Input data and parameters
QualiMap command line
| qualimap bamqc -bam /opt/tsinghua/zhangwei/Pipeline_test/o_WGBS-PE/intermediate_result/step_06_bamsort/case4.pair1_sorted.bam -nw 400 -hm 3 |
Alignment
| Command line: | "bismark -q --phred33-quals --bowtie2 --un --multicore 12 --output_dir /opt/tsinghua/zhangwei/Pipeline_test/o_WGBS-PE/intermediate_result/step_04_bismark --temp_dir /opt/tsinghua/zhangwei/Pipeline_test/o_WGBS-PE/intermediate_result/step_04_bismark --genome_folder /home/zhangwei/Genome/hg19_bismark -1 /opt/tsinghua/zhangwei/Pipeline_test/o_WGBS-PE/intermediate_result/step_03_adapterremoval/case4.pair1.truncated.gz -2 /opt/tsinghua/zhangwei/Pipeline_test/o_WGBS-PE/intermediate_result/step_03_adapterremoval/case4.pair2.truncated.gz" |
| Draw chromosome limits: | no |
| Analyze overlapping paired-end reads: | no |
| Program: | Bismark (v0.23.0) |
| Analysis date: | Tue Jan 12 17:46:51 CST 2021 |
| Size of a homopolymer: | 3 |
| Skip duplicate alignments: | no |
| Number of windows: | 400 |
| BAM file: | /opt/tsinghua/zhangwei/Pipeline_test/o_WGBS-PE/intermediate_result/step_06_bamsort/case4.pair1_sorted.bam |
Summary
Globals
| Reference size | 3,137,161,264 |
| Number of reads | 7,180,310 |
| Mapped reads | 7,180,310 / 100% |
| Unmapped reads | 0 / 0% |
| Mapped paired reads | 7,180,310 / 100% |
| Mapped reads, first in pair | 3,590,155 / 50% |
| Mapped reads, second in pair | 3,590,155 / 50% |
| Mapped reads, both in pair | 7,180,310 / 100% |
| Mapped reads, singletons | 0 / 0% |
| Secondary alignments | 0 |
| Read min/max/mean length | 16 / 150 / 147.54 |
| Duplicated reads (estimated) | 673,620 / 9.38% |
| Duplication rate | 9.45% |
| Clipped reads | 0 / 0% |
ACGT Content
| Number/percentage of A's | 418,083,805 / 39.48% |
| Number/percentage of C's | 111,302,197 / 10.51% |
| Number/percentage of T's | 419,905,744 / 39.65% |
| Number/percentage of G's | 109,783,667 / 10.37% |
| Number/percentage of N's | 17,881 / 0% |
| GC Percentage | 20.88% |
Coverage
| Mean | 0.3377 |
| Standard Deviation | 1.8975 |
Mapping Quality
| Mean Mapping Quality | 34.92 |
Insert size
| Mean | 182.34 |
| Standard Deviation | 54.74 |
| P25/Median/P75 | 158 / 169 / 183 |
Mismatches and indels
| General error rate | 14.91% |
| Mismatches | 157,677,516 |
| Insertions | 167,683 |
| Mapped reads with at least one insertion | 2.29% |
| Deletions | 172,794 |
| Mapped reads with at least one deletion | 2.36% |
| Homopolymer indels | 80.7% |
Chromosome stats
