Summary 

Globals

Reference size 942,353,201
Number of reads 14,990,294
Mapped reads 14,990,294 / 100%
Unmapped reads 0 / 0%
Mapped paired reads 14,990,294 / 100%
Mapped reads, first in pair 7,495,147 / 50%
Mapped reads, second in pair 7,495,147 / 50%
Mapped reads, both in pair 14,990,294 / 100%
Mapped reads, singletons 0 / 0%
Read min/max/mean length 20 / 101 / 89.19
Duplicated reads (estimated) 4,998,789 / 33.35%
Duplication rate 27.53%
Clipped reads 0 / 0%

ACGT Content

Number/percentage of A's 502,073,672 / 37.96%
Number/percentage of C's 161,337,485 / 12.2%
Number/percentage of T's 499,971,965 / 37.8%
Number/percentage of G's 159,149,829 / 12.03%
Number/percentage of N's 84,176 / 0.01%
GC Percentage 24.23%

Coverage

Mean 1.4107
Standard Deviation 11.1269

Mapping Quality

Mean Mapping Quality 19.71

Insert size

Mean 160.63
Standard Deviation 94.81
P25/Median/P75 94 / 129 / 197

Mismatches and indels

General error rate 21.13%
Mismatches 262,632,201
Insertions 5,255,067
Mapped reads with at least one insertion 21%
Deletions 3,246,933
Mapped reads with at least one deletion 16.71%
Homopolymer indels 40.07%

Chromosome stats

Name Length Mapped bases Mean coverage Standard deviation
PGA_scaffold1__77_contigs__length_89643857 89643857 130649928 1.4574 6.0002
PGA_scaffold2__36_contigs__length_69596280 69596280 104227843 1.4976 7.566
PGA_scaffold3__111_contigs__length_57743597 57743597 82616076 1.4307 5.4391
PGA_scaffold4__129_contigs__length_65288255 65288255 90371380 1.3842 11.8247
PGA_scaffold5__109_contigs__length_67248332 67248332 85093262 1.2654 6.9888
PGA_scaffold6__104_contigs__length_61759565 61759565 82144727 1.3301 9.9136
PGA_scaffold7__69_contigs__length_43120122 43120122 58457371 1.3557 5.2681
PGA_scaffold8__63_contigs__length_61151155 61151155 85285701 1.3947 5.6097
PGA_scaffold9__45_contigs__length_38581958 38581958 62235356 1.6131 17.4162
PGA_scaffold10__49_contigs__length_53961475 53961475 71545786 1.3259 5.7105
PGA_scaffold11__79_contigs__length_51449921 51449921 62274416 1.2104 6.5893
PGA_scaffold12__71_contigs__length_50438331 50438331 74982490 1.4866 7.7309
PGA_scaffold13__52_contigs__length_44396874 44396874 62143497 1.3997 7.223
PGA_scaffold14__91_contigs__length_45393038 45393038 83489939 1.8393 28.5482
PGA_scaffold15__101_contigs__length_47938513 47938513 55976578 1.1677 5.4587
PGA_scaffold16__33_contigs__length_31980953 31980953 50508862 1.5793 25.9256
PGA_scaffold17__51_contigs__length_34923512 34923512 50481645 1.4455 7.3498
PGA_scaffold18__69_contigs__length_27737463 27737463 36920896 1.3311 10.9002

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