What do you mean with direct sequencing? Sanger sequencing? What is your target: gDNA, PCR product or product cloned into a plasmid? From my experience GC-rich templates forms more stable secondary structures and addition of 5-10% DMSO to the sequencing reaction solve this problem.

someone told me to use GC-rich when i would like to do PCR from human genomic DNA, due to it will make easier to get amplified PCR fragment. I will sequencing this PCR product to determine single nucleotide polymorphisms (SNPs). I'm just curious does GC-rich will distract my sequencing result by inserting to PCR fragment ?

For primer specificity the choosing the more GC- rich stretches of DNA (in your target gene) are better (but not repeats, of curse). I think someone who advise use of GC-rich sequence, means primer construction.

Bad performance of sequencing reaction could be due to: 1. target amount and purity; 2. unspecificity of reaction (primers anneals to several places in your DNA); 3. any repeats in the sequence (for example ATATATATATTTTTT), then you see in your chromatogram, that sequence stops at the repeat;  3. Sequencing of GC-rich sequence could also be affected by secondary structures. 4. Other protocol issues like loss of the product at the purification step. Nb 3.and 4. could be solved by addition of DMSO.

If you see some difference in your sequence from expected template, there could be variation in your DNA sample from reference gene or you amplification is not specific. Microsatellites are usually stable if any present in a gene, only repeat length could vary by alleles. Do you see clear difference, or your chromatograms are with pure quality/unexpected stops?

The chromatograms shows to many C (cytosin) peak whereas it does not appear in reference gene sequence