## Cycle-specific base calls and read quality

Per-cycle base call should usually be approximately uniform across cycles. Genome Analyzer `control' lane results often show a deline in A and increase in T as cycles progress. This is likely an artifact of the underlying technology.

      perCycle <- qa[["perCycle"]]
      ShortRead:::.plotCycleBaseCall(perCycle$baseCall)

@CYCLE_BASE_CALL_FIGURE@

Per-cycle quality score. Reported quality scores are `calibrated', i.e., incorporating phred-like adjustments following sequence alignment. These typically decline with cycle, in an accelerating manner. Abrupt transitions in quality between cycles toward the end of the read might result when only some of the cycles are used for alignment: the cycles included in the alignment are calibrated more effectively than the reads excluded from the alignment.

      perCycle <- qa[["perCycle"]]
      ShortRead:::.plotCycleQuality(perCycle$quality)

@CYCLE_QUALITY_FIGURE@