Input data and parameters
QualiMap command line
| qualimap bamqc -bam /opt/tsinghua/zhangwei/Pipeline_test/o_WGBS-PE/intermediate_result/step_06_bamsort/case3.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/case3.pair1.truncated.gz -2 /opt/tsinghua/zhangwei/Pipeline_test/o_WGBS-PE/intermediate_result/step_03_adapterremoval/case3.pair2.truncated.gz" |
| Draw chromosome limits: | no |
| Analyze overlapping paired-end reads: | no |
| Program: | Bismark (v0.23.0) |
| Analysis date: | Tue Jan 12 17:45:10 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/case3.pair1_sorted.bam |
Summary
Globals
| Reference size | 3,137,161,264 |
| Number of reads | 6,967,966 |
| Mapped reads | 6,967,966 / 100% |
| Unmapped reads | 0 / 0% |
| Mapped paired reads | 6,967,966 / 100% |
| Mapped reads, first in pair | 3,483,983 / 50% |
| Mapped reads, second in pair | 3,483,983 / 50% |
| Mapped reads, both in pair | 6,967,966 / 100% |
| Mapped reads, singletons | 0 / 0% |
| Secondary alignments | 0 |
| Read min/max/mean length | 16 / 150 / 147.77 |
| Duplicated reads (estimated) | 637,869 / 9.15% |
| Duplication rate | 9.05% |
| Clipped reads | 0 / 0% |
ACGT Content
| Number/percentage of A's | 407,365,880 / 39.57% |
| Number/percentage of C's | 107,531,610 / 10.45% |
| Number/percentage of T's | 409,116,580 / 39.74% |
| Number/percentage of G's | 105,366,081 / 10.24% |
| Number/percentage of N's | 17,066 / 0% |
| GC Percentage | 20.68% |
Coverage
| Mean | 0.3282 |
| Standard Deviation | 2.002 |
Mapping Quality
| Mean Mapping Quality | 34.57 |
Insert size
| Mean | 183.93 |
| Standard Deviation | 55.73 |
| P25/Median/P75 | 159 / 169 / 183 |
Mismatches and indels
| General error rate | 14.8% |
| Mismatches | 152,147,393 |
| Insertions | 164,500 |
| Mapped reads with at least one insertion | 2.32% |
| Deletions | 169,325 |
| Mapped reads with at least one deletion | 2.39% |
| Homopolymer indels | 80.57% |
Chromosome stats
| Name | Length | Mapped bases | Mean coverage | Standard deviation |
| chr1 | 249250621 | 80451118 | 0.3228 | 2.0751 |
| chr2 | 243199373 | 90241857 | 0.3711 | 0.9159 |
| chr3 | 198022430 | 75588424 | 0.3817 | 0.9263 |
| chr4 | 191154276 | 78862986 | 0.4126 | 0.9616 |
| chr5 | 180915260 | 68806466 | 0.3803 | 0.9142 |
| chr6 | 171115067 | 64281675 | 0.3757 | 0.9749 |
| chr7 | 159138663 | 57723661 | 0.3627 | 1.4128 |
| chr8 | 146364022 | 54123222 | 0.3698 | 0.9107 |
| chr9 | 141213431 | 40359366 | 0.2858 | 0.8122 |
| chr10 | 135534747 | 49613776 | 0.3661 | 5.4646 |
| chr11 | 135006516 | 46407027 | 0.3437 | 0.8714 |
| chr12 | 133851895 | 48047946 | 0.359 | 0.8854 |
| chr13 | 115169878 | 39592624 | 0.3438 | 0.8772 |
| chr14 | 107349540 | 32572224 | 0.3034 | 0.8272 |
| chr15 | 102531392 | 27894182 | 0.2721 | 0.7922 |
| chr16 | 90354753 | 26812883 | 0.2968 | 4.3427 |
| chr17 | 81195210 | 21993741 | 0.2709 | 0.7778 |
| chr18 | 78077248 | 29041943 | 0.372 | 0.9064 |
| chr19 | 59128983 | 13835214 | 0.234 | 0.9313 |
| chr20 | 63025520 | 18128797 | 0.2876 | 0.8062 |
| chr21 | 48129895 | 13891334 | 0.2886 | 0.8942 |
| chr22 | 51304566 | 8286487 | 0.1615 | 0.613 |
| chrX | 155270560 | 29873275 | 0.1924 | 0.6306 |
| chrY | 59373566 | 5322124 | 0.0896 | 4.5199 |
| chrM | 16571 | 5910 | 0.3566 | 0.7373 |
| chr1_gl000191_random | 106433 | 4605 | 0.0433 | 0.276 |
| chr1_gl000192_random | 547496 | 101645 | 0.1857 | 0.6538 |
| chr4_ctg9_hap1 | 590426 | 13291 | 0.0225 | 0.2051 |
| chr4_gl000193_random | 189789 | 126521 | 0.6666 | 1.4762 |
