1 0.3679 0.3679 0.6321
2 0.1839 0.7358 0.2642
3 0.0613 0.9197 0.0803
4 0.0153 0.9810 0.0190
5 0.0031 0.9963 0.0037
^top

sequencing redundancy 2-fold

φ Ph,φ - Ph,φ+1 1-Ph,φ Ph,φ
0 0.1353 0.0000 1.0000
1 0.2707 0.1353 0.8647
2 0.2707 0.4060 0.5940
3 0.1804 0.6767 0.3233
4 0.0902 0.8571 0.1429
5 0.0361 0.9473 0.0527
6 0.0120 0.9834 0.0166
7 0.0034 0.9955 0.0045
8 0.0009 0.9989 0.0011
9 0.0002 0.9998 0.0002
^top

sequencing redundancy 3-fold

φ Ph,φ - Ph,φ+1 1-Ph,φ Ph,φ
0 0.0498 0.0000 1.0000
1 0.1494 0.0498 0.9502
2 0.2240 0.1991 0.8009
3 0.2240 0.4232 0.5768
4 0.1680 0.6472 0.3528
5 0.1008 0.8153 0.1847
6 0.0504 0.9161 0.0839
7 0.0216 0.9665 0.0335
8 0.0081 0.9881 0.0119
9 0.0027 0.9962 0.0038
10 0.0008 0.9989 0.0011
11 0.0002 0.9997 0.0003
^top

sequencing redundancy 4-fold

φ Ph,φ - Ph,φ+1 1-Ph,φ Ph,φ
0 0.0183 0.0000 1.0000
1 0.0733 0.0183 0.9817
2 0.1465 0.0916 0.9084
3 0.1954 0.2381 0.7619
4 0.1954 0.4335 0.5665
5 0.1563 0.6288 0.3712
6 0.1042 0.7851 0.2149
7 0.0595 0.8893 0.1107
8 0.0298 0.9489 0.0511
9 0.0132 0.9786 0.0214
10 0.0053 0.9919 0.0081
11 0.0019 0.9972 0.0028
12 0.0006 0.9991 0.0009
13 0.0002 0.9997 0.0003
^top

sequencing redundancy 5-fold

φ Ph,φ - Ph,φ+1 1-Ph,φ Ph,φ
0 0.0067 0.0000 1.0000
1 0.0337 0.0067 0.9933
2 0.0842 0.0404 0.9596
3 0.1404 0.1247 0.8753
4 0.1755 0.2650 0.7350
5 0.1755 0.4405 0.5595
6 0.1462 0.6160 0.3840
7 0.1044 0.7622 0.2378
8 0.0653 0.8666 0.1334
9 0.0363 0.9319 0.0681
10 0.0181 0.9682 0.0318
11 0.0082 0.9863 0.0137
12 0.0034 0.9945 0.0055
13 0.0013 0.9980 0.0020
14 0.0005 0.9993 0.0007
15 0.0002 0.9998 0.0002
^top

sequencing redundancy 6-fold

φ Ph,φ - Ph,φ+1 1-Ph,φ Ph,φ
0 0.0025 0.0000 1.0000
1 0.0149 0.0025 0.9975
2 0.0446 0.0174 0.9826
3 0.0892 0.0620 0.9380
4 0.1339 0.1512 0.8488
5 0.1606 0.2851 0.7149
6 0.1606 0.4457 0.5543
7 0.1377 0.6063 0.3937
8 0.1033 0.7440 0.2560
9 0.0688 0.8472 0.1528
10 0.0413 0.9161 0.0839
11 0.0225 0.9574 0.0426
12 0.0113 0.9799 0.0201
13 0.0052 0.9912 0.0088
14 0.0022 0.9964 0.0036
15 0.0009 0.9986 0.0014
16 0.0003 0.9995 0.0005
17 0.0001 0.9998 0.0002
^top

sequencing redundancy 7-fold

φ Ph,φ - Ph,φ+1 1-Ph,φ Ph,φ
0 0.0009 0.0000 1.0000
1 0.0064 0.0009 0.9991
2 0.0223 0.0073 0.9927
3 0.0521 0.0296 0.9704
4 0.0912 0.0818 0.9182
5 0.1277 0.1730 0.8270
6 0.1490 0.3007 0.6993
7 0.1490 0.4497 0.5503
8 0.1304 0.5987 0.4013
9 0.1014 0.7291 0.2709
10 0.0710 0.8305 0.1695
11 0.0452 0.9015 0.0985
12 0.0263 0.9467 0.0533
13 0.0142 0.9730 0.0270
14 0.0071 0.9872 0.0128
15 0.0033 0.9943 0.0057
16 0.0014 0.9976 0.0024
17 0.0006 0.9990 0.0010
18 0.0002 0.9996 0.0004
19 0.0001 0.9999 0.0001
^top

