BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1781848.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 = 189,366,380 number of mapped reads = 184,519,441 (97.44%) number of supplementary alignments = 601,123 (0.32%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 93,016,007 number of mapped paired reads (second in pair) = 91,503,434 number of mapped paired reads (both in pair) = 182,331,266 number of mapped paired reads (singletons) = 2,188,175 number of mapped bases = 18,321,792,985 bp number of sequenced bases = 18,318,088,464 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 13,662,892 duplication rate = 7.14% >>>>>>> Insert size mean insert size = 36,069.7955 std insert size = 1,838,394.0705 median insert size = 193 >>>>>>> Mapping quality mean mapping quality = 53.8975 >>>>>>> ACTG content number of A's = 5,449,449,271 bp (29.75%) number of C's = 3,696,490,711 bp (20.18%) number of T's = 5,434,448,615 bp (29.67%) number of G's = 3,735,617,523 bp (20.39%) number of N's = 2,082,344 bp (0.01%) GC percentage = 40.57% >>>>>>> Mismatches and indels general error rate = 0.0042 number of mismatches = 72,854,594 number of insertions = 1,990,116 mapped reads with insertion percentage = 1.06% number of deletions = 1,651,006 mapped reads with deletion percentage = 0.88% homopolymer indels = 46.86% >>>>>>> Coverage mean coverageData = 5.9185X std coverageData = 7.2693X There is a 84.45% of reference with a coverageData >= 1X There is a 75.5% of reference with a coverageData >= 2X There is a 65.72% of reference with a coverageData >= 3X There is a 56.24% of reference with a coverageData >= 4X There is a 47.57% of reference with a coverageData >= 5X There is a 39.96% of reference with a coverageData >= 6X There is a 33.44% of reference with a coverageData >= 7X There is a 27.94% of reference with a coverageData >= 8X There is a 23.36% of reference with a coverageData >= 9X There is a 19.55% of reference with a coverageData >= 10X There is a 16.4% of reference with a coverageData >= 11X There is a 13.8% of reference with a coverageData >= 12X There is a 11.65% of reference with a coverageData >= 13X There is a 9.86% of reference with a coverageData >= 14X There is a 8.38% of reference with a coverageData >= 15X There is a 7.14% of reference with a coverageData >= 16X There is a 6.11% of reference with a coverageData >= 17X There is a 5.24% of reference with a coverageData >= 18X There is a 4.51% of reference with a coverageData >= 19X There is a 3.9% of reference with a coverageData >= 20X There is a 3.38% of reference with a coverageData >= 21X There is a 2.93% of reference with a coverageData >= 22X There is a 2.55% of reference with a coverageData >= 23X There is a 2.23% of reference with a coverageData >= 24X There is a 1.95% of reference with a coverageData >= 25X There is a 1.71% of reference with a coverageData >= 26X There is a 1.51% of reference with a coverageData >= 27X There is a 1.33% of reference with a coverageData >= 28X There is a 1.18% of reference with a coverageData >= 29X There is a 1.04% of reference with a coverageData >= 30X There is a 0.93% of reference with a coverageData >= 31X There is a 0.82% of reference with a coverageData >= 32X There is a 0.74% of reference with a coverageData >= 33X There is a 0.66% of reference with a coverageData >= 34X There is a 0.59% of reference with a coverageData >= 35X There is a 0.53% of reference with a coverageData >= 36X There is a 0.48% of reference with a coverageData >= 37X There is a 0.43% of reference with a coverageData >= 38X There is a 0.39% of reference with a coverageData >= 39X There is a 0.35% of reference with a coverageData >= 40X There is a 0.32% of reference with a coverageData >= 41X There is a 0.29% of reference with a coverageData >= 42X There is a 0.27% of reference with a coverageData >= 43X There is a 0.24% of reference with a coverageData >= 44X There is a 0.22% of reference with a coverageData >= 45X There is a 0.2% of reference with a coverageData >= 46X There is a 0.19% of reference with a coverageData >= 47X There is a 0.17% of reference with a coverageData >= 48X There is a 0.16% of reference with a coverageData >= 49X There is a 0.15% of reference with a coverageData >= 50X There is a 0.13% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1475418315 5.919416806588417 8.802151369329676 chr2 243199373 1282260542 5.2724664795908005 8.224289245008617 chr3 198022430 1304413683 6.587201677102942 6.3832734571259095 chr4 191154276 1228606884 6.427305262059636 6.482494578119474 chr5 180915260 1156175137 6.390699916635004 6.0422742785616235 chr6 171115067 1118767859 6.538102568139134 6.57569248826405 chr7 159138663 976326824 6.135069916981771 6.901441204275531 chr8 146364022 933600994 6.378623525390687 6.2584645604245 chr9 141213431 755098410 5.3472138213255365 7.188132776778261 chr10 135534747 1012645071 7.471479405941563 9.865357322615715 chr11 135006516 862100946 6.38562472051349 6.6124597339163085 chr12 133851895 1249385107 9.334086058325884 8.969307852302304 chr13 115169878 591405543 5.135071368227029 5.726273529818547 chr14 107349540 556921014 5.18792175541693 6.146262862570679 chr15 102531392 513786296 5.011014538844845 6.132378296755514 chr16 90354753 422967003 4.681181553337875 5.954788433053121 chr17 81195210 385675106 4.749973625291442 5.74882291487346 chr18 78077248 241768647 3.0965313608389478 4.824551503379782 chr19 59128983 244046677 4.127361314501215 6.395621028643314 chr20 63025520 348900900 5.535867058296385 7.1817076888418985 chr21 48129895 214012236 4.446555223110294 8.07316924156007 chr22 51304566 157564135 3.071152283015122 4.881664891102281 chrMT 16571 685934 41.393639490676485 13.23288690779378 chrX 155270560 1272635366 8.196243808227393 8.20958171353293 chrY 59373566 16624356 0.2799959160276814 2.8845611427014766