TABLE 1.

Within-patient V. cholerae diversity profiles from 15 metagenomes^a

Patient and/or day	Total no. of iSNVs	No. of nonsynonymous iSNVs	No. of synonymous iSNVs	No. of intergenic iSNVs	Mean coverage (×)	iRep value	DNA repair and proofreading genes with NS mutation
A	93	6	0	87	451.3	3.34
B	18	7	5	6	111.4	1.7
C	6	0	1	5	111.8	1.7
D	41	22	9	10	10	5.43	DNA polymerase II
E
Day 1	8	2	1	5	351	3.25
Day 2	21	7	1	13	258	1.23
F	207	133	47	27	18.2	2.48	DNA mismatch repair endonuclease MutL; nuclease SbcCD subunit C
G	16	12	3	1	7.7	1.73
H	32	21	11	0	98.5	4.75	Excinuclease ABC subunit UvrB
I	75	55	20	0	13	2.79	MutT/nudix family protein
J	6	1	0	5	424.6	1.84
K	25	13	6	6	18	1.69	Formamidopyrimidine-DNA glycosylase mutM
L	13	9	1	3	164.4	2.67
M	2	0	1	1	113	2.65
N	7	2	1	3	6.7	2.27

^aMutations segregating within patients are denoted iSNVs. The number of iSNVs and mean coverage values were computed with InStrain (27), and replication rates were determined with iRep (39).