The debate over the city’s statue of Robert E. Lee and the white supremacist march last year set Charlottesville apart, and spurred it to confront its Confederate past. But the city has not fully come to terms with another aspect of its Jim Crow legacy: a school system that segregates students from the time they start, and steers them into separate and unequal tracks.

Charlottesville is “beautiful physically and aesthetically pleasing, but a very ugly-in-the-soul place,” said Nikuyah Walker, who became its first black female mayor during the self-recrimination that swept the city after last year’s white nationalist rallies. “No one has ever attempted to undo that, and that affects whether our children can learn here.”

Today, white students make up 40 percent of Charlottesville’s enrollment, and African-American students about a third. But white children are about four times as likely to be in Charlottesville’s gifted program, while black students are more than four times as likely to be held back a grade and almost five times as likely to be suspended from school, according to a ProPublica/New York Times examination of newly available district and federal data.

Since 2005, the academic gulf between white and black students in Charlottesville has widened in nearly all subjects, including reading, writing, history and science. As of last year, half of all black students in Charlottesville could not read at grade level, compared with only a tenth of white students, according to state data. Black students in Charlottesville lag on average about three and a half grades behind their white peers in reading and math, compared with a national gap of about two grades.

Over the decades, school board members have often brushed aside findings of racial inequality in Charlottesville schools, including a 2004 audit — commissioned by the district’s first African-American superintendent — that blamed inadequate leadership and a history of racism for the persistent underachievement of its black students.

Officials in the 4,500-student district — which spends about $16,000 per pupil, one of the highest rates in the state — instead point to socioeconomic differences. The vast majority of Charlottesville’s black children qualify for free or reduced-price meals at school because of low family income.