BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094007.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP024468/ERP024468.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 = 488,452 number of mapped reads = 369,286 (75.6%) number of supplementary alignments = 19,381 (3.97%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 185,163 number of mapped paired reads (second in pair) = 184,123 number of mapped paired reads (both in pair) = 365,018 number of mapped paired reads (singletons) = 4,268 number of mapped bases = 47,184,257 bp number of sequenced bases = 46,100,163 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 368,168 duplication rate = 44.43% >>>>>>> Insert size mean insert size = 741,402.6233 std insert size = 7,978,121.0252 median insert size = 184 >>>>>>> Mapping quality mean mapping quality = 30.5267 >>>>>>> ACTG content number of A's = 12,645,945 bp (27.43%) number of C's = 10,205,678 bp (22.14%) number of T's = 11,751,604 bp (25.49%) number of G's = 11,496,622 bp (24.94%) number of N's = 314 bp (0%) GC percentage = 47.08% >>>>>>> Mismatches and indels general error rate = 0.0396 number of mismatches = 1,782,042 number of insertions = 23,074 mapped reads with insertion percentage = 6.13% number of deletions = 136,419 mapped reads with deletion percentage = 35.74% homopolymer indels = 28.84% >>>>>>> Coverage mean coverageData = 0.0152X std coverageData = 9.7664X There is a 0.01% 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 545172 0.002187244299784513 0.9660934060235161 chr2 243199373 3157076 0.01298143149406886 10.318107848524456 chr3 198022430 723646 0.0036543638011108134 1.6253560223817696 chr4 191154276 654943 0.003426253462412737 3.17366997260067 chr5 180915260 271014 0.0014980162535763982 0.8965074020067401 chr6 171115067 1390294 0.008124906966842376 5.293990932552262 chr7 159138663 584111 0.0036704531066721353 1.888780572699312 chr8 146364022 127962 8.742722306442221E-4 0.3322927246940403 chr9 141213431 1054975 0.007470783710368173 3.213057712792733 chr10 135534747 267841 0.0019761795844131396 1.4377047889031758 chr11 135006516 434671 0.003219629784387592 3.2435565239712 chr12 133851895 454299 0.00339404234807434 1.3159400601875328 chr13 115169878 913283 0.007929877289615606 4.364292256191495 chr14 107349540 240835 0.0022434655984552893 0.9202770589044473 chr15 102531392 455525 0.0044427856787509525 2.963035762547925 chr16 90354753 374703 0.004147020356527343 1.4333491942714556 chr17 81195210 240165 0.002957871529613631 1.061895648791618 chr18 78077248 563793 0.007220964038076752 3.391094273226339 chr19 59128983 72361 0.00122378225243617 0.3005911747664485 chr20 63025520 29387 4.662714405212365E-4 0.1983130371615949 chr21 48129895 424286 0.008815435811775612 4.023823099055793 chr22 51304566 213161 0.0041548153823189925 1.4977971432644932 chrMT 16571 1710077 103.19697061130891 505.3208133087762 chrX 155270560 31892645 0.20540046355213765 39.957237157491626 chrY 59373566 388032 0.006535433630514967 1.8933000820200518