BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1781807.sorted.bam outfile = /home/yangyx/scDNA/SRP052954/SRP052954.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 = 145,286,944 number of mapped reads = 142,058,080 (97.78%) number of supplementary alignments = 500,554 (0.34%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 71,767,216 number of mapped paired reads (second in pair) = 70,290,864 number of mapped paired reads (both in pair) = 140,099,332 number of mapped paired reads (singletons) = 1,958,748 number of mapped bases = 14,105,840,133 bp number of sequenced bases = 14,102,900,938 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 8,301,481 duplication rate = 5.59% >>>>>>> Insert size mean insert size = 35,483.5162 std insert size = 1,828,768.5682 median insert size = 197 >>>>>>> Mapping quality mean mapping quality = 53.9726 >>>>>>> ACTG content number of A's = 4,158,365,980 bp (29.49%) number of C's = 2,878,698,071 bp (20.41%) number of T's = 4,145,656,020 bp (29.4%) number of G's = 2,918,845,963 bp (20.7%) number of N's = 1,334,904 bp (0.01%) GC percentage = 41.11% >>>>>>> Mismatches and indels general error rate = 0.0048 number of mismatches = 65,762,177 number of insertions = 1,311,907 mapped reads with insertion percentage = 0.91% number of deletions = 1,304,346 mapped reads with deletion percentage = 0.9% homopolymer indels = 46.25% >>>>>>> Coverage mean coverageData = 4.5566X std coverageData = 5.9076X There is a 81.38% of reference with a coverageData >= 1X There is a 69.81% of reference with a coverageData >= 2X There is a 58.1% of reference with a coverageData >= 3X There is a 47.45% of reference with a coverageData >= 4X There is a 38.29% of reference with a coverageData >= 5X There is a 30.67% of reference with a coverageData >= 6X There is a 24.49% of reference with a coverageData >= 7X There is a 19.53% of reference with a coverageData >= 8X There is a 15.59% of reference with a coverageData >= 9X There is a 12.47% of reference with a coverageData >= 10X There is a 10% of reference with a coverageData >= 11X There is a 8.05% of reference with a coverageData >= 12X There is a 6.5% of reference with a coverageData >= 13X There is a 5.27% of reference with a coverageData >= 14X There is a 4.3% of reference with a coverageData >= 15X There is a 3.52% of reference with a coverageData >= 16X There is a 2.89% of reference with a coverageData >= 17X There is a 2.39% of reference with a coverageData >= 18X There is a 1.98% of reference with a coverageData >= 19X There is a 1.65% of reference with a coverageData >= 20X There is a 1.38% of reference with a coverageData >= 21X There is a 1.16% of reference with a coverageData >= 22X There is a 0.98% of reference with a coverageData >= 23X There is a 0.83% of reference with a coverageData >= 24X There is a 0.71% of reference with a coverageData >= 25X There is a 0.6% of reference with a coverageData >= 26X There is a 0.52% of reference with a coverageData >= 27X There is a 0.45% of reference with a coverageData >= 28X There is a 0.39% of reference with a coverageData >= 29X There is a 0.34% of reference with a coverageData >= 30X There is a 0.3% of reference with a coverageData >= 31X There is a 0.26% of reference with a coverageData >= 32X There is a 0.23% of reference with a coverageData >= 33X There is a 0.2% of reference with a coverageData >= 34X There is a 0.18% of reference with a coverageData >= 35X There is a 0.16% of reference with a coverageData >= 36X There is a 0.14% of reference with a coverageData >= 37X There is a 0.13% of reference with a coverageData >= 38X There is a 0.11% of reference with a coverageData >= 39X There is a 0.1% of reference with a coverageData >= 40X There is a 0.09% of reference with a coverageData >= 41X There is a 0.08% of reference with a coverageData >= 42X There is a 0.08% of reference with a coverageData >= 43X There is a 0.07% of reference with a coverageData >= 44X There is a 0.06% of reference with a coverageData >= 45X There is a 0.06% of reference with a coverageData >= 46X There is a 0.05% of reference with a coverageData >= 47X There is a 0.05% of reference with a coverageData >= 48X There is a 0.05% of reference with a coverageData >= 49X There is a 0.04% of reference with a coverageData >= 50X There is a 0.04% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1131168057 4.538275782269766 8.739354547265268 chr2 243199373 1157828596 4.760820645701253 5.542145895562854 chr3 198022430 955728153 4.826363119571859 4.762778216894968 chr4 191154276 880984648 4.608762442750692 5.412812214559487 chr5 180915260 846402757 4.678448667072087 4.578311251081049 chr6 171115067 824496024 4.818371862017271 5.353988712550165 chr7 159138663 719362789 4.520352096963388 5.387314266526814 chr8 146364022 691953763 4.72762194933397 4.844426454889245 chr9 141213431 577520566 4.08969998045016 5.809800125914209 chr10 135534747 784332092 5.786944745615676 8.940818926273746 chr11 135006516 634574198 4.7003227459036125 4.978176720172847 chr12 133851895 937534107 7.004264728564358 6.5753213238437755 chr13 115169878 430733764 3.739986283566264 4.307226841272389 chr14 107349540 420607831 3.9181148889878803 4.622885721950941 chr15 102531392 391211978 3.815533666021037 4.612644167076647 chr16 90354753 349929948 3.872844940431634 4.820423777265254 chr17 81195210 321749489 3.9626658887882673 5.139365604249974 chr18 78077248 349276098 4.473468352778008 6.026140165342955 chr19 59128983 209706782 3.546598831236451 6.0296923298933445 chr20 63025520 277658221 4.405488776609856 5.4124613144531075 chr21 48129895 166050693 3.450053090703813 7.636595834411622 chr22 51304566 136973505 2.6698112015994835 4.273973731183911 chrMT 16571 467226 28.195401605213927 8.130007025546568 chrX 155270560 896788811 5.775652583464631 5.768704936546452 chrY 59373566 12800037 0.21558477723908312 2.465653281323412