BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472744.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 19,725,626 number of mapped reads = 19,502,094 (98.87%) number of supplementary alignments = 108,962 (0.55%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,795,425 number of mapped paired reads (second in pair) = 9,706,669 number of mapped paired reads (both in pair) = 19,366,730 number of mapped paired reads (singletons) = 135,364 number of mapped bases = 1,922,205,106 bp number of sequenced bases = 1,921,921,199 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 12,630,769 duplication rate = 47.34% >>>>>>> Insert size mean insert size = 37,354.4457 std insert size = 1,897,018.7222 median insert size = 250 >>>>>>> Mapping quality mean mapping quality = 55.0601 >>>>>>> ACTG content number of A's = 532,631,966 bp (27.71%) number of C's = 431,037,933 bp (22.43%) number of T's = 530,327,530 bp (27.59%) number of G's = 427,551,976 bp (22.25%) number of N's = 371,794 bp (0.02%) GC percentage = 44.67% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 12,459,646 number of insertions = 123,297 mapped reads with insertion percentage = 0.63% number of deletions = 109,712 mapped reads with deletion percentage = 0.56% homopolymer indels = 45.26% >>>>>>> Coverage mean coverageData = 0.6209X std coverageData = 21.1604X There is a 5.45% of reference with a coverageData >= 1X There is a 2.34% of reference with a coverageData >= 2X There is a 1.06% of reference with a coverageData >= 3X There is a 0.74% of reference with a coverageData >= 4X There is a 0.56% of reference with a coverageData >= 5X There is a 0.49% of reference with a coverageData >= 6X There is a 0.44% of reference with a coverageData >= 7X There is a 0.42% of reference with a coverageData >= 8X There is a 0.39% of reference with a coverageData >= 9X There is a 0.38% of reference with a coverageData >= 10X There is a 0.36% of reference with a coverageData >= 11X There is a 0.35% of reference with a coverageData >= 12X There is a 0.34% of reference with a coverageData >= 13X There is a 0.33% of reference with a coverageData >= 14X There is a 0.32% of reference with a coverageData >= 15X There is a 0.31% of reference with a coverageData >= 16X There is a 0.3% of reference with a coverageData >= 17X There is a 0.3% of reference with a coverageData >= 18X There is a 0.29% of reference with a coverageData >= 19X There is a 0.28% of reference with a coverageData >= 20X There is a 0.28% of reference with a coverageData >= 21X There is a 0.27% of reference with a coverageData >= 22X There is a 0.27% of reference with a coverageData >= 23X There is a 0.26% of reference with a coverageData >= 24X There is a 0.26% of reference with a coverageData >= 25X There is a 0.25% of reference with a coverageData >= 26X There is a 0.25% of reference with a coverageData >= 27X There is a 0.24% of reference with a coverageData >= 28X There is a 0.24% of reference with a coverageData >= 29X There is a 0.24% of reference with a coverageData >= 30X There is a 0.23% of reference with a coverageData >= 31X There is a 0.23% of reference with a coverageData >= 32X There is a 0.22% of reference with a coverageData >= 33X There is a 0.22% of reference with a coverageData >= 34X There is a 0.22% of reference with a coverageData >= 35X There is a 0.22% of reference with a coverageData >= 36X There is a 0.21% of reference with a coverageData >= 37X There is a 0.21% of reference with a coverageData >= 38X There is a 0.21% of reference with a coverageData >= 39X There is a 0.2% of reference with a coverageData >= 40X There is a 0.2% of reference with a coverageData >= 41X There is a 0.2% of reference with a coverageData >= 42X There is a 0.2% of reference with a coverageData >= 43X There is a 0.19% of reference with a coverageData >= 44X There is a 0.19% of reference with a coverageData >= 45X There is a 0.19% of reference with a coverageData >= 46X There is a 0.19% of reference with a coverageData >= 47X There is a 0.18% of reference with a coverageData >= 48X There is a 0.18% of reference with a coverageData >= 49X There is a 0.18% of reference with a coverageData >= 50X There is a 0.18% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 179296424 0.719341934959512 23.16183320175612 chr2 243199373 133685005 0.5496930495787092 16.14111471964785 chr3 198022430 239368026 1.2087924888104848 28.086993016435034 chr4 191154276 75348022 0.394173876602164 14.9254491435516 chr5 180915260 80385866 0.4443288310781523 16.84619029731649 chr6 171115067 159183647 0.9302725340954342 26.942004286621664 chr7 159138663 62792091 0.39457470495400604 16.144870350498767 chr8 146364022 106401730 0.7269664262164099 23.66404102450383 chr9 141213431 101985115 0.7222054890798596 20.396738372830036 chr10 135534747 37397080 0.2759224540405126 8.376412994048248 chr11 135006516 57053487 0.42259802482422404 11.514467048766896 chr12 133851895 129955069 0.9708870315209209 32.12756871170625 chr13 115169878 52129056 0.4526275177611979 19.158193021124198 chr14 107349540 69254453 0.6451304122961309 36.02867718769621 chr15 102531392 50033729 0.4879844896673206 17.532135449764642 chr16 90354753 67307138 0.7449208344357934 22.421604541639994 chr17 81195210 86094064 1.0603342734134193 29.474526147898942 chr18 78077248 26200044 0.33556566952769645 10.179080491290929 chr19 59128983 39510660 0.6682113913577712 15.742633132082398 chr20 63025520 41229653 0.654173944141992 18.55115889961079 chr21 48129895 8438154 0.1753204323425181 6.728005982646534 chr22 51304566 15663822 0.30531048639998243 9.430870533449484 chrMT 16571 6084 0.36714742622654034 0.9925114468927102 chrX 155270560 100793668 0.6491486087253114 23.568716657464858 chrY 59373566 2693019 0.04535720492179971 1.9094521824048696