| Name | Length | Mapped bases | Mean coverage | Standard deviation |
| chr1 | 249250621 | 82708989 | 0.3318 | 2.348 |
| chr2 | 243199373 | 93147946 | 0.383 | 0.9216 |
| chr3 | 198022430 | 77755495 | 0.3927 | 0.928 |
| chr4 | 191154276 | 81029254 | 0.4239 | 0.9707 |
| chr5 | 180915260 | 70594912 | 0.3902 | 0.9127 |
| chr6 | 171115067 | 66200416 | 0.3869 | 0.9917 |
| chr7 | 159138663 | 59211422 | 0.3721 | 1.5036 |
| chr8 | 146364022 | 56084269 | 0.3832 | 0.9173 |
| chr9 | 141213431 | 41902810 | 0.2967 | 0.8155 |
| chr10 | 135534747 | 51075345 | 0.3768 | 5.0073 |
| chr11 | 135006516 | 48024725 | 0.3557 | 0.877 |
| chr12 | 133851895 | 49059753 | 0.3665 | 0.8837 |
| chr13 | 115169878 | 40733232 | 0.3537 | 0.8811 |
| chr14 | 107349540 | 33609095 | 0.3131 | 0.8313 |
| chr15 | 102531392 | 28694379 | 0.2799 | 0.7952 |
| chr16 | 90354753 | 27392809 | 0.3032 | 3.9129 |
| chr17 | 81195210 | 22706273 | 0.2797 | 0.7802 |
| chr18 | 78077248 | 29949009 | 0.3836 | 0.9082 |
| chr19 | 59128983 | 14071019 | 0.238 | 1.0294 |
| chr20 | 63025520 | 18964618 | 0.3009 | 0.8127 |
| chr21 | 48129895 | 14474045 | 0.3007 | 0.9143 |
| chr22 | 51304566 | 8762906 | 0.1708 | 0.6226 |
| chrX | 155270560 | 30275478 | 0.195 | 0.6324 |
| chrY | 59373566 | 5247285 | 0.0884 | 4.0606 |
| chrM | 16571 | 2748 | 0.1658 | 0.6314 |
| chr1_gl000191_random | 106433 | 7433 | 0.0698 | 0.356 |
| chr1_gl000192_random | 547496 | 102178 | 0.1866 | 0.6603 |
| chr4_ctg9_hap1 | 590426 | 13428 | 0.0227 | 0.2159 |
| chr4_gl000193_random | 189789 | 140584 | 0.7407 | 1.4786 |
| chr4_gl000194_random | 191469 | 68455 | 0.3575 | 1.0348 |
| chr6_apd_hap1 | 4622290 | 1200 | 0.0003 | 0.0212 |
| chr6_cox_hap2 | 4795371 | 23170 | 0.0048 | 0.105 |
| chr6_dbb_hap3 | 4610396 | 13014 | 0.0028 | 0.0724 |
| chr6_mann_hap4 | 4683263 | 13128 | 0.0028 | 0.0738 |
| chr6_mcf_hap5 | 4833398 | 8926 | 0.0018 | 0.0613 |
| chr6_qbl_hap6 | 4611984 | 10849 | 0.0024 | 0.0644 |
| chr6_ssto_hap7 | 4928567 | 17725 | 0.0036 | 0.0846 |
| chr7_gl000195_random | 182896 | 211322 | 1.1554 | 2.1149 |
| chr8_gl000196_random | 38914 | 600 | 0.0154 | 0.2371 |
| chr8_gl000197_random | 37175 | 0 | 0 | 0 |
| chr9_gl000198_random | 90085 | 56551 | 0.6278 | 1.5303 |
| chr9_gl000199_random | 169874 | 166165 | 0.9782 | 3.7259 |
| chr9_gl000200_random | 187035 | 0 | 0 | 0 |
| chr9_gl000201_random | 36148 | 294 | 0.0081 | 0.1208 |
| chr11_gl000202_random | 40103 | 2288 | 0.0571 | 0.3588 |
| chr17_ctg5_hap1 | 1680828 | 9154 | 0.0054 | 0.1007 |
| chr17_gl000203_random | 37498 | 10716 | 0.2858 | 1.0071 |
