BamQC report ----------------------------------- >>>>>>> Input bam file = SRR23117306.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP418207/SRP418207.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 = 8,236,235 number of mapped reads = 7,611,162 (92.41%) number of supplementary alignments = 82,573 (1%) number of secondary alignments = 0 number of mapped bases = 1,927,783,601 bp number of sequenced bases = 1,923,798,169 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 4,323,078 duplication rate = 35.3% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 51.992 >>>>>>> ACTG content number of A's = 545,239,017 bp (28.34%) number of C's = 407,863,821 bp (21.2%) number of T's = 551,984,863 bp (28.69%) number of G's = 418,710,468 bp (21.76%) number of N's = 0 bp (0%) GC percentage = 42.97% >>>>>>> Mismatches and indels general error rate = 0.0118 number of mismatches = 13,440,782 number of insertions = 7,923,304 mapped reads with insertion percentage = 47.21% number of deletions = 3,099,982 mapped reads with deletion percentage = 27.02% homopolymer indels = 31.18% >>>>>>> Coverage mean coverageData = 0.6227X std coverageData = 9.3782X There is a 14.66% of reference with a coverageData >= 1X There is a 8.9% of reference with a coverageData >= 2X There is a 6.4% of reference with a coverageData >= 3X There is a 4.96% of reference with a coverageData >= 4X There is a 3.98% of reference with a coverageData >= 5X There is a 3.26% of reference with a coverageData >= 6X There is a 2.71% of reference with a coverageData >= 7X There is a 2.27% of reference with a coverageData >= 8X There is a 1.92% of reference with a coverageData >= 9X There is a 1.62% of reference with a coverageData >= 10X There is a 1.38% of reference with a coverageData >= 11X There is a 1.17% of reference with a coverageData >= 12X There is a 1.01% of reference with a coverageData >= 13X There is a 0.86% of reference with a coverageData >= 14X There is a 0.74% of reference with a coverageData >= 15X There is a 0.64% of reference with a coverageData >= 16X There is a 0.55% of reference with a coverageData >= 17X There is a 0.47% of reference with a coverageData >= 18X There is a 0.41% of reference with a coverageData >= 19X There is a 0.35% of reference with a coverageData >= 20X There is a 0.31% of reference with a coverageData >= 21X There is a 0.27% of reference with a coverageData >= 22X There is a 0.23% of reference with a coverageData >= 23X There is a 0.2% of reference with a coverageData >= 24X There is a 0.18% of reference with a coverageData >= 25X There is a 0.15% of reference with a coverageData >= 26X There is a 0.13% of reference with a coverageData >= 27X There is a 0.12% of reference with a coverageData >= 28X There is a 0.1% of reference with a coverageData >= 29X There is a 0.09% of reference with a coverageData >= 30X There is a 0.08% of reference with a coverageData >= 31X There is a 0.07% of reference with a coverageData >= 32X There is a 0.06% of reference with a coverageData >= 33X There is a 0.05% of reference with a coverageData >= 34X There is a 0.05% of reference with a coverageData >= 35X There is a 0.04% of reference with a coverageData >= 36X There is a 0.04% of reference with a coverageData >= 37X There is a 0.03% of reference with a coverageData >= 38X There is a 0.03% of reference with a coverageData >= 39X There is a 0.03% of reference with a coverageData >= 40X There is a 0.03% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.02% of reference with a coverageData >= 44X There is a 0.02% of reference with a coverageData >= 45X There is a 0.02% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 176160665 0.7067611879691165 27.22616732197545 chr2 243199373 179001709 0.7360286615541562 5.032479339380307 chr3 198022430 116794421 0.5898039984662343 2.358485250152157 chr4 191154276 113597241 0.5942699445551508 4.985969756638414 chr5 180915260 122469044 0.6769414807794544 2.6464887926224447 chr6 171115067 132617633 0.7750201973739694 2.9809776750092665 chr7 159138663 96430769 0.6059543745192832 8.094345546555322 chr8 146364022 86550065 0.5913342897887843 2.410080861243546 chr9 141213431 94319162 0.6679192009717546 3.5014767408659875 chr10 135534747 106018331 0.782222517447869 15.39798676054667 chr11 135006516 82106551 0.6081673198647686 2.5280597990175795 chr12 133851895 98464111 0.7356198505818689 2.8760860998717264 chr13 115169878 59553246 0.5170904670056176 2.338266222674448 chr14 107349540 58871421 0.5484086936935174 2.3858954506733827 chr15 102531392 48324866 0.47131775993053915 2.1491161233666465 chr16 90354753 43085065 0.4768433709292526 3.892101644841536 chr17 81195210 38557926 0.4748793186199038 2.245930839997948 chr18 78077248 52599412 0.673684246657874 3.9122523469648907 chr19 59128983 27091521 0.4581766779245975 16.41256809090426 chr20 63025520 39224608 0.6223607199115533 4.434704307293697 chr21 48129895 25682222 0.5336022860635786 4.718125822884745 chr22 51304566 21839123 0.42567601098116686 2.1469444037429177 chrMT 16571 436704 26.353509142477822 82.33687310368865 chrX 155270560 104225241 0.6712492116985989 2.8376382980533457 chrY 59373566 3762544 0.06337069260754861 4.122767579188673