BamQC report ----------------------------------- >>>>>>> Input bam file = SRR926981.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 26,733,388 number of mapped reads = 26,127,359 (97.73%) number of supplementary alignments = 763,103 (2.85%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 13,168,583 number of mapped paired reads (second in pair) = 12,958,776 number of mapped paired reads (both in pair) = 25,726,022 number of mapped paired reads (singletons) = 401,337 number of mapped bases = 2,373,511,154 bp number of sequenced bases = 2,371,658,246 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,568,748 duplication rate = 7.7% >>>>>>> Insert size mean insert size = 335,783.0848 std insert size = 5,713,338.533 median insert size = 166 >>>>>>> Mapping quality mean mapping quality = 52.6132 >>>>>>> ACTG content number of A's = 678,346,870 bp (28.6%) number of C's = 460,715,186 bp (19.43%) number of T's = 692,382,116 bp (29.19%) number of G's = 540,032,923 bp (22.77%) number of N's = 181,151 bp (0.01%) GC percentage = 42.2% >>>>>>> Mismatches and indels general error rate = 0.0098 number of mismatches = 22,396,950 number of insertions = 420,945 mapped reads with insertion percentage = 1.58% number of deletions = 1,258,199 mapped reads with deletion percentage = 4.69% homopolymer indels = 51.74% >>>>>>> Coverage mean coverageData = 0.7667X std coverageData = 2.9722X There is a 32.13% of reference with a coverageData >= 1X There is a 17.46% of reference with a coverageData >= 2X There is a 9.58% of reference with a coverageData >= 3X There is a 5.71% of reference with a coverageData >= 4X There is a 3.51% of reference with a coverageData >= 5X There is a 2.23% of reference with a coverageData >= 6X There is a 1.46% of reference with a coverageData >= 7X There is a 0.98% of reference with a coverageData >= 8X There is a 0.67% of reference with a coverageData >= 9X There is a 0.47% of reference with a coverageData >= 10X There is a 0.33% of reference with a coverageData >= 11X There is a 0.24% of reference with a coverageData >= 12X There is a 0.18% of reference with a coverageData >= 13X There is a 0.13% of reference with a coverageData >= 14X There is a 0.1% of reference with a coverageData >= 15X There is a 0.08% of reference with a coverageData >= 16X There is a 0.06% of reference with a coverageData >= 17X There is a 0.05% of reference with a coverageData >= 18X There is a 0.04% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 188697714 0.7570601559303638 3.5714240692674695 chr2 243199373 215119197 0.8845384523256974 5.226292806199055 chr3 198022430 167576245 0.8462488062589677 1.7124752119158066 chr4 191154276 138865846 0.7264595326133327 2.5954096602252803 chr5 180915260 134105103 0.7412592116331148 1.568070264002976 chr6 171115067 145933383 0.8528377165057008 2.65670484533345 chr7 159138663 114460089 0.7192475218922758 2.5834378023719236 chr8 146364022 111351519 0.7607847712739132 1.9210565304193028 chr9 141213431 102124810 0.723194736342041 3.412251299824771 chr10 135534747 115302922 0.8507259175390647 3.7451469979633814 chr11 135006516 108294718 0.8021443794609143 3.6590253723933945 chr12 133851895 112257616 0.8386703527805863 2.1852633894045566 chr13 115169878 69146136 0.6003838607869325 1.5342163064943728 chr14 107349540 76783235 0.7152637542741217 1.7067514211178276 chr15 102531392 71175797 0.6941854159163273 1.684475329890584 chr16 90354753 77831546 0.8613995768435115 4.378041602236176 chr17 81195210 62033677 0.7640066082715963 2.9035614068461753 chr18 78077248 65863099 0.8435632746686973 3.5832515719668474 chr19 59128983 39319474 0.6649780193242966 2.2204040955865736 chr20 63025520 49678607 0.788230021743573 1.776747823720867 chr21 48129895 32015379 0.665186969553954 2.484634493600911 chr22 51304566 24993140 0.4871523520927942 1.4091342838526857 chrMT 16571 406290 24.51813408967473 23.830612408600643 chrX 155270560 145618303 0.937835884664807 2.2446491681808127 chrY 59373566 4557309 0.07675653168617158 2.511537851237966