BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9717009.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 = 2,623,846 number of mapped reads = 2,346,497 (89.43%) number of supplementary alignments = 35,001 (1.33%) number of secondary alignments = 0 number of mapped bases = 184,840,532 bp number of sequenced bases = 184,762,104 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 119,099 duplication rate = 2.99% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.8171 >>>>>>> ACTG content number of A's = 46,239,245 bp (25.03%) number of C's = 33,665,152 bp (18.22%) number of T's = 57,427,111 bp (31.08%) number of G's = 47,420,405 bp (25.67%) number of N's = 10,191 bp (0.01%) GC percentage = 43.89% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 1,541,986 number of insertions = 17,186 mapped reads with insertion percentage = 0.72% number of deletions = 44,821 mapped reads with deletion percentage = 1.88% homopolymer indels = 43.7% >>>>>>> Coverage mean coverageData = 0.0597X std coverageData = 0.7421X There is a 4.86% of reference with a coverageData >= 1X There is a 0.7% of reference with a coverageData >= 2X There is a 0.15% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% 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 16079714 0.06451223244896148 1.2103447173382345 chr2 243199373 16262126 0.06686746680058259 1.3268330504520376 chr3 198022430 14079627 0.0711011727307861 0.3341697349519212 chr4 191154276 7848523 0.04105857930167359 0.26758764944053715 chr5 180915260 11412637 0.0630827769863084 0.3057702423087649 chr6 171115067 13341240 0.07796648322032332 0.4543370649767866 chr7 159138663 9764560 0.06135881636758504 1.021823287628071 chr8 146364022 12844462 0.08775696256830111 0.9622557250589712 chr9 141213431 7971160 0.05644760518565688 0.6762306634799878 chr10 135534747 8762781 0.0646533910599324 0.63095933507356 chr11 135006516 7291481 0.05400836356668889 0.5012168021097241 chr12 133851895 6856339 0.051223324107589216 0.2804674340873103 chr13 115169878 8233233 0.07148772876185559 0.32041092863996673 chr14 107349540 4302171 0.04007628723886474 0.3333246259116161 chr15 102531392 2184610 0.0213067428168731 0.18387215047486247 chr16 90354753 4650307 0.05146720947817764 0.36446139817734957 chr17 81195210 5674971 0.0698929284128953 0.39793523829320737 chr18 78077248 5604715 0.07178422835804868 1.6064981538910155 chr19 59128983 3763015 0.06364078678640557 0.9542482721207751 chr20 63025520 3359118 0.05329774351722921 0.39783381523606215 chr21 48129895 3824604 0.07946420826390749 0.35777025563902715 chr22 51304566 2728570 0.05318376535920799 0.2781938077299737 chrMT 16571 135500 8.176935610403717 6.059318460455177 chrX 155270560 7457331 0.04802797774413901 0.41728022176088275 chrY 59373566 407737 0.006867315330192564 0.1720066886073637