Qualimap Report: BAM QC

Summary 

Globals

Reference size 942,353,201
Number of reads 23,227,490
Mapped reads 23,227,490 / 100%
Unmapped reads 0 / 0%
Mapped paired reads 23,227,490 / 100%
Mapped reads, first in pair 11,613,745 / 50%
Mapped reads, second in pair 11,613,745 / 50%
Mapped reads, both in pair 23,227,490 / 100%
Mapped reads, singletons 0 / 0%
Read min/max/mean length 20 / 101 / 91.73
Duplicated reads (estimated) 7,889,216 / 33.96%
Duplication rate 29.14%
Clipped reads 0 / 0%

ACGT Content

Number/percentage of A's 825,956,145 / 38.86%
Number/percentage of C's 238,322,603 / 11.21%
Number/percentage of T's 824,035,289 / 38.77%
Number/percentage of G's 236,925,468 / 11.15%
Number/percentage of N's 28,643 / 0%
GC Percentage 22.36%

Coverage

Mean 2.2601
Standard Deviation 8.8666

Mapping Quality

Mean Mapping Quality 24.76

Insert size

Mean 156.34
Standard Deviation 86.56
P25/Median/P75 97 / 135 / 194

Mismatches and indels

General error rate 18.62%
Mismatches 388,490,579
Insertions 2,448,292
Mapped reads with at least one insertion 9.21%
Deletions 2,450,870
Mapped reads with at least one deletion 9.54%
Homopolymer indels 51.01%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
PGA_scaffold1__77_contigs__length_89643857 89643857 216845195 2.419 5.7279
PGA_scaffold2__36_contigs__length_69596280 69596280 172945920 2.485 7.0463
PGA_scaffold3__111_contigs__length_57743597 57743597 137272775 2.3773 6.7583
PGA_scaffold4__129_contigs__length_65288255 65288255 147655249 2.2616 8.7174
PGA_scaffold5__109_contigs__length_67248332 67248332 133178555 1.9804 6.15
PGA_scaffold6__104_contigs__length_61759565 61759565 131191044 2.1242 7.7882
PGA_scaffold7__69_contigs__length_43120122 43120122 96119910 2.2291 6.2236
PGA_scaffold8__63_contigs__length_61151155 61151155 139704667 2.2846 6.7231
PGA_scaffold9__45_contigs__length_38581958 38581958 95107763 2.4651 14.4146
PGA_scaffold10__49_contigs__length_53961475 53961475 114491300 2.1217 5.4101
PGA_scaffold11__79_contigs__length_51449921 51449921 101711036 1.9769 6.2882
PGA_scaffold12__71_contigs__length_50438331 50438331 121752315 2.4139 8.0342
PGA_scaffold13__52_contigs__length_44396874 44396874 98914436 2.228 7.2355
PGA_scaffold14__91_contigs__length_45393038 45393038 126338581 2.7832 22.954
PGA_scaffold15__101_contigs__length_47938513 47938513 89138309 1.8594 6.0601
PGA_scaffold16__33_contigs__length_31980953 31980953 74471271 2.3286 10.5291
PGA_scaffold17__51_contigs__length_34923512 34923512 78574277 2.2499 6.0228
PGA_scaffold18__69_contigs__length_27737463 27737463 54415024 1.9618 7.6466

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 13:41:26
    Generated by QualiMap v.2.2.1