BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068089.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 4,373,237 number of mapped reads = 4,115,675 (94.11%) number of supplementary alignments = 26,000 (0.59%) number of secondary alignments = 0 number of mapped bases = 265,531,919 bp number of sequenced bases = 265,429,602 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 614,429 duplication rate = 12.63% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.2502 >>>>>>> ACTG content number of A's = 70,629,833 bp (26.61%) number of C's = 46,898,428 bp (17.67%) number of T's = 87,417,827 bp (32.93%) number of G's = 60,453,355 bp (22.78%) number of N's = 30,159 bp (0.01%) GC percentage = 40.44% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 1,388,663 number of insertions = 17,154 mapped reads with insertion percentage = 0.41% number of deletions = 59,003 mapped reads with deletion percentage = 1.42% homopolymer indels = 45.81% >>>>>>> Coverage mean coverageData = 0.0858X std coverageData = 0.923X There is a 6% of reference with a coverageData >= 1X There is a 1.65% of reference with a coverageData >= 2X There is a 0.5% of reference with a coverageData >= 3X There is a 0.16% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% 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 22930827 0.09199907670440668 2.0486896253409617 chr2 243199373 23508563 0.0966637483888579 1.3622465598237468 chr3 198022430 16285317 0.08223975940503306 0.38834501626073875 chr4 191154276 13347717 0.06982693392639566 0.37568771755385416 chr5 180915260 14325448 0.07918319328065526 0.38214953779371785 chr6 171115067 17718132 0.10354513083292659 0.6035271875002104 chr7 159138663 18156945 0.11409512093236576 1.4179108718503648 chr8 146364022 12553099 0.0857662889313058 0.9733511081171388 chr9 141213431 9003181 0.06375584061830493 0.5966641163508215 chr10 135534747 15088789 0.11132782798495208 0.6119276003242852 chr11 135006516 13461623 0.09971091321251487 0.6826474985486634 chr12 133851895 13312724 0.0994586143139774 0.4464728487169534 chr13 115169878 7763766 0.06741142853342261 0.4027027636117941 chr14 107349540 7100346 0.06614230484825552 0.3785476799427016 chr15 102531392 6328418 0.061721760297568186 0.37105485592439275 chr16 90354753 4829939 0.05345528419517676 0.3503973033869471 chr17 81195210 8187440 0.10083649023138187 0.47322396463483757 chr18 78077248 7921837 0.10146152948423592 1.1404131219433578 chr19 59128983 6705980 0.1134127404153053 1.2627641835158117 chr20 63025520 4944423 0.07845112582966392 0.38859437132802266 chr21 48129895 5544307 0.11519466227798751 0.4724165928109994 chr22 51304566 3801656 0.07409975946390425 0.3623275876597696 chrMT 16571 266445 16.078993422243677 10.066484053709337 chrX 155270560 12033013 0.07749706705508114 0.4724777890301714 chrY 59373566 411984 0.0069388454788112276 0.2310923764930163