While crime in New York City has dropped to historic low levels, the Bronx continues to have large pockets of problems that make it lag behind the rest of the city.

Through July 3, the Bronx has seen a 19.5 percent increase in killings this year compared to 2015, at a time when the city as a whole is witnessing a nearly 9 percent drop, according to most currently available police data.

Overall, some Bronx precincts are seeing serious crimes increase by more than 38 percent even though citywide there is actually a slight decrease.

All police precincts in the Bronx are up a combined 9 percent.

Monday, NYPD Commissioner William Bratton will release half-year crime statistics that will show serious felonies at their lowest levels since the Compstat era started in 1994, with shootings at a historic low level, officials said.

“When you look at shooting numbers, we are far and away the best that we have seen in the modern era, by far, over 100 shootings fewer this year than last,” NYPD Deputy Commissioner Dermot Shea said in an interview.

But Shea and other officials acknowledge that the Bronx continues to have crime problems, particularly in the area of the 40th Precinct, which covers south Bronx communities like Melrose and Concourse Village.

This year serious felonies are up 38.5 percent in the precinct, with killings up over 100 percent, from four in 2015 to nine. Shootings were up about 54 percent, from 11 at the same time last year to 17.

“The crime numbers really separate it from the rest of the boroughs,” said Shea who, as the NYPD’s head of operations, watches crime trends constantly. “The same story, unfortunately, a lot of it driven by gangs. Gangs don’t just commit shootings, they are also out there robbing people, and in that environment in the Bronx, you have a formula that is a challenge at times.”

Shea said the poor neighborhoods and dense public housing areas contribute to making the precinct a difficult command.

“When the 4-0 heats up, it is a challenge,” he said, adding that to combat it, the NYPD has had to bring in resources from other precincts, a common practice in other boroughs.

The 40th Precinct has proved a struggle for able commanders over the years, Shea said. More than a year ago, Inspector Carlos Valdez took over as commander after a scandal erupted in which some precinct cops were accused of fudging crime data to make things look better than they were.

Part of the problem in the 40th Precinct, Shea said, is that the police haven’t been as successful in taking out some of the people driving crime in that area, with a couple of gangs in particular causing problems this year.

“There are things in the works,” he said, hinting that big gang takedowns may be imminent.

While serious crimes have risen in the precinct this year — except for rape and auto theft — historically it is down as much as 80 percent from where things were 20 years ago, police data showed.

Other Bronx precincts, such as the 46th and the 49th, are up in serious crimes by around 19 percent respectively this year. But overall, a big bright spot for the borough is a decline in shootings, with the Bronx seeing a drop of 23 percent, better than the 21-percent citywide number.

“They are having career shooting numbers in the borough,” Shea said of the drop.

Shea stressed that crime trends aren’t the only indicator of changes in the Bronx. After President Jimmy Carter visited a burned out and dilapidated Charlotte Street in the 42nd Precinct in 1976, the borough earned a reputation as a symbol of urban decay. But today, even with crime a problem in some areas, Charlotte Street is now an area of new homes and the Bronx is seeing a growing population.

“Historically, we are doing a lot better,” said John DeSio, spokesman for Bronx Borough President Ruben Diaz Jr.