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India, who had lost 2-4 against Tajikistan and 2-5 against North Korea, collected their first points of the tournament though they ended at the bottom of the table with just one point.
Returning after a three-year hiatus, the 129th edition of the tournament will feature six I-League and five Indian Super League teams, including defending champions of the respective tournaments -- Chennai City FC and Bengaluru FC.
The champions got richer by USD 50,000 while the runners-up received USD 25,000.
The loss put the home side virtually out of reckoning for a berth in the final as they occupy the bottom of the points table.
The All India Football Federation's (AIFF) plan to merge the franchise-based Indian Super League (ISL) with the I-League has faced major obstacles, leaving fans and stakeholders confused about the future of club football.
The 87-ranked Oman turned it around in the last eight minutes of regulation time by scoring twice through Rabia Alawi Al Mandhar, leaving the hosts distraught.
Despite playing without their talismanic captain Sunil Chhetri who was laid low by fever, the young Indians denied Qatar, who won the Asian Cup title in January, any goal despite the home side having more than one dozen shots on target.
With just three points from five matches, India still remain at fourth spot in the Group E table, headed by Asian champions Qatar who have 13 points from five matches. Oman are at second spot with 12 points.
The result meant the 106-ranked India remained winless in their qualifying campaign so far.
The sixth Indian Super League will have a new team with Hyderabad FC, a city with a storied past in football, replacing FC Pune City, a club that has been plagued by financial problems in recent years.
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