BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472684.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 = 16,830,184 number of mapped reads = 16,692,652 (99.18%) number of supplementary alignments = 91,752 (0.55%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,364,457 number of mapped paired reads (second in pair) = 8,328,195 number of mapped paired reads (both in pair) = 16,601,918 number of mapped paired reads (singletons) = 90,734 number of mapped bases = 1,640,815,060 bp number of sequenced bases = 1,640,596,807 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,148,472 duplication rate = 49.18% >>>>>>> Insert size mean insert size = 23,610.9847 std insert size = 1,507,648.457 median insert size = 219 >>>>>>> Mapping quality mean mapping quality = 54.7931 >>>>>>> ACTG content number of A's = 438,740,902 bp (26.74%) number of C's = 384,534,544 bp (23.44%) number of T's = 436,640,674 bp (26.61%) number of G's = 380,370,563 bp (23.18%) number of N's = 310,124 bp (0.02%) GC percentage = 46.62% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 10,348,884 number of insertions = 107,597 mapped reads with insertion percentage = 0.64% number of deletions = 88,787 mapped reads with deletion percentage = 0.52% homopolymer indels = 46.76% >>>>>>> Coverage mean coverageData = 0.53X std coverageData = 19.7205X There is a 3.62% of reference with a coverageData >= 1X There is a 1.65% of reference with a coverageData >= 2X There is a 0.79% of reference with a coverageData >= 3X There is a 0.6% of reference with a coverageData >= 4X There is a 0.47% of reference with a coverageData >= 5X There is a 0.42% of reference with a coverageData >= 6X There is a 0.38% of reference with a coverageData >= 7X There is a 0.36% of reference with a coverageData >= 8X There is a 0.34% of reference with a coverageData >= 9X There is a 0.33% of reference with a coverageData >= 10X There is a 0.32% of reference with a coverageData >= 11X There is a 0.31% of reference with a coverageData >= 12X There is a 0.3% of reference with a coverageData >= 13X There is a 0.29% of reference with a coverageData >= 14X There is a 0.28% of reference with a coverageData >= 15X There is a 0.27% of reference with a coverageData >= 16X There is a 0.27% of reference with a coverageData >= 17X There is a 0.26% of reference with a coverageData >= 18X There is a 0.25% of reference with a coverageData >= 19X There is a 0.25% of reference with a coverageData >= 20X There is a 0.24% of reference with a coverageData >= 21X There is a 0.24% of reference with a coverageData >= 22X There is a 0.23% of reference with a coverageData >= 23X There is a 0.23% of reference with a coverageData >= 24X There is a 0.22% of reference with a coverageData >= 25X There is a 0.22% of reference with a coverageData >= 26X There is a 0.22% of reference with a coverageData >= 27X There is a 0.21% of reference with a coverageData >= 28X There is a 0.21% of reference with a coverageData >= 29X There is a 0.21% of reference with a coverageData >= 30X There is a 0.2% of reference with a coverageData >= 31X There is a 0.2% of reference with a coverageData >= 32X There is a 0.2% of reference with a coverageData >= 33X There is a 0.19% of reference with a coverageData >= 34X There is a 0.19% of reference with a coverageData >= 35X There is a 0.19% of reference with a coverageData >= 36X There is a 0.19% of reference with a coverageData >= 37X There is a 0.18% of reference with a coverageData >= 38X There is a 0.18% of reference with a coverageData >= 39X There is a 0.18% of reference with a coverageData >= 40X There is a 0.18% of reference with a coverageData >= 41X There is a 0.17% of reference with a coverageData >= 42X There is a 0.17% of reference with a coverageData >= 43X There is a 0.17% of reference with a coverageData >= 44X There is a 0.17% of reference with a coverageData >= 45X There is a 0.16% of reference with a coverageData >= 46X There is a 0.16% of reference with a coverageData >= 47X There is a 0.16% of reference with a coverageData >= 48X There is a 0.16% of reference with a coverageData >= 49X There is a 0.16% of reference with a coverageData >= 50X There is a 0.16% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 181543849 0.7283586627453177 22.741814795708382 chr2 243199373 131117032 0.5391339228493817 21.352164641214475 chr3 198022430 170352366 0.8602680312528233 23.996003143409034 chr4 191154276 49582173 0.25938301793468643 14.068972563241367 chr5 180915260 52562852 0.29053852063115077 12.28067870407187 chr6 171115067 112702563 0.6586361153106406 20.549186590712868 chr7 159138663 91243795 0.5733603216208999 18.781832548249888 chr8 146364022 64830720 0.4429416403984854 13.748212819866572 chr9 141213431 110369212 0.781577299116824 21.840183668914072 chr10 135534747 34692685 0.25596893614299515 11.135812892155 chr11 135006516 63587016 0.470992200109808 28.01939218758863 chr12 133851895 65129843 0.48658140402121314 18.85426875556644 chr13 115169878 57216444 0.496800422068694 19.10478958350718 chr14 107349540 18234795 0.16986374603934026 6.6965476663537995 chr15 102531392 27834071 0.27146877124227475 16.635778764499264 chr16 90354753 102440759 1.133761707034936 30.426651852921022 chr17 81195210 45237360 0.5571432107879271 18.0727386626528 chr18 78077248 8718889 0.11167003478401288 3.9794181726930904 chr19 59128983 54619836 0.9237404945726869 31.527083797792073 chr20 63025520 82335137 1.306377749838478 35.110825601425034 chr21 48129895 11391765 0.23668792545672498 12.184402092464234 chr22 51304566 29113051 0.5674553606008479 21.41550801957043 chrMT 16571 4721 0.28489529901635385 0.7263254691007174 chrX 155270560 75179933 0.4841866545725088 15.470780713799048 chrY 59373566 774193 0.013039354921009797 0.7457395451243618