sequencing redundancy 8-fold

φ Ph,φ - Ph,φ+1 1-Ph,φ Ph,φ
0 0.0003 0.0000 1.0000
1 0.0027 0.0003 0.9997
2 0.0107 0.0030 0.9970
3 0.0286 0.0138 0.9862
4 0.0573 0.0424 0.9576
5 0.0916 0.0996 0.9004
6 0.1221 0.1912 0.8088
7 0.1396 0.3134 0.6866
8 0.1396 0.4530 0.5470
9 0.1241 0.5925 0.4075
10 0.0993 0.7166 0.2834
11 0.0722 0.8159 0.1841
12 0.0481 0.8881 0.1119
13 0.0296 0.9362 0.0638
14 0.0169 0.9658 0.0342
15 0.0090 0.9827 0.0173
16 0.0045 0.9918 0.0082
17 0.0021 0.9963 0.0037
18 0.0009 0.9984 0.0016
19 0.0004 0.9993 0.0007
20 0.0002 0.9997 0.0003
^top

sequencing redundancy 9-fold

φ Ph,φ - Ph,φ+1 1-Ph,φ Ph,φ
0 0.0001 0.0000 1.0000
1 0.0011 0.0001 0.9999
2 0.0050 0.0012 0.9988
3 0.0150 0.0062 0.9938
4 0.0337 0.0212 0.9788
5 0.0607 0.0550 0.9450
6 0.0911 0.1157 0.8843
7 0.1171 0.2068 0.7932
8 0.1318 0.3239 0.6761
9 0.1318 0.4557 0.5443
10 0.1186 0.5874 0.4126
11 0.0970 0.7060 0.2940
12 0.0728 0.8030 0.1970
13 0.0504 0.8758 0.1242
14 0.0324 0.9261 0.0739
15 0.0194 0.9585 0.0415
16 0.0109 0.9780 0.0220
17 0.0058 0.9889 0.0111
18 0.0029 0.9947 0.0053
19 0.0014 0.9976 0.0024
20 0.0006 0.9989 0.0011
21 0.0003 0.9996 0.0004
22 0.0001 0.9998 0.0002
^top

sequencing redundancy 10-fold

φ Ph,φ - Ph,φ+1 1-Ph,φ Ph,φ
1 0.0005 0.0000 1.0000
2 0.0023 0.0005 0.9995
3 0.0076 0.0028 0.9972
4 0.0189 0.0103 0.9897
5 0.0378 0.0293 0.9707
6 0.0631 0.0671 0.9329
7 0.0901 0.1301 0.8699
8 0.1126 0.2202 0.7798
9 0.1251 0.3328 0.6672
10 0.1251 0.4579 0.5421
11 0.1137 0.5830 0.4170
12 0.0948 0.6968 0.3032
13 0.0729 0.7916 0.2084
14 0.0521 0.8645 0.1355
15 0.0347 0.9165 0.0835
16 0.0217 0.9513 0.0487
17 0.0128 0.9730 0.0270
18 0.0071 0.9857 0.0143
19 0.0037 0.9928 0.0072
20 0.0019 0.9965 0.0035
21 0.0009 0.9984 0.0016
22 0.0004 0.9993 0.0007
23 0.0002 0.9997 0.0003
24 0.0001 0.9999 0.0001
^top

sequencing redundancy 15-fold

φ Ph,φ - Ph,φ+1 1-Ph,φ Ph,φ
3 0.0002 0.0000 1.0000
4 0.0006 0.0002 0.9998
5 0.0019 0.0009 0.9991
6 0.0048 0.0028 0.9972
7 0.0104 0.0076 0.9924
8 0.0194 0.0180 0.9820
9 0.0324 0.0374 0.9626
10 0.0486 0.0699 0.9301
11 0.0663 0.1185 0.8815
12 0.0829 0.1848 0.8152
13 0.0956 0.2676 0.7324
14 0.1024 0.3632 0.6368
15 0.1024 0.4657 0.5343
16 0.0960 0.5681 0.4319
17 0.0847 0.6641 0.3359
18 0.0706 0.7489 0.2511
19 0.0557 0.8195 0.1805
20 0.0418 0.8752 0.1248
21 0.0299 0.9170 0.0830
22 0.0204 0.9469 0.0531
23 0.0133 0.9673 0.0327
24 0.0083 0.9805 0.0195
25 0.0050 0.9888 0.0112
26 0.0029 0.9938 0.0062
27 0.0016 0.9967 0.0033
28 0.0009 0.9983 0.0017
29 0.0004 0.9991 0.0009
30 0.0002 0.9996 0.0004
31 0.0001 0.9998 0.0002
^top

