E2348-69.bam

5841578 reads, size:374843846 bytes, created 2025-02-06 09:35:39

Mapping stats:

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

Number Percentage
MAPQ >= 30 5424813.0 92.9
MAPQ < 30 9706.0 0.2
MAPQ < 20 1824.0 0.0
MAPQ < 10 1862.0 0.0
MAPQ < 3 520.0 0.0
Unmapped 402853.0 6.9
Total 5841578.0 100.0

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

Read Length Distributions

  • MAPQ >= 30
  • MAPQ < 30
  • MAPQ < 20
  • MAPQ < 10
  • MAPQ < 3
  • Unmapped
  • MAPQ >= 30
  • MAPQ < 30
  • MAPQ < 20
  • MAPQ < 10
  • MAPQ < 3
  • Unmapped
  • MAPQ >= 30
  • MAPQ < 30
  • MAPQ < 20
  • MAPQ < 10
  • MAPQ < 3
  • Unmapped
  • MAPQ >= 30
  • MAPQ < 30
  • MAPQ < 20
  • MAPQ < 10
  • MAPQ < 3
  • Unmapped
  • MAPQ >= 30
  • MAPQ < 30
  • MAPQ < 20
  • MAPQ < 10
  • MAPQ < 3
  • Unmapped
  • MAPQ >= 30
  • MAPQ < 30
  • MAPQ < 20
  • MAPQ < 10
  • MAPQ < 3
  • Unmapped
  • MAPQ >= 30
  • MAPQ < 30
  • MAPQ < 20
  • MAPQ < 10
  • MAPQ < 3
  • Unmapped

Distribution of read lengths separated by mapping quality thresholds.

Base Quality Distributions

  • MAPQ >= 30
  • MAPQ < 30
  • MAPQ < 20
  • MAPQ < 10
  • MAPQ < 3
  • Unmapped
  • MAPQ >= 30
  • MAPQ < 30
  • MAPQ < 20
  • MAPQ < 10
  • MAPQ < 3
  • Unmapped
  • MAPQ >= 30
  • MAPQ < 30
  • MAPQ < 20
  • MAPQ < 10
  • MAPQ < 3
  • Unmapped
  • MAPQ >= 30
  • MAPQ < 30
  • MAPQ < 20
  • MAPQ < 10
  • MAPQ < 3
  • Unmapped
  • MAPQ >= 30
  • MAPQ < 30
  • MAPQ < 20
  • MAPQ < 10
  • MAPQ < 3
  • Unmapped
  • MAPQ >= 30
  • MAPQ < 30
  • MAPQ < 20
  • MAPQ < 10
  • MAPQ < 3
  • Unmapped
  • MAPQ >= 30
  • MAPQ < 30
  • MAPQ < 20
  • MAPQ < 10
  • MAPQ < 3
  • Unmapped
  • MAPQ >= 30
  • MAPQ < 30
  • MAPQ < 20
  • 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):

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  • G
  • T
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Distribution of Mismatches in MAPQ >= 30 reads.

Distribution of Mismatches (MAPQ < 30):

  • A
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  • G
  • T
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Distribution of Mismatches in MAPQ < 30 reads.

Distribution of Mismatches (MAPQ < 20):

  • A
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  • G
  • T
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Distribution of Mismatches in MAPQ < 20 reads.

Distribution of Mismatches (MAPQ < 10):

  • A
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Distribution of Mismatches in MAPQ < 10 reads.

Distribution of Mismatches(MAPQ < 3):

  • A
  • C
  • G
  • T
  • A
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Distribution of Mismatches in MAPQ < 3 reads.

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

  • Errors
  • Errors
  • Errors
  • Errors
  • Errors
  • 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 < 30):

  • Errors
  • Errors
  • Errors
  • Errors
  • Errors
  • 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 < 20):

  • Errors
  • Errors
  • Errors
  • Errors
  • Errors
  • Errors

Barplot shows the percentage of reads (y-axis) with 0, 1, 2 ... errors (x axis) for MAPQ < 20 reads.

Number of Errors Per Read(MAPQ < 10):

  • Errors
  • Errors
  • Errors
  • Errors
  • Errors
  • 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
  • Errors
  • Errors
  • Errors
  • Errors
  • Errors

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