. 2020 Aug 12;5(4):e00388-20. doi: 10.1128/mSphere.00388-20

TABLE 3.

Distribution of mutation types arising during serial dilution experiments

Serial dilution initiated from	No. total new mutations^a	No. nonsynonymous new mutations^a	No. synonymous new mutations^a	dN/dS^b	P value^c
Population 2 sample 1	41	14	5	0.86	N/A
Population 2 sample 4	18	1	0	N/A	N/A
Clone 2_1	12	10	0	N/A	N/A
Clone 2_2	362	160	104	0.47	<0.0001
Clone 2_6	24	13	8	0.5	N/A
Clone 2_13	4317	2259	1089	0.64	<0.0001
Population 4 sample 1	249	102	65	0.48	<0.0001
Population 4 sample 4	312	119	74	0.49	<0.0001
Clone 4_1	286	122	68	0.55	<0.0001
Clone 4_4	336	182	50	1.12	0.39
Clone 4_5	252	106	86	0.38	<0.0001
Clone 4_9	322	160	70	0.7	0.017

New mutations are mutations that did not appear in the ancestral clone with which the serial dilution experiments were initiated. In the case of whole population samples, new mutations are those mutations that were never seen in our sequencing of clones from that population at any of the six sequenced time points up to and including day 127. The sum of the nonsynonymous and synonymous new mutations does not match the total number of new mutations, as mutations can also be noncoding, frameshift, or nonsense.

dN/dS (the ratio of the rates of nonsynonymous to synonymous mutations) was calculated as $\frac{dN}{dS} = \frac{\frac{# non - syn new mutations}{# non - syn sites}}{\frac{# syn new mutations}{# syn sites}}$ , where numbers of syn (synonymous) and nonsynonymous new mutations are given in the previous two columns of the table and the number of synonymous and nonsynonymous sites are calculated based on a combination of all E. coli protein-coding genes (see the Materials and Methods section).

χ² P value with which it is possible to reject the null hypothesis that there is no enrichment in nonsynonymous or synonymous mutations, relative to random expectations based on the number of nonsynonymous and synonymous sites within E. coli protein coding genes. N/A, not applicable.