BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524635.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 1,639,719 number of mapped reads = 1,518,916 (92.63%) number of supplementary alignments = 3,364 (0.21%) number of secondary alignments = 0 number of mapped bases = 88,285,484 bp number of sequenced bases = 88,256,737 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 80,375 duplication rate = 4.27% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0974 >>>>>>> ACTG content number of A's = 21,650,192 bp (24.53%) number of C's = 16,338,942 bp (18.51%) number of T's = 28,459,869 bp (32.25%) number of G's = 21,807,212 bp (24.71%) number of N's = 522 bp (0%) GC percentage = 43.22% >>>>>>> Mismatches and indels general error rate = 0.0048 number of mismatches = 411,301 number of insertions = 5,672 mapped reads with insertion percentage = 0.37% number of deletions = 16,461 mapped reads with deletion percentage = 1.08% homopolymer indels = 43.12% >>>>>>> Coverage mean coverageData = 0.0285X std coverageData = 0.2485X There is a 2.45% of reference with a coverageData >= 1X There is a 0.3% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 8334862 0.03343968398778834 0.4021378071700269 chr2 243199373 8027636 0.03300845681045403 0.2909576705351954 chr3 198022430 5826716 0.02942452529241258 0.19582456086435834 chr4 191154276 4089620 0.02139434223276282 0.1937731773871565 chr5 180915260 5550345 0.030679252817037102 0.19948698959696595 chr6 171115067 5925261 0.03462734815748282 0.2263320417932099 chr7 159138663 4544085 0.028554248944519536 0.29698256440301773 chr8 146364022 7786403 0.053198886540573476 0.33894517326026863 chr9 141213431 3345308 0.023689729626355443 0.21363277493853158 chr10 135534747 3829223 0.028252703345511835 0.2529659688449379 chr11 135006516 4538921 0.03362001431101296 0.24651339474296713 chr12 133851895 2961839 0.022127733044048425 0.17350200993067041 chr13 115169878 2199432 0.019097285142561322 0.15712512842612167 chr14 107349540 1629510 0.015179478179412785 0.1455303131899867 chr15 102531392 2385650 0.023267508159842402 0.18229359001403764 chr16 90354753 2673760 0.02959180243677939 0.20282845318034487 chr17 81195210 2083600 0.025661612304469686 0.18827795154157148 chr18 78077248 2364478 0.03028382865133771 0.32676040471279866 chr19 59128983 1806817 0.030557214217602897 0.28737765515906377 chr20 63025520 1679071 0.026641128863355668 0.18866850827312853 chr21 48129895 794430 0.016505957471962072 0.1614141685666172 chr22 51304566 1620709 0.031589956340338204 0.20368675558455826 chrMT 16571 4471 0.2698087019491883 0.5718374652227507 chrX 155270560 4057420 0.02613128979505194 0.20223367366870645 chrY 59373566 225917 0.0038050097917312225 0.11135304282631457