Qualimap Report: BAM QC

Summary 

Globals

Reference size 942,353,201
Number of reads 14,413,552
Mapped reads 14,413,552 / 100%
Unmapped reads 0 / 0%
Mapped paired reads 14,413,552 / 100%
Mapped reads, first in pair 7,206,776 / 50%
Mapped reads, second in pair 7,206,776 / 50%
Mapped reads, both in pair 14,413,552 / 100%
Mapped reads, singletons 0 / 0%
Read min/max/mean length 20 / 101 / 90.02
Duplicated reads (estimated) 4,789,811 / 33.23%
Duplication rate 26.97%
Clipped reads 0 / 0%

ACGT Content

Number/percentage of A's 488,485,381 / 38.06%
Number/percentage of C's 155,196,944 / 12.09%
Number/percentage of T's 486,587,859 / 37.91%
Number/percentage of G's 153,172,621 / 11.93%
Number/percentage of N's 80,905 / 0.01%
GC Percentage 24.03%

Coverage

Mean 1.3691
Standard Deviation 9.3638

Mapping Quality

Mean Mapping Quality 19.98

Insert size

Mean 165
Standard Deviation 96.65
P25/Median/P75 96 / 133 / 205

Mismatches and indels

General error rate 21.01%
Mismatches 253,398,514
Insertions 5,086,046
Mapped reads with at least one insertion 21.04%
Deletions 3,154,195
Mapped reads with at least one deletion 16.87%
Homopolymer indels 40.16%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
PGA_scaffold1__77_contigs__length_89643857 89643857 126253204 1.4084 5.037
PGA_scaffold2__36_contigs__length_69596280 69596280 100957133 1.4506 6.4118
PGA_scaffold3__111_contigs__length_57743597 57743597 81097432 1.4044 5.3185
PGA_scaffold4__129_contigs__length_65288255 65288255 87705726 1.3434 10.7837
PGA_scaffold5__109_contigs__length_67248332 67248332 81602547 1.2135 6.3993
PGA_scaffold6__104_contigs__length_61759565 61759565 79466626 1.2867 7.7352
PGA_scaffold7__69_contigs__length_43120122 43120122 58049178 1.3462 4.9537
PGA_scaffold8__63_contigs__length_61151155 61151155 83350288 1.363 5.2557
PGA_scaffold9__45_contigs__length_38581958 38581958 60192393 1.5601 15.1298
PGA_scaffold10__49_contigs__length_53961475 53961475 69329468 1.2848 5.2448
PGA_scaffold11__79_contigs__length_51449921 51449921 61086227 1.1873 5.7138
PGA_scaffold12__71_contigs__length_50438331 50438331 72440256 1.4362 7.5944
PGA_scaffold13__52_contigs__length_44396874 44396874 60650462 1.3661 6.5723
PGA_scaffold14__91_contigs__length_45393038 45393038 79737267 1.7566 24.4397
PGA_scaffold15__101_contigs__length_47938513 47938513 55103718 1.1495 5.0456
PGA_scaffold16__33_contigs__length_31980953 31980953 47826600 1.4955 17.8039
PGA_scaffold17__51_contigs__length_34923512 34923512 49335579 1.4127 6.4467
PGA_scaffold18__69_contigs__length_27737463 27737463 35951330 1.2961 9.1203

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
    • 2019/08/12 17:00:27
    Generated by QualiMap v.2.2.1