Qualimap Report: BAM QC

Summary 

Globals

Reference size 942,353,201
Number of reads 16,420,530
Mapped reads 16,420,530 / 100%
Unmapped reads 0 / 0%
Mapped paired reads 16,420,530 / 100%
Mapped reads, first in pair 8,210,265 / 50%
Mapped reads, second in pair 8,210,265 / 50%
Mapped reads, both in pair 16,420,530 / 100%
Mapped reads, singletons 0 / 0%
Read min/max/mean length 20 / 101 / 91.63
Duplicated reads (estimated) 5,535,382 / 33.71%
Duplication rate 28.03%
Clipped reads 0 / 0%

ACGT Content

Number/percentage of A's 578,212,549 / 38.54%
Number/percentage of C's 173,561,618 / 11.57%
Number/percentage of T's 576,582,298 / 38.43%
Number/percentage of G's 172,107,132 / 11.47%
Number/percentage of N's 137,476 / 0.01%
GC Percentage 23.04%

Coverage

Mean 1.5959
Standard Deviation 9.2641

Mapping Quality

Mean Mapping Quality 24.36

Insert size

Mean 159.01
Standard Deviation 90.85
P25/Median/P75 96 / 135 / 198

Mismatches and indels

General error rate 18.6%
Mismatches 273,623,002
Insertions 1,802,138
Mapped reads with at least one insertion 9.55%
Deletions 1,753,764
Mapped reads with at least one deletion 9.64%
Homopolymer indels 50.1%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
PGA_scaffold1__77_contigs__length_89643857 89643857 152871014 1.7053 5.2476
PGA_scaffold2__36_contigs__length_69596280 69596280 121320892 1.7432 6.8664
PGA_scaffold3__111_contigs__length_57743597 57743597 95627995 1.6561 5.2738
PGA_scaffold4__129_contigs__length_65288255 65288255 101681770 1.5574 7.5253
PGA_scaffold5__109_contigs__length_67248332 67248332 93649126 1.3926 5.6851
PGA_scaffold6__104_contigs__length_61759565 61759565 91403588 1.48 9.1166
PGA_scaffold7__69_contigs__length_43120122 43120122 67265434 1.56 5.0117
PGA_scaffold8__63_contigs__length_61151155 61151155 98355807 1.6084 5.7868
PGA_scaffold9__45_contigs__length_38581958 38581958 68196474 1.7676 13.7836
PGA_scaffold10__49_contigs__length_53961475 53961475 81570728 1.5116 4.6317
PGA_scaffold11__79_contigs__length_51449921 51449921 71100407 1.3819 5.8454
PGA_scaffold12__71_contigs__length_50438331 50438331 85306165 1.6913 6.8399
PGA_scaffold13__52_contigs__length_44396874 44396874 70576509 1.5897 6.0799
PGA_scaffold14__91_contigs__length_45393038 45393038 92384075 2.0352 25.8137
PGA_scaffold15__101_contigs__length_47938513 47938513 62507910 1.3039 5.0769
PGA_scaffold16__33_contigs__length_31980953 31980953 54722982 1.7111 18.2544
PGA_scaffold17__51_contigs__length_34923512 34923512 55777543 1.5971 5.7678
PGA_scaffold18__69_contigs__length_27737463 27737463 39549183 1.4258 8.0847

Coverage across reference 

Coverage Histogram 

Coverage Histogram (0-50X) 

Genome Fraction Coverage 

Duplication Rate Histogram 

Mapped Reads Nucleotide Content 

Mapped Reads GC-content Distribution 

Homopolymer Indels 

Mapping Quality Across Reference 

Mapping Quality Histogram 

Insert Size Across Reference 

Insert Size Histogram 

Contents

  • Summary
  • Coverage across reference
  • Coverage Histogram
  • Coverage Histogram (0-50X)
  • Genome Fraction Coverage
  • Duplication Rate Histogram
  • Mapped Reads Nucleotide Content
  • Mapped Reads GC-content Distribution
  • Homopolymer Indels
  • Mapping Quality Across Reference
  • Mapping Quality Histogram
  • Insert Size Across Reference
  • Insert Size Histogram
    • 2019/09/12 12:47:08
    Generated by QualiMap v.2.2.1