sequencing redundancy 20-fold

φ Ph,φ - Ph,φ+1 1-Ph,φ Ph,φ
6 0.0002 0.0001 0.9999
7 0.0005 0.0003 0.9997
8 0.0013 0.0008 0.9992
9 0.0029 0.0021 0.9979
10 0.0058 0.0050 0.9950
11 0.0106 0.0108 0.9892
12 0.0176 0.0214 0.9786
13 0.0271 0.0390 0.9610
14 0.0387 0.0661 0.9339
15 0.0516 0.1049 0.8951
16 0.0646 0.1565 0.8435
17 0.0760 0.2211 0.7789
18 0.0844 0.2970 0.7030
19 0.0888 0.3814 0.6186
20 0.0888 0.4703 0.5297
21 0.0846 0.5591 0.4409
22 0.0769 0.6437 0.3563
23 0.0669 0.7206 0.2794
24 0.0557 0.7875 0.2125
25 0.0446 0.8432 0.1568
26 0.0343 0.8878 0.1122
27 0.0254 0.9221 0.0779
28 0.0181 0.9475 0.0525
29 0.0125 0.9657 0.0343
30 0.0083 0.9782 0.0218
31 0.0054 0.9865 0.0135
32 0.0034 0.9919 0.0081
33 0.0020 0.9953 0.0047
34 0.0012 0.9973 0.0027
35 0.0007 0.9985 0.0015
36 0.0004 0.9992 0.0008
37 0.0002 0.9996 0.0004
38 0.0001 0.9998 0.0002
39 0.0001 0.9999 0.0001
^top

sequencing redundancy 25-fold

φ Ph,φ - Ph,φ+1 1-Ph,φ Ph,φ
9 0.0001 0.0001 0.9999
10 0.0004 0.0002 0.9998
11 0.0008 0.0006 0.9994
12 0.0017 0.0014 0.9986
13 0.0033 0.0031 0.9969
14 0.0059 0.0065 0.9935
15 0.0099 0.0124 0.9876
16 0.0155 0.0223 0.9777
17 0.0227 0.0377 0.9623
18 0.0316 0.0605 0.9395
19 0.0415 0.0920 0.9080
20 0.0519 0.1336 0.8664
21 0.0618 0.1855 0.8145
22 0.0702 0.2473 0.7527
23 0.0763 0.3175 0.6825
24 0.0795 0.3939 0.6061
25 0.0795 0.4734 0.5266
26 0.0765 0.5529 0.4471
27 0.0708 0.6294 0.3706
28 0.0632 0.7002 0.2998
29 0.0545 0.7634 0.2366
30 0.0454 0.8179 0.1821
31 0.0366 0.8633 0.1367
32 0.0286 0.8999 0.1001
33 0.0217 0.9285 0.0715
34 0.0159 0.9502 0.0498
35 0.0114 0.9662 0.0338
36 0.0079 0.9775 0.0225
37 0.0053 0.9854 0.0146
38 0.0035 0.9908 0.0092
39 0.0023 0.9943 0.0057
40 0.0014 0.9966 0.0034
41 0.0009 0.9980 0.0020
42 0.0005 0.9988 0.0012
43 0.0003 0.9993 0.0007
44 0.0002 0.9996 0.0004
45 0.0001 0.9998 0.0002
46 0.0001 0.9999 0.0001
^top

