Qualimap Report: Multi-sample BAM QC

Input data and parameters 

Samples (with groups)

EPI-168 (Day135-Super.Low) /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0807/EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted_stats
EPI-136 (Day10-Ambient) /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0809-005/EPI-136_S36_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted_stats
EPI-182 (Day145-Ambient) /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0807-003/EPI-182_S17_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted_stats
EPI-42 (Day0-Field) /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0809-005/EPI-42_S39_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted_stats
EPI-220 (Day145-Super.Low) /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0807-004/EPI-220_S32_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted_stats
EPI-181 (Day145-Ambient) /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0807-003/EPI-181_S16_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted_stats
EPI-187 (Day145-Super.Low) /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0807-003/EPI-187_S20_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted_stats
EPI-185 (Day145-Ambient) /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0807-003/EPI-185_S19_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted_stats
EPI-127 (Day10-Low) /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0809-005/EPI-127_S33_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted_stats
EPI-104 (Day10-Low) /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0809-005/EPI-104_S28_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted_stats
EPI-176 (Day145-Low) /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0807-003/EPI-176_S15_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted_stats
EPI-153 (Day135-Ambient) /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0807/EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted_stats
EPI-152 (Day135-Ambient) /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0807/EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted_stats
EPI-209 (Day145-Low) /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0807-004/EPI-209_S29_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted_stats
EPI-208 (Day145-Low) /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0807-004/EPI-208_S28_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted_stats
EPI-175 (Day145-Low) /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0807-003/EPI-175_S14_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted_stats
EPI-44 (Day0-Field) /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0809-005/EPI-44_S41_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted_stats
EPI-226 (Day145-Ambient) /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0807-004/EPI-226_S34_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted_stats
EPI-128 (Day10-Low) /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0809-005/EPI-128_S34_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted_stats
EPI-199 (Day145-Super.Low) /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0807-003/EPI-199_S24_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted_stats
EPI-230 (Day145-Low) /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0807-004/EPI-230_S37_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted_stats
EPI-205 (Day145-Ambient) /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0807-004/EPI-205_S26_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted_stats
EPI-103 (Day10-Low) /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0809-005/EPI-103_S27_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted_stats
EPI-120 (Day10-Ambient) /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0809-005/EPI-120_S32_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted_stats
EPI-135 (Day10-Ambient) /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0809-005/EPI-135_S35_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted_stats
EPI-159 (Day135-Low) /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0807/EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted_stats
EPI-167 (Day135-Super.Low) /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0807/EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted_stats
EPI-145 (Day10-Super.Low) /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0809-005/EPI-145_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted_stats
EPI-169 (Day135-Super.Low) /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0807/EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted_stats
EPI-200 (Day145-Super.Low) /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0807-003/EPI-200_S25_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted_stats
EPI-41 (Day0-Field) /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0809-005/EPI-41_S38_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted_stats
EPI-43 (Day0-Field) /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0809-005/EPI-43_S40_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted_stats
EPI-111 (Day10-Super.Low) /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0809-005/EPI-111_S29_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted_stats
EPI-221 (Day145-Super.Low) /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0807-004/EPI-221_S33_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted_stats
EPI-188 (Day145-Super.Low) /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0807-003/EPI-188_S21_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted_stats
EPI-119 (Day10-Ambient) /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0809-005/EPI-119_S31_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted_stats
EPI-194 (Day145-Low) /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0807-003/EPI-194_S23_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted_stats
EPI-162 (Day135-Low) /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0807/EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted_stats
EPI-161 (Day135-Low) /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0807/EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted_stats
EPI-193 (Day145-Low) /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0807-003/EPI-193_S22_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted_stats
EPI-214 (Day145-Super.Low) /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0807-004/EPI-214_S30_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted_stats
EPI-184 (Day145-Ambient) /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0807-003/EPI-184_S18_L003_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted_stats
EPI-215 (Day145-Super.Low) /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0807-004/EPI-215_S31_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted_stats
EPI-227 (Day145-Ambient) /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0807-004/EPI-227_S35_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted_stats
EPI-229 (Day145-Low) /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0807-004/EPI-229_S36_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted_stats
EPI-151 (Day135-Ambient) /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0807/EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted_stats
EPI-113 (Day10-Super.Low) /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0809-005/EPI-113_S30_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted_stats
EPI-154 (Day135-Ambient) /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0807/EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted_stats
EPI-206 (Day145-Ambient) /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0807-004/EPI-206_S27_L004_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted_stats
EPI-160 (Day135-Low) /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0807/EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted_stats
EPI-170 (Day135-Super.Low) /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0807/EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted_stats
EPI-143 (Day10-Super.Low) /Volumes/web/metacarcinus/Pgenerosa/analyses/20190822/dedup_bams/0809-005/EPI-143_S37_L005_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted_stats

Summary 

Globals

Number of samples 52
Number of groups 10
Total number of mapped reads 773,985,936
Mean samples coverage 1.4
Mean samples GC-content 23.04
Mean samples mapping quality 24.31
Mean samples insert size 123.96

