BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779006.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 = 16,585,450 number of mapped reads = 15,906,117 (95.9%) number of supplementary alignments = 84,175 (0.51%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 8,062,860 number of mapped paired reads (second in pair) = 7,843,257 number of mapped paired reads (both in pair) = 15,627,472 number of mapped paired reads (singletons) = 278,645 number of mapped bases = 1,589,541,609 bp number of sequenced bases = 1,589,158,164 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 281,599 duplication rate = 1.49% >>>>>>> Insert size mean insert size = 75,199.0162 std insert size = 2,632,642.8303 median insert size = 270 >>>>>>> Mapping quality mean mapping quality = 53.6099 >>>>>>> ACTG content number of A's = 486,575,638 bp (30.62%) number of C's = 305,941,094 bp (19.25%) number of T's = 485,547,485 bp (30.55%) number of G's = 310,564,639 bp (19.54%) number of N's = 529,308 bp (0.03%) GC percentage = 38.79% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 7,899,288 number of insertions = 140,019 mapped reads with insertion percentage = 0.87% number of deletions = 171,419 mapped reads with deletion percentage = 1.06% homopolymer indels = 47.13% >>>>>>> Coverage mean coverageData = 0.5135X std coverageData = 1.3307X There is a 29.64% of reference with a coverageData >= 1X There is a 11.55% of reference with a coverageData >= 2X There is a 4.82% of reference with a coverageData >= 3X There is a 2.18% of reference with a coverageData >= 4X There is a 1.06% of reference with a coverageData >= 5X There is a 0.56% of reference with a coverageData >= 6X There is a 0.31% of reference with a coverageData >= 7X There is a 0.19% of reference with a coverageData >= 8X There is a 0.12% of reference with a coverageData >= 9X There is a 0.08% of reference with a coverageData >= 10X There is a 0.06% of reference with a coverageData >= 11X There is a 0.05% of reference with a coverageData >= 12X There is a 0.04% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% 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% 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 130276396 0.5226723025897697 1.324034926931645 chr2 243199373 150232005 0.6177318763070989 1.2803485220134962 chr3 198022430 102535176 0.51779576687348 0.9803106679110494 chr4 191154276 116687753 0.6104375766095863 1.087729947589643 chr5 180915260 108481944 0.5996284890506196 1.0801710159478726 chr6 171115067 94705598 0.5534614786434908 1.051194944923454 chr7 159138663 149580636 0.9399390014983349 3.4697950038499656 chr8 146364022 99082705 0.6769607971008067 1.18004288371432 chr9 141213431 65134059 0.46124549583389135 1.035778911612886 chr10 135534747 38502226 0.2840764221148397 1.47297821877139 chr11 135006516 66549756 0.4929373631121627 0.9965570995110588 chr12 133851895 63173587 0.4719663251685753 1.0153278007590327 chr13 115169878 54813328 0.4759345842148066 0.9655414366109946 chr14 107349540 52574145 0.4897472779110185 1.0455534694810162 chr15 102531392 37693830 0.36763209066741237 0.9330826567338751 chr16 90354753 24021468 0.2658572703972751 0.7220996441696835 chr17 81195210 26628959 0.3279621913657222 0.8836771106251196 chr18 78077248 44172058 0.565748142147633 1.0641533440897568 chr19 59128983 14917135 0.25228127126759475 0.8394322986018415 chr20 63025520 27523283 0.4367006095308694 0.9923978916597492 chr21 48129895 18095086 0.37596354614943583 0.9198243675577735 chr22 51304566 6253928 0.12189807823342663 0.4960233237194645 chrMT 16571 798 0.04815641783839237 0.22266309378076912 chrX 155270560 96940052 0.6243298922860844 1.2161126748504307 chrY 59373566 965698 0.016264780188543836 0.28133358402040654