sequencing redundancy 30-fold

φ Ph,φ - Ph,φ+1 1-Ph,φ Ph,φ
12 0.0001 0.0001 0.9999
13 0.0002 0.0002 0.9998
14 0.0005 0.0004 0.9996
15 0.0010 0.0009 0.9991
16 0.0019 0.0019 0.9981
17 0.0034 0.0039 0.9961
18 0.0057 0.0073 0.9927
19 0.0089 0.0129 0.9871
20 0.0134 0.0219 0.9781
21 0.0192 0.0353 0.9647
22 0.0261 0.0544 0.9456
23 0.0341 0.0806 0.9194
24 0.0426 0.1146 0.8854
25 0.0511 0.1572 0.8428
26 0.0590 0.2084 0.7916
27 0.0655 0.2673 0.7327
28 0.0702 0.3329 0.6671
29 0.0726 0.4031 0.5969
30 0.0726 0.4757 0.5243
31 0.0703 0.5484 0.4516
32 0.0659 0.6186 0.3814
33 0.0599 0.6845 0.3155
34 0.0529 0.7444 0.2556
35 0.0453 0.7973 0.2027
36 0.0378 0.8426 0.1574
37 0.0306 0.8804 0.1196
38 0.0242 0.9110 0.0890
39 0.0186 0.9352 0.0648
40 0.0139 0.9537 0.0463
41 0.0102 0.9677 0.0323
42 0.0073 0.9779 0.0221
43 0.0051 0.9852 0.0148
44 0.0035 0.9903 0.0097
45 0.0023 0.9937 0.0063
46 0.0015 0.9960 0.0040
47 0.0010 0.9975 0.0025
48 0.0006 0.9985 0.0015
49 0.0004 0.9991 0.0009
50 0.0002 0.9995 0.0005
51 0.0001 0.9997 0.0003
52 0.0001 0.9998 0.0002
^top

sequencing redundancy 40-fold

φ Ph,φ - Ph,φ+1 1-Ph,φ Ph,φ
20 0.0002 0.0002 0.9998
21 0.0004 0.0004 0.9996
22 0.0007 0.0007 0.9993
23 0.0012 0.0014 0.9986
24 0.0019 0.0026 0.9974
25 0.0031 0.0045 0.9955
26 0.0047 0.0076 0.9924
27 0.0070 0.0123 0.9877
28 0.0100 0.0193 0.9807
29 0.0138 0.0294 0.9706
30 0.0185 0.0432 0.9568
31 0.0238 0.0617 0.9383
32 0.0298 0.0855 0.9145
33 0.0361 0.1153 0.8847
34 0.0425 0.1514 0.8486
35 0.0485 0.1939 0.8061
36 0.0539 0.2424 0.7576
37 0.0583 0.2963 0.7037
38 0.0614 0.3547 0.6453
39 0.0629 0.4160 0.5840
40 0.0629 0.4790 0.5210
41 0.0614 0.5419 0.4581
42 0.0585 0.6033 0.3967
43 0.0544 0.6618 0.3382
44 0.0495 0.7162 0.2838
45 0.0440 0.7657 0.2343
46 0.0382 0.8097 0.1903
47 0.0325 0.8479 0.1521
48 0.0271 0.8804 0.1196
49 0.0221 0.9075 0.0925
50 0.0177 0.9297 0.0703
51 0.0139 0.9474 0.0526
52 0.0107 0.9613 0.0387
53 0.0081 0.9719 0.0281
54 0.0060 0.9800 0.0200
55 0.0043 0.9860 0.0140
56 0.0031 0.9903 0.0097
57 0.0022 0.9934 0.0066
58 0.0015 0.9956 0.0044
59 0.0010 0.9971 0.0029
60 0.0007 0.9981 0.0019
61 0.0004 0.9988 0.0012
62 0.0003 0.9992 0.0008
63 0.0002 0.9995 0.0005
64 0.0001 0.9997 0.0003
65 0.0001 0.9998 0.0002
66 0.0000 0.9999 0.0001
^top