| chr17_gl000204_random | 81310 | 7624 | 0.0938 | 0.4271 |
| chr17_gl000205_random | 174588 | 152571 | 0.8739 | 1.8398 |
| chr17_gl000206_random | 41001 | 600 | 0.0146 | 0.1584 |
| chr18_gl000207_random | 4262 | 300 | 0.0704 | 0.3442 |
| chr19_gl000208_random | 92689 | 62104 | 0.67 | 2.1238 |
| chr19_gl000209_random | 159169 | 2100 | 0.0132 | 0.1629 |
| chr21_gl000210_random | 27682 | 294 | 0.0106 | 0.1406 |
| chrUn_gl000211 | 166566 | 68006 | 0.4083 | 0.9978 |
| chrUn_gl000212 | 186858 | 79615 | 0.4261 | 3.1371 |
| chrUn_gl000213 | 164239 | 10386 | 0.0632 | 0.3362 |
| chrUn_gl000214 | 137718 | 208623 | 1.5149 | 2.4996 |
| chrUn_gl000215 | 172545 | 1496 | 0.0087 | 0.1352 |
| chrUn_gl000216 | 172294 | 178567 | 1.0364 | 1.6282 |
| chrUn_gl000217 | 172149 | 35017 | 0.2034 | 0.7228 |
| chrUn_gl000218 | 161147 | 117137 | 0.7269 | 1.357 |
| chrUn_gl000219 | 179198 | 191885 | 1.0708 | 1.9586 |
| chrUn_gl000220 | 161802 | 4862354 | 30.0513 | 103.747 |
| chrUn_gl000221 | 155397 | 40609 | 0.2613 | 0.9233 |
| chrUn_gl000222 | 186861 | 15296 | 0.0819 | 0.447 |
| chrUn_gl000223 | 180455 | 900 | 0.005 | 0.097 |
| chrUn_gl000224 | 179693 | 208724 | 1.1616 | 5.1366 |
| chrUn_gl000225 | 211173 | 88133 | 0.4173 | 1.2805 |
| chrUn_gl000226 | 15008 | 118369 | 7.8871 | 25.2155 |
| chrUn_gl000227 | 128374 | 3594 | 0.028 | 0.2264 |
| chrUn_gl000228 | 129120 | 17276 | 0.1338 | 1.0428 |
| chrUn_gl000229 | 19913 | 24775 | 1.2442 | 2.3606 |
| chrUn_gl000230 | 43691 | 13886 | 0.3178 | 0.9228 |
| chrUn_gl000231 | 27386 | 25943 | 0.9473 | 1.5865 |
| chrUn_gl000232 | 40652 | 70198 | 1.7268 | 2.4637 |
| chrUn_gl000233 | 45941 | 19606 | 0.4268 | 1.1493 |
| chrUn_gl000234 | 40531 | 47119 | 1.1625 | 2.1154 |
| chrUn_gl000235 | 34474 | 37093 | 1.076 | 2.008 |
| chrUn_gl000236 | 41934 | 1200 | 0.0286 | 0.2182 |
| chrUn_gl000237 | 45867 | 15950 | 0.3477 | 1.1857 |
| chrUn_gl000238 | 39939 | 890 | 0.0223 | 0.2063 |
| chrUn_gl000239 | 33824 | 3268 | 0.0966 | 0.892 |
| chrUn_gl000240 | 41933 | 11823 | 0.2819 | 0.7743 |
| chrUn_gl000241 | 42152 | 61955 | 1.4698 | 2.1272 |
| chrUn_gl000242 | 43523 | 300 | 0.0069 | 0.1148 |
| chrUn_gl000243 | 43341 | 8297 | 0.1914 | 0.8839 |
| chrUn_gl000244 | 39929 | 900 | 0.0225 | 0.1819 |
| chrUn_gl000245 | 36651 | 2070 | 0.0565 | 0.3591 |
| chrUn_gl000246 | 38154 | 3546 | 0.0929 | 0.4204 |
| chrUn_gl000247 | 36422 | 4174 | 0.1146 | 0.6707 |
| chrUn_gl000248 | 39786 | 1198 | 0.0301 | 0.2244 |
| chrUn_gl000249 | 38502 | 286 | 0.0074 | 0.1217 |
