IGV visualization of alignments in region chr1:1,510,446–1,510,622 from the (a) Trio NA12878 Illumina reads from 1000 Genomes and (b) NA12878 HiSeq reads before (left) and after (right) multiple sequence realignment. Reads are depicted as arrows oriented by increasing machine cycle; highlighted bases indicate mismatches to the reference: A is green, G is orange, T is red, and deleted bases are dashes; a coverage histogram per base is shown above the reads. Both the 4bp indel (rs34877486) and the C/T polymorphism (rs28788874) are present in dbSNP, as are the artifactual A/G polymorphisms (rs28782535 and rs28783181) resulting from the mis-modeled indel, indicating that these sites are common misalignment errors.