BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714055.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 272,526 number of mapped reads = 256,618 (94.16%) number of supplementary alignments = 7,208 (2.64%) number of secondary alignments = 0 number of mapped bases = 32,691,461 bp number of sequenced bases = 31,980,045 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 246,221 duplication rate = 32.92% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 27.0258 >>>>>>> ACTG content number of A's = 9,101,832 bp (28.46%) number of C's = 6,781,306 bp (21.2%) number of T's = 8,490,275 bp (26.55%) number of G's = 7,606,454 bp (23.79%) number of N's = 178 bp (0%) GC percentage = 44.99% >>>>>>> Mismatches and indels general error rate = 0.0459 number of mismatches = 1,383,429 number of insertions = 32,255 mapped reads with insertion percentage = 12.28% number of deletions = 135,243 mapped reads with deletion percentage = 49.56% homopolymer indels = 29.38% >>>>>>> Coverage mean coverageData = 0.0106X std coverageData = 15.4731X There is a 0.02% of reference with a coverageData >= 1X There is a 0.01% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1568388 0.00629241361047602 3.7220490218978535 chr2 243199373 725277 0.0029822321951463253 1.3797139547178685 chr3 198022430 196474 9.92180532276066E-4 0.2763831650428263 chr4 191154276 382328 0.00200010173981146 1.0384731163322856 chr5 180915260 545385 0.003014588155802888 1.0056006273142226 chr6 171115067 194749 0.0011381171945542353 0.5976050014622606 chr7 159138663 94329 5.927472194484882E-4 0.18311978195455383 chr8 146364022 180354 0.0012322290514809712 0.37851155900154543 chr9 141213431 114664 8.119907517862093E-4 0.21655209982814075 chr10 135534747 325396 0.002400830836390612 0.8560768327669153 chr11 135006516 19384096 0.1435789662181935 71.80605582079231 chr12 133851895 1499838 0.011205205574414916 5.563834736349232 chr13 115169878 1788515 0.015529364370777574 10.05150074325388 chr14 107349540 1930771 0.017985833940229273 11.852778672106135 chr15 102531392 141453 0.0013796067452200396 0.4694548989682137 chr16 90354753 144024 0.0015939836612690425 0.8450506389928347 chr17 81195210 274466 0.003380322558436637 1.1953760993147202 chr18 78077248 150450 0.0019269377937091226 0.5515922795632258 chr19 59128983 60533 0.0010237449881388963 0.3145084626364682 chr20 63025520 1781367 0.028264217415421563 11.76460952052507 chr21 48129895 36974 7.682127708776426E-4 0.1892984686331572 chr22 51304566 56099 0.001093450434801456 0.33336069106241534 chrMT 16571 12916 0.7794339508780399 5.535327430035604 chrX 155270560 1096210 0.0070599990107590264 2.137748507300026 chrY 59373566 6405 1.0787628959325097E-4 0.02517115566220975