| chr4_gl000194_random | 191469 | 73615 | 0.3845 | 1.0788 |
| chr6_apd_hap1 | 4622290 | 1791 | 0.0004 | 0.0299 |
| chr6_cox_hap2 | 4795371 | 23869 | 0.005 | 0.1024 |
| chr6_dbb_hap3 | 4610396 | 11552 | 0.0025 | 0.0715 |
| chr6_mann_hap4 | 4683263 | 14507 | 0.0031 | 0.0845 |
| chr6_mcf_hap5 | 4833398 | 12456 | 0.0026 | 0.0715 |
| chr6_qbl_hap6 | 4611984 | 11489 | 0.0025 | 0.0686 |
| chr6_ssto_hap7 | 4928567 | 15046 | 0.0031 | 0.0807 |
| chr7_gl000195_random | 182896 | 198934 | 1.0877 | 1.9981 |
| chr8_gl000196_random | 38914 | 900 | 0.0231 | 0.2615 |
| chr8_gl000197_random | 37175 | 0 | 0 | 0 |
| chr9_gl000198_random | 90085 | 60455 | 0.6711 | 1.8004 |
| chr9_gl000199_random | 169874 | 158084 | 0.9306 | 3.5331 |
| chr9_gl000200_random | 187035 | 0 | 0 | 0 |
| chr9_gl000201_random | 36148 | 300 | 0.0083 | 0.1246 |
| chr11_gl000202_random | 40103 | 3543 | 0.0883 | 0.4567 |
| chr17_ctg5_hap1 | 1680828 | 9798 | 0.0058 | 0.1104 |
| chr17_gl000203_random | 37498 | 7915 | 0.2111 | 0.756 |
| chr17_gl000204_random | 81310 | 7613 | 0.0936 | 0.4125 |
| chr17_gl000205_random | 174588 | 145235 | 0.8319 | 1.7938 |
| chr17_gl000206_random | 41001 | 1178 | 0.0287 | 0.2192 |
| chr18_gl000207_random | 4262 | 582 | 0.1366 | 0.4984 |
| chr19_gl000208_random | 92689 | 58911 | 0.6356 | 1.634 |
| chr19_gl000209_random | 159169 | 2698 | 0.017 | 0.177 |
| chr21_gl000210_random | 27682 | 0 | 0 | 0 |
| chrUn_gl000211 | 166566 | 61791 | 0.371 | 0.889 |
| chrUn_gl000212 | 186858 | 74844 | 0.4005 | 2.9007 |
| chrUn_gl000213 | 164239 | 10658 | 0.0649 | 0.3465 |
| chrUn_gl000214 | 137718 | 211190 | 1.5335 | 2.6132 |
| chrUn_gl000215 | 172545 | 2408 | 0.014 | 0.1497 |
| chrUn_gl000216 | 172294 | 186104 | 1.0802 | 1.799 |
| chrUn_gl000217 | 172149 | 38260 | 0.2222 | 0.775 |
| chrUn_gl000218 | 161147 | 130298 | 0.8086 | 1.5824 |
| chrUn_gl000219 | 179198 | 189253 | 1.0561 | 2.0797 |
| chrUn_gl000220 | 161802 | 5183257 | 32.0346 | 115.9875 |
| chrUn_gl000221 | 155397 | 32757 | 0.2108 | 0.8536 |
| chrUn_gl000222 | 186861 | 17018 | 0.0911 | 0.5089 |
| chrUn_gl000223 | 180455 | 300 | 0.0017 | 0.0407 |
| chrUn_gl000224 | 179693 | 178384 | 0.9927 | 4.6534 |
| chrUn_gl000225 | 211173 | 74475 | 0.3527 | 1.1162 |
| chrUn_gl000226 | 15008 | 107287 | 7.1487 | 22.2709 |
| chrUn_gl000227 | 128374 | 3300 | 0.0257 | 0.2224 |
| chrUn_gl000228 | 129120 | 9081 | 0.0703 | 0.4596 |
| chrUn_gl000229 | 19913 | 23681 | 1.1892 | 2.058 |
| chrUn_gl000230 | 43691 | 14939 | 0.3419 | 0.9045 |
| chrUn_gl000231 | 27386 | 22489 | 0.8212 | 1.5024 |
| chrUn_gl000232 | 40652 | 56214 | 1.3828 | 2.705 |
| chrUn_gl000233 | 45941 | 16792 | 0.3655 | 0.9649 |
| chrUn_gl000234 | 40531 | 49703 | 1.2263 | 2.1668 |
| chrUn_gl000235 | 34474 | 33690 | 0.9773 | 1.862 |
| chrUn_gl000236 | 41934 | 1784 | 0.0425 | 0.2843 |
| chrUn_gl000237 | 45867 | 20153 | 0.4394 | 1.334 |
| chrUn_gl000238 | 39939 | 1778 | 0.0445 | 0.2755 |
| chrUn_gl000239 | 33824 | 3608 | 0.1067 | 0.8104 |
| chrUn_gl000240 | 41933 | 12542 | 0.2991 | 0.8675 |
| chrUn_gl000241 | 42152 | 73710 | 1.7487 | 2.2396 |
| chrUn_gl000242 | 43523 | 1498 | 0.0344 | 0.291 |
| chrUn_gl000243 | 43341 | 5701 | 0.1315 | 0.6094 |
| chrUn_gl000244 | 39929 | 1500 | 0.0376 | 0.2764 |
| chrUn_gl000245 | 36651 | 1810 | 0.0494 | 0.3935 |
| chrUn_gl000246 | 38154 | 2993 | 0.0784 | 0.4198 |
| chrUn_gl000247 | 36422 | 2091 | 0.0574 | 0.3934 |
| chrUn_gl000248 | 39786 | 900 | 0.0226 | 0.2053 |
| chrUn_gl000249 | 38502 | 300 | 0.0078 | 0.1203 |
