Qualimap Report: BAM QC

Summary 

Globals

Reference size 942,353,201
Number of reads 14,420,554
Mapped reads 14,420,554 / 100%
Unmapped reads 0 / 0%
Mapped paired reads 14,420,554 / 100%
Mapped reads, first in pair 7,210,277 / 50%
Mapped reads, second in pair 7,210,277 / 50%
Mapped reads, both in pair 14,420,554 / 100%
Mapped reads, singletons 0 / 0%
Read min/max/mean length 20 / 101 / 90.69
Duplicated reads (estimated) 4,858,965 / 33.69%
Duplication rate 28.88%
Clipped reads 0 / 0%

ACGT Content

Number/percentage of A's 501,321,250 / 38.44%
Number/percentage of C's 152,380,355 / 11.68%
Number/percentage of T's 499,743,542 / 38.31%
Number/percentage of G's 150,859,618 / 11.57%
Number/percentage of N's 70,201 / 0.01%
GC Percentage 23.25%

Coverage

Mean 1.3872
Standard Deviation 8.3587

Mapping Quality

Mean Mapping Quality 23.99

Insert size

Mean 152.07
Standard Deviation 88.41
P25/Median/P75 91 / 128 / 188

Mismatches and indels

General error rate 18.58%
Mismatches 237,427,615
Insertions 1,573,542
Mapped reads with at least one insertion 9.48%
Deletions 1,500,935
Mapped reads with at least one deletion 9.39%
Homopolymer indels 48.43%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
PGA_scaffold1__77_contigs__length_89643857 89643857 130849166 1.4597 4.6862
PGA_scaffold2__36_contigs__length_69596280 69596280 105144492 1.5108 6.7631
PGA_scaffold3__111_contigs__length_57743597 57743597 83587858 1.4476 4.9879
PGA_scaffold4__129_contigs__length_65288255 65288255 89192710 1.3661 6.5845
PGA_scaffold5__109_contigs__length_67248332 67248332 81303967 1.209 5.0996
PGA_scaffold6__104_contigs__length_61759565 61759565 80684110 1.3064 8.2385
PGA_scaffold7__69_contigs__length_43120122 43120122 58443998 1.3554 4.6287
PGA_scaffold8__63_contigs__length_61151155 61151155 85557000 1.3991 5.5046
PGA_scaffold9__45_contigs__length_38581958 38581958 59455436 1.541 11.728
PGA_scaffold10__49_contigs__length_53961475 53961475 69617181 1.2901 4.1967
PGA_scaffold11__79_contigs__length_51449921 51449921 61288257 1.1912 5.5101
PGA_scaffold12__71_contigs__length_50438331 50438331 73912153 1.4654 6.0232
PGA_scaffold13__52_contigs__length_44396874 44396874 61013881 1.3743 5.6892
PGA_scaffold14__91_contigs__length_45393038 45393038 80799265 1.78 21.5538
PGA_scaffold15__101_contigs__length_47938513 47938513 55015804 1.1476 4.7316
PGA_scaffold16__33_contigs__length_31980953 31980953 47474018 1.4844 19.0069
PGA_scaffold17__51_contigs__length_34923512 34923512 49327030 1.4124 5.6708
PGA_scaffold18__69_contigs__length_27737463 27737463 34528061 1.2448 7.966

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 13:18:30
    Generated by QualiMap v.2.2.1