BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716159.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 = 7,268,879 number of mapped reads = 6,627,117 (91.17%) number of supplementary alignments = 29,967 (0.41%) number of secondary alignments = 0 number of mapped bases = 382,583,058 bp number of sequenced bases = 382,482,682 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 659,462 duplication rate = 7.44% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4467 >>>>>>> ACTG content number of A's = 93,712,954 bp (24.5%) number of C's = 79,242,511 bp (20.72%) number of T's = 120,769,175 bp (31.58%) number of G's = 88,749,333 bp (23.2%) number of N's = 8,709 bp (0%) GC percentage = 43.92% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 1,854,041 number of insertions = 22,986 mapped reads with insertion percentage = 0.35% number of deletions = 59,655 mapped reads with deletion percentage = 0.89% homopolymer indels = 42.6% >>>>>>> Coverage mean coverageData = 0.1236X std coverageData = 0.8307X There is a 8.72% of reference with a coverageData >= 1X There is a 2.28% of reference with a coverageData >= 2X There is a 0.71% of reference with a coverageData >= 3X There is a 0.25% of reference with a coverageData >= 4X There is a 0.1% of reference with a coverageData >= 5X There is a 0.05% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% 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 30831712 0.123697633635986 1.6358485666590905 chr2 243199373 32340607 0.1329798124109473 0.9179698143001684 chr3 198022430 25527866 0.1289140124176842 0.4864798247356879 chr4 191154276 24325427 0.12725546877120342 0.5869376161473671 chr5 180915260 23013350 0.12720513460279692 0.49745596991387003 chr6 171115067 21851624 0.1277013437980888 0.5655753404728233 chr7 159138663 20621258 0.12958044017248027 0.9375958918879107 chr8 146364022 19297766 0.1318477432930888 0.7608794815288258 chr9 141213431 16567096 0.11731954873329294 0.8455459476634244 chr10 135534747 18150189 0.13391539366654073 0.71050199296798 chr11 135006516 17518980 0.12976395894847031 0.8483686094360597 chr12 133851895 17327212 0.12945062899557755 0.5036069348621962 chr13 115169878 11869067 0.10305704239783947 0.43181166939464016 chr14 107349540 11504109 0.10716495850843888 0.49947375884032585 chr15 102531392 11168045 0.10892317740112219 0.4533106603076555 chr16 90354753 11413325 0.12631681921591884 0.564355146102836 chr17 81195210 10531017 0.1296999786071124 0.565407446581791 chr18 78077248 10232735 0.13105911468600942 1.6687939884678091 chr19 59128983 7728829 0.1307113467518966 1.0677849688072192 chr20 63025520 8319143 0.13199641986293806 0.529229596015711 chr21 48129895 5071735 0.10537598305585333 0.5435148445604904 chr22 51304566 4742389 0.0924360026746937 0.41700303227952046 chrMT 16571 20955 1.2645585661698147 1.4952454690018855 chrX 155270560 21529715 0.13865935049116845 0.6660213766684978 chrY 59373566 1078907 0.018171504133674573 0.35051141497351324