BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779092.sorted.bam outfile = /home/yangyx/scDNA/SRP052627/SRP052627.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 = 50,873,340 number of mapped reads = 49,083,838 (96.48%) number of supplementary alignments = 236,842 (0.47%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 24,864,429 number of mapped paired reads (second in pair) = 24,219,409 number of mapped paired reads (both in pair) = 48,277,766 number of mapped paired reads (singletons) = 806,072 number of mapped bases = 4,906,302,659 bp number of sequenced bases = 4,905,149,889 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,441,341 duplication rate = 4.39% >>>>>>> Insert size mean insert size = 61,122.3653 std insert size = 2,406,685.9891 median insert size = 290 >>>>>>> Mapping quality mean mapping quality = 53.4249 >>>>>>> ACTG content number of A's = 1,506,579,803 bp (30.71%) number of C's = 940,077,854 bp (19.17%) number of T's = 1,500,038,676 bp (30.58%) number of G's = 956,833,085 bp (19.51%) number of N's = 1,620,471 bp (0.03%) GC percentage = 38.67% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 24,030,906 number of insertions = 420,031 mapped reads with insertion percentage = 0.84% number of deletions = 513,956 mapped reads with deletion percentage = 1.03% homopolymer indels = 47.41% >>>>>>> Coverage mean coverageData = 1.5849X std coverageData = 3.9757X There is a 43.01% of reference with a coverageData >= 1X There is a 27.77% of reference with a coverageData >= 2X There is a 19.25% of reference with a coverageData >= 3X There is a 13.91% of reference with a coverageData >= 4X There is a 10.35% of reference with a coverageData >= 5X There is a 7.87% of reference with a coverageData >= 6X There is a 6.09% of reference with a coverageData >= 7X There is a 4.79% of reference with a coverageData >= 8X There is a 3.82% of reference with a coverageData >= 9X There is a 3.08% of reference with a coverageData >= 10X There is a 2.51% of reference with a coverageData >= 11X There is a 2.06% of reference with a coverageData >= 12X There is a 1.71% of reference with a coverageData >= 13X There is a 1.43% of reference with a coverageData >= 14X There is a 1.2% of reference with a coverageData >= 15X There is a 1.02% of reference with a coverageData >= 16X There is a 0.87% of reference with a coverageData >= 17X There is a 0.74% of reference with a coverageData >= 18X There is a 0.64% of reference with a coverageData >= 19X There is a 0.56% of reference with a coverageData >= 20X There is a 0.48% of reference with a coverageData >= 21X There is a 0.42% of reference with a coverageData >= 22X There is a 0.37% of reference with a coverageData >= 23X There is a 0.33% of reference with a coverageData >= 24X There is a 0.29% of reference with a coverageData >= 25X There is a 0.26% of reference with a coverageData >= 26X There is a 0.23% of reference with a coverageData >= 27X There is a 0.21% of reference with a coverageData >= 28X There is a 0.18% of reference with a coverageData >= 29X There is a 0.17% of reference with a coverageData >= 30X There is a 0.15% of reference with a coverageData >= 31X There is a 0.14% of reference with a coverageData >= 32X There is a 0.12% of reference with a coverageData >= 33X There is a 0.11% of reference with a coverageData >= 34X There is a 0.1% of reference with a coverageData >= 35X There is a 0.09% of reference with a coverageData >= 36X There is a 0.09% of reference with a coverageData >= 37X There is a 0.08% of reference with a coverageData >= 38X There is a 0.07% of reference with a coverageData >= 39X There is a 0.07% of reference with a coverageData >= 40X There is a 0.06% of reference with a coverageData >= 41X There is a 0.06% of reference with a coverageData >= 42X There is a 0.06% of reference with a coverageData >= 43X There is a 0.05% of reference with a coverageData >= 44X There is a 0.05% of reference with a coverageData >= 45X There is a 0.05% of reference with a coverageData >= 46X There is a 0.04% of reference with a coverageData >= 47X There is a 0.04% of reference with a coverageData >= 48X There is a 0.04% of reference with a coverageData >= 49X There is a 0.04% of reference with a coverageData >= 50X There is a 0.03% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 369901773 1.4840555723229272 4.03213549431826 chr2 243199373 556637271 2.2888104690960698 4.338514069146623 chr3 198022430 203747070 1.028909048333565 2.4754125365715742 chr4 191154276 191058739 0.9995002099769926 2.3607326983926114 chr5 180915260 277303257 1.5327798053077446 3.092645805935851 chr6 171115067 287873029 1.6823359511643705 3.4119269429726815 chr7 159138663 412986039 2.595133270662202 8.79001177555821 chr8 146364022 349820209 2.390069664797815 4.100663340063643 chr9 141213431 216379867 1.5322895667055918 3.4139810512152495 chr10 135534747 121613864 0.8972891947774839 4.069237542295702 chr11 135006516 289788055 2.1464745820120266 3.974455182082026 chr12 133851895 175095710 1.3081302285634433 3.0619883529508405 chr13 115169878 236898366 2.056947268798878 3.7848581130590317 chr14 107349540 160893228 1.4987789235054012 3.5104966629760272 chr15 102531392 139049434 1.3561645003317617 3.351114447734327 chr16 90354753 83387351 0.9228883731218877 2.2106565182695794 chr17 81195210 81253853 1.0007222470389572 2.5830588876230216 chr18 78077248 184978494 2.369172822279802 3.7719513127353523 chr19 59128983 45843870 0.7753197784578841 2.336281820548622 chr20 63025520 86411240 1.3710515994156018 3.0868086071827427 chr21 48129895 51785065 1.0759438598401263 2.464250925750916 chr22 51304566 21413072 0.417371662397456 1.433068991268051 chrMT 16571 303 0.018284955645404624 0.1583397924027701 chrX 155270560 359621870 2.3160982352353208 4.798163893874195 chrY 59373566 2561630 0.04314428410784692 0.7020667564850978