polipo.bam

230194 reads, size:14680064 bytes, created 2017-04-03 15:04:17

Mapping stats:

Number of alignments in various mapping quality (MAPQ) intervals and number of unmapped sequences.

Number Percentage
MAPQ >= 30 190549.0 82.8
MAPQ < 30 0.0 0.0
MAPQ < 20 0.0 0.0
MAPQ < 10 24861.0 10.8
MAPQ < 3 7607.0 3.3
Unmapped 7177.0 3.1
Total 230194.0 100.0

Number of alignments in various mapping quality (MAPQ) intervals and number of unmapped sequences.

Read Length Distributions

  • MAPQ >= 30
  • MAPQ < 10
  • MAPQ < 3
  • Unmapped
  • MAPQ >= 30
  • MAPQ < 10
  • MAPQ < 3
  • Unmapped
  • MAPQ >= 30
  • MAPQ < 10
  • MAPQ < 3
  • Unmapped
  • MAPQ >= 30
  • MAPQ < 10
  • MAPQ < 3
  • Unmapped

Distribution of read lengths separated by mapping quality thresholds.

Base Quality Distributions

  • MAPQ >= 30
  • MAPQ < 10
  • MAPQ < 3
  • Unmapped
  • MAPQ >= 30
  • MAPQ < 10
  • MAPQ < 3
  • Unmapped
  • MAPQ >= 30
  • MAPQ < 10
  • MAPQ < 3
  • Unmapped
  • MAPQ >= 30
  • MAPQ < 10
  • MAPQ < 3
  • Unmapped

Base quality distributions separated by mapping quality thresholds.

Composition of MAPQ >= 20 Reads.

  • A
  • C
  • G
  • T

A HMM was trained on a subset of the sequences. Shown are log2 odds ratios comparing emission probabilities in match states to background nucleotide probabilities. Values above 0 indicate positional enrichment of a particular nucleotide. "L" indicates the emission probabilities for a state modelling residiues in the middle of the reads.

Composition of 0 >= MAPQ < 20 Reads.

  • A
  • C
  • G
  • T

A HMM was trained on a subset of the sequences. Shown are log2 odds ratios comparing emission probabilities in match states to background nucleotide probabilities. Values above 0 indicate positional enrichment of a particular nucleotide. "L" indicates the emission probabilities for a state modelling residiues in the middle of the reads.

Composition of unmapped reads.

  • A
  • C
  • G
  • T

A HMM was trained on a subset of the sequences. Shown are log2 odds ratios comparing emission probabilities in match states to background nucleotide probabilities. Values above 0 indicate positional enrichment of a particular nucleotide. "L" indicates the emission probabilities for a state modelling residiues in the middle of the reads.

Distribution of Mismatches (MAPQ >= 30):

  • A
  • T
  • A
  • T
  • A
  • T
  • A
  • T

Distribution of Mismatches in MAPQ >= 30 reads.

Distribution of Mismatches (MAPQ < 30):

  • A
  • T
  • A
  • T
  • A
  • T
  • A
  • T

Distribution of Mismatches in MAPQ < 30 reads.

Distribution of Mismatches (MAPQ < 20):

  • A
  • T
  • A
  • T
  • A
  • T
  • A
  • T

Distribution of Mismatches in MAPQ < 20 reads.

Distribution of Mismatches (MAPQ < 10):

  • A
  • T
  • A
  • T
  • A
  • T
  • A
  • T

Distribution of Mismatches in MAPQ < 10 reads.

Distribution of Mismatches(MAPQ < 3):

  • A
  • T
  • A
  • T
  • A
  • T
  • A
  • T

Distribution of Mismatches in MAPQ < 3 reads.

Number of Errors Per Read (MAPQ >= 30):

  • Errors

Barplot shows the percentage of reads (y-axis) with 0, 1, 2 ... errors (x axis) for MAPQ >= 30 reads.

Number of Errors Per Read(MAPQ < 10):

  • Errors

Barplot shows the percentage of reads (y-axis) with 0, 1, 2 ... errors (x axis) for MAPQ < 10 reads.

Number of Errors Per Read(MAPQ < 3):

  • Errors

Barplot shows the percentage of reads (y-axis) with 0, 1, 2 ... errors (x axis) for MAPQ < 3 reads.