Qualimap Report: BAM QC

Summary 

Globals

Reference size 942,353,201
Number of reads 17,407,756
Mapped reads 17,407,756 / 100%
Unmapped reads 0 / 0%
Mapped paired reads 17,407,756 / 100%
Mapped reads, first in pair 8,703,878 / 50%
Mapped reads, second in pair 8,703,878 / 50%
Mapped reads, both in pair 17,407,756 / 100%
Mapped reads, singletons 0 / 0%
Read min/max/mean length 20 / 101 / 88.39
Duplicated reads (estimated) 6,140,300 / 35.27%
Duplication rate 32.06%
Clipped reads 0 / 0%

ACGT Content

Number/percentage of A's 591,495,789 / 38.55%
Number/percentage of C's 177,076,827 / 11.54%
Number/percentage of T's 590,023,407 / 38.45%
Number/percentage of G's 175,918,484 / 11.46%
Number/percentage of N's 91,964 / 0.01%
GC Percentage 23%

Coverage

Mean 1.632
Standard Deviation 8.9033

Mapping Quality

Mean Mapping Quality 24.52

Insert size

Mean 146.92
Standard Deviation 90.2
P25/Median/P75 84 / 123 / 184

Mismatches and indels

General error rate 18.66%
Mismatches 280,868,503
Insertions 1,851,369
Mapped reads with at least one insertion 9.29%
Deletions 1,788,851
Mapped reads with at least one deletion 9.29%
Homopolymer indels 50.25%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
PGA_scaffold1__77_contigs__length_89643857 89643857 156416098 1.7449 5.1137
PGA_scaffold2__36_contigs__length_69596280 69596280 124192753 1.7845 7.255
PGA_scaffold3__111_contigs__length_57743597 57743597 97875416 1.695 5.3168
PGA_scaffold4__129_contigs__length_65288255 65288255 105223238 1.6117 7.7492
PGA_scaffold5__109_contigs__length_67248332 67248332 96221590 1.4308 5.5351
PGA_scaffold6__104_contigs__length_61759565 61759565 94632337 1.5323 7.823
PGA_scaffold7__69_contigs__length_43120122 43120122 68331955 1.5847 4.8872
PGA_scaffold8__63_contigs__length_61151155 61151155 100424476 1.6422 5.618
PGA_scaffold9__45_contigs__length_38581958 38581958 69639774 1.805 14.3741
PGA_scaffold10__49_contigs__length_53961475 53961475 82497740 1.5288 4.434
PGA_scaffold11__79_contigs__length_51449921 51449921 74008504 1.4385 6.0837
PGA_scaffold12__71_contigs__length_50438331 50438331 87500135 1.7348 6.5382
PGA_scaffold13__52_contigs__length_44396874 44396874 71303270 1.606 6.0061
PGA_scaffold14__91_contigs__length_45393038 45393038 93341868 2.0563 24.5216
PGA_scaffold15__101_contigs__length_47938513 47938513 63894653 1.3328 4.9163
PGA_scaffold16__33_contigs__length_31980953 31980953 55344215 1.7305 15.7533
PGA_scaffold17__51_contigs__length_34923512 34923512 56873873 1.6285 5.3762
PGA_scaffold18__69_contigs__length_27737463 27737463 40195298 1.4491 8.9462

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 13:08:35
    Generated by QualiMap v.2.2.1