sequencing redundancy 50-fold

φ Ph,φ - Ph,φ+1 1-Ph,φ Ph,φ
27 0.0001 0.0001 0.9999
28 0.0002 0.0003 0.9997
29 0.0004 0.0005 0.9995
30 0.0007 0.0009 0.9991
31 0.0011 0.0016 0.9984
32 0.0017 0.0027 0.9973
33 0.0026 0.0044 0.9956
34 0.0038 0.0070 0.9930
35 0.0054 0.0108 0.9892
36 0.0075 0.0162 0.9838
37 0.0102 0.0238 0.9762
38 0.0134 0.0340 0.9660
39 0.0172 0.0474 0.9526
40 0.0215 0.0646 0.9354
41 0.0262 0.0861 0.9139
42 0.0312 0.1123 0.8877
43 0.0363 0.1435 0.8565
44 0.0412 0.1798 0.8202
45 0.0458 0.2210 0.7790
46 0.0498 0.2669 0.7331
47 0.0530 0.3167 0.6833
48 0.0552 0.3697 0.6303
49 0.0563 0.4249 0.5751
50 0.0563 0.4812 0.5188
51 0.0552 0.5375 0.4625
52 0.0531 0.5927 0.4073
53 0.0501 0.6458 0.3542
54 0.0464 0.6959 0.3041
55 0.0422 0.7423 0.2577
56 0.0376 0.7845 0.2155
57 0.0330 0.8221 0.1779
58 0.0285 0.8551 0.1449
59 0.0241 0.8836 0.1164
60 0.0201 0.9077 0.0923
61 0.0165 0.9278 0.0722
62 0.0133 0.9443 0.0557
63 0.0105 0.9576 0.0424
64 0.0082 0.9682 0.0318
65 0.0063 0.9764 0.0236
66 0.0048 0.9827 0.0173
67 0.0036 0.9875 0.0125
68 0.0026 0.9911 0.0089
69 0.0019 0.9938 0.0062
70 0.0014 0.9957 0.0043
71 0.0010 0.9970 0.0030
72 0.0007 0.9980 0.0020
73 0.0005 0.9987 0.0013
74 0.0003 0.9991 0.0009
75 0.0002 0.9994 0.0006
76 0.0001 0.9996 0.0004
77 0.0001 0.9998 0.0002
78 0.0001 0.9999 0.0001
^top

sequencing redundancy 100-fold

φ Ph,φ - Ph,φ+1 1-Ph,φ Ph,φ
66 0.0001 0.0001 0.9999
67 0.0001 0.0002 0.9998
68 0.0002 0.0003 0.9997
69 0.0002 0.0004 0.9996
70 0.0003 0.0007 0.9993
71 0.0004 0.0010 0.9990
72 0.0006 0.0014 0.9986
73 0.0008 0.0020 0.9980
74 0.0011 0.0028 0.9972
75 0.0015 0.0040 0.9960
76 0.0020 0.0055 0.9945
77 0.0026 0.0074 0.9926
78 0.0033 0.0100 0.9900
79 0.0042 0.0133 0.9867
80 0.0052 0.0175 0.9825
81 0.0064 0.0226 0.9774
82 0.0078 0.0291 0.9709
83 0.0094 0.0369 0.9631
84 0.0112 0.0463 0.9537
85 0.0132 0.0575 0.9425
86 0.0154 0.0708 0.9292
87 0.0176 0.0861 0.9139
88 0.0201 0.1038 0.8962
89 0.0225 0.1238 0.8762
90 0.0250 0.1463 0.8537
91 0.0275 0.1714 0.8286
92 0.0299 0.1989 0.8011
93 0.0322 0.2288 0.7712
94 0.0342 0.2610 0.7390
95 0.0360 0.2952 0.7048
96 0.0375 0.3312 0.6688
97 0.0387 0.3687 0.6313
98 0.0395 0.4074 0.5926
99 0.0399 0.4468 0.5532
100 0.0399 0.4867 0.5133
101 0.0395 0.5266 0.4734
102 0.0387 0.5660 0.4340
103 0.0376 0.6047 0.3953
104 0.0361 0.6423 0.3577
105 0.0344 0.6784 0.3216
106 0.0325 0.7128 0.2872
107 0.0303 0.7453 0.2547
108 0.0281 0.7756 0.2244
109 0.0258 0.8037 0.1963
110 0.0234 0.8294 0.1706
111 0.0211 0.8529 0.1471
112 0.0188 0.8740 0.1260
113 0.0167 0.8928 0.1072
114 0.0146 0.9095 0.0905
115 0.0127 0.9241 0.0759
116 0.0110 0.9368 0.0632
117 0.0094 0.9478 0.0522
118 0.0079 0.9572 0.0428
119 0.0067 0.9651 0.0349
120 0.0056 0.9718 0.0282
121 0.0046 0.9773 0.0227
122 0.0038 0.9819 0.0181
123 0.0031 0.9857 0.0143
124 0.0025 0.9888 0.0112
125 0.0020 0.9912 0.0088
126 0.0016 0.9932 0.0068
127 0.0012 0.9948 0.0052
128 0.0010 0.9960 0.0040
129 0.0007 0.9970 0.0030
130 0.0006 0.9977 0.0023
131 0.0004 0.9983 0.0017
132 0.0003 0.9987 0.0013
133 0.0003 0.9991 0.0009
134 0.0002 0.9993 0.0007
135 0.0001 0.9995 0.0005
136 0.0001 0.9996 0.0004
137 0.0001 0.9997 0.0003
138 0.0001 0.9998 0.0002
139 0.0000 0.9999 0.0001