Qualimap Report: BAM QC

Summary 

Globals

Reference size 942,353,201
Number of reads 13,539,046
Mapped reads 13,539,046 / 100%
Unmapped reads 0 / 0%
Mapped paired reads 13,539,046 / 100%
Mapped reads, first in pair 6,769,523 / 50%
Mapped reads, second in pair 6,769,523 / 50%
Mapped reads, both in pair 13,539,046 / 100%
Mapped reads, singletons 0 / 0%
Read min/max/mean length 20 / 101 / 90.33
Duplicated reads (estimated) 4,452,332 / 32.89%
Duplication rate 29.1%
Clipped reads 0 / 0%

ACGT Content

Number/percentage of A's 471,192,707 / 38.64%
Number/percentage of C's 139,985,651 / 11.48%
Number/percentage of T's 469,692,468 / 38.51%
Number/percentage of G's 138,677,151 / 11.37%
Number/percentage of N's 65,360 / 0.01%
GC Percentage 22.85%

Coverage

Mean 1.2971
Standard Deviation 7.8308

Mapping Quality

Mean Mapping Quality 24.12

Insert size

Mean 149.34
Standard Deviation 87.42
P25/Median/P75 89 / 125 / 184

Mismatches and indels

General error rate 18.58%
Mismatches 222,019,117
Insertions 1,538,696
Mapped reads with at least one insertion 9.92%
Deletions 1,468,226
Mapped reads with at least one deletion 9.79%
Homopolymer indels 49.4%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
PGA_scaffold1__77_contigs__length_89643857 89643857 122960880 1.3717 4.1666
PGA_scaffold2__36_contigs__length_69596280 69596280 99152062 1.4247 6.3795
PGA_scaffold3__111_contigs__length_57743597 57743597 77989152 1.3506 4.4341
PGA_scaffold4__129_contigs__length_65288255 65288255 82834850 1.2688 6.5028
PGA_scaffold5__109_contigs__length_67248332 67248332 75756895 1.1265 4.601
PGA_scaffold6__104_contigs__length_61759565 61759565 75271262 1.2188 6.422
PGA_scaffold7__69_contigs__length_43120122 43120122 55209059 1.2804 4.0819
PGA_scaffold8__63_contigs__length_61151155 61151155 79467010 1.2995 4.6187
PGA_scaffold9__45_contigs__length_38581958 38581958 55927117 1.4496 11.6885
PGA_scaffold10__49_contigs__length_53961475 53961475 65859743 1.2205 3.7953
PGA_scaffold11__79_contigs__length_51449921 51449921 58548861 1.138 5.1332
PGA_scaffold12__71_contigs__length_50438331 50438331 69223995 1.3724 6.2215
PGA_scaffold13__52_contigs__length_44396874 44396874 57128990 1.2868 5.0829
PGA_scaffold14__91_contigs__length_45393038 45393038 73373929 1.6164 22.9405
PGA_scaffold15__101_contigs__length_47938513 47938513 51261006 1.0693 4.2366
PGA_scaffold16__33_contigs__length_31980953 31980953 44254503 1.3838 13.6689
PGA_scaffold17__51_contigs__length_34923512 34923512 45463827 1.3018 4.589
PGA_scaffold18__69_contigs__length_27737463 27737463 32642364 1.1768 7.4277

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 13:24:04
    Generated by QualiMap v.2.2.1