Sample statistics

Sample Group Coverage mean Coverage std GC percentage Mapping quality mean Insert size median
EPI-175 Day145-Low 1.5224 8.4272 23.0 24.2795 128.0
EPI-176 Day145-Low 1.9316 10.5072 22.37 24.5799 126.0
EPI-181 Day145-Ambient 1.5959 9.2641 23.04 24.3568 135.0
EPI-182 Day145-Ambient 1.9805 9.9461 22.56 24.5085 130.0
EPI-184 Day145-Ambient 1.1695 8.2159 23.24 23.9969 118.0
EPI-185 Day145-Ambient 0.5186 5.528 23.62 23.0983 120.0
EPI-187 Day145-Super.Low 1.3446 7.8846 23.45 24.3043 127.0
EPI-188 Day145-Super.Low 1.0929 7.0497 23.17 24.4004 106.0
EPI-193 Day145-Low 1.4582 8.7388 23.08 24.4278 110.0
EPI-194 Day145-Low 1.7534 9.344 23.06 24.4256 139.0
EPI-199 Day145-Super.Low 0.7981 5.8196 23.57 23.7657 118.0
EPI-200 Day145-Super.Low 1.3391 7.3512 23.42 24.1978 110.0
EPI-205 Day145-Ambient 0.8157 5.6512 23.72 24.4252 103.0
EPI-206 Day145-Ambient 1.1926 8.3493 23.74 24.279 110.0
EPI-208 Day145-Low 1.4916 9.1584 23.61 24.3855 103.0
EPI-209 Day145-Low 1.6549 9.8777 23.26 24.4109 119.0
EPI-214 Day145-Super.Low 1.632 8.9033 23.0 24.5176 123.0
EPI-215 Day145-Super.Low 1.1499 6.7645 23.51 24.4351 115.0
EPI-220 Day145-Super.Low 0.8073 5.9892 23.35 23.8446 119.0
EPI-221 Day145-Super.Low 0.8763 6.0043 23.49 24.2053 113.0
EPI-226 Day145-Ambient 0.6568 4.968 23.38 24.0451 129.0
EPI-227 Day145-Ambient 0.7727 5.4738 23.34 24.2119 119.0
EPI-229 Day145-Low 1.1076 7.6795 23.55 24.0295 117.0
EPI-230 Day145-Low 1.3137 8.0112 23.13 24.1291 112.0
EPI-151 Day135-Ambient 1.3872 8.3587 23.25 23.9914 128.0
EPI-152 Day135-Ambient 1.6242 8.1547 22.79 24.3637 130.0
EPI-153 Day135-Ambient 1.2605 8.0758 23.32 23.5555 119.0
EPI-154 Day135-Ambient 1.2971 7.8308 22.85 24.1212 125.0
EPI-159 Day135-Low 0.8862 5.8505 23.1 24.026 127.0
EPI-160 Day135-Low 1.6408 9.7083 23.1 24.0295 113.0
EPI-161 Day135-Low 1.1672 7.2429 22.82 24.0216 114.0
EPI-162 Day135-Low 1.1591 7.9099 23.1 23.9259 110.0
EPI-167 Day135-Super.Low 1.4883 9.2124 22.66 24.0374 131.0
EPI-168 Day135-Super.Low 1.2516 8.9775 23.03 23.6522 127.0
EPI-169 Day135-Super.Low 1.175 8.0202 23.57 23.7504 114.0
EPI-170 Day135-Super.Low 1.4152 8.8242 23.11 24.2489 112.0
EPI-103 Day10-Low 1.555 8.0501 22.41 24.5284 144.0
EPI-104 Day10-Low 2.2601 8.8666 22.36 24.7599 135.0
EPI-111 Day10-Super.Low 2.0268 7.952 22.33 25.0252 134.0
EPI-113 Day10-Super.Low 1.9288 7.8777 22.31 24.9444 141.0
EPI-119 Day10-Ambient 2.0494 9.2873 22.2 24.9509 146.0
EPI-120 Day10-Ambient 1.8595 7.5851 22.32 25.0272 143.0
EPI-127 Day10-Low 1.6702 7.2294 22.38 24.9635 146.0
EPI-128 Day10-Low 1.8249 7.3432 22.4 25.0932 145.0
EPI-135 Day10-Ambient 2.0005 7.9608 22.73 24.9555 130.0
EPI-136 Day10-Ambient 1.9595 8.3779 22.55 24.856 130.0
EPI-143 Day10-Super.Low 1.5427 6.8618 22.4 24.7913 141.0
EPI-145 Day10-Super.Low 1.8353 7.3341 22.37 25.0553 144.0
EPI-41 Day0-Field 1.159 7.0888 23.52 23.6661 118.0
EPI-42 Day0-Field 1.5499 6.8682 23.66 24.2309 116.0
EPI-43 Day0-Field 1.1606 6.1383 23.32 24.1267 116.0
EPI-44 Day0-Field 0.727 3.7995 23.51 24.2825 118.0

PCA 

Coverage Across Reference 

Coverage Histogram (0 - 18078X) 

Global Coverage Histogram 

Genome Fraction Coverage 

Duplication Rate Histogram 

Mapped reads GC-content 

Mapped Reads Clipping Profile 

Mapped Reads GC-content Distribution 

Mapping Quality Across Reference 

Mapping Quality Histogram 

Insert Size Across Reference 

Insert Size Histogram 

Contents

  • Input data & parameters
  • Summary
  • PCA
  • Coverage Across Reference
  • Coverage Histogram (0 - 18078X)
  • Global Coverage Histogram
  • Genome Fraction Coverage
  • Duplication Rate Histogram
  • Mapped reads GC-content
  • Mapped Reads Clipping Profile
  • Mapped Reads GC-content Distribution
  • Mapping Quality Across Reference
  • Mapping Quality Histogram
  • Insert Size Across Reference
  • Insert Size Histogram
    • 2019/09/12 15:19:20
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