BamQC report ----------------------------------- >>>>>>> Input bam file = SRR2976563.sorted.bam outfile = /home/yangyx/scDNA/SRP067062/SRP067062.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 = 378,668,658 number of mapped reads = 375,539,683 (99.17%) number of supplementary alignments = 12,801,002 (3.38%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 188,846,400 number of mapped paired reads (second in pair) = 186,693,283 number of mapped paired reads (both in pair) = 373,035,086 number of mapped paired reads (singletons) = 2,504,597 number of mapped bases = 85,869,827,699 bp number of sequenced bases = 85,841,190,941 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 61,515,664 duplication rate = 14.3% >>>>>>> Insert size mean insert size = 77,925.7079 std insert size = 2,712,283.0082 median insert size = 538 >>>>>>> Mapping quality mean mapping quality = 55.4751 >>>>>>> ACTG content number of A's = 25,067,467,018 bp (29.2%) number of C's = 17,865,028,744 bp (20.81%) number of T's = 24,841,394,026 bp (28.94%) number of G's = 18,065,538,413 bp (21.05%) number of N's = 1,762,740 bp (0%) GC percentage = 41.86% >>>>>>> Mismatches and indels general error rate = 0.0081 number of mismatches = 677,116,270 number of insertions = 8,156,613 mapped reads with insertion percentage = 2.06% number of deletions = 10,405,823 mapped reads with deletion percentage = 2.64% homopolymer indels = 46.54% >>>>>>> Coverage mean coverageData = 27.7385X std coverageData = 47.6202X There is a 90.46% of reference with a coverageData >= 1X There is a 88.66% of reference with a coverageData >= 2X There is a 86.75% of reference with a coverageData >= 3X There is a 84.74% of reference with a coverageData >= 4X There is a 82.66% of reference with a coverageData >= 5X There is a 80.51% of reference with a coverageData >= 6X There is a 78.32% of reference with a coverageData >= 7X There is a 76.1% of reference with a coverageData >= 8X There is a 73.86% of reference with a coverageData >= 9X There is a 71.61% of reference with a coverageData >= 10X There is a 69.37% of reference with a coverageData >= 11X There is a 67.14% of reference with a coverageData >= 12X There is a 64.94% of reference with a coverageData >= 13X There is a 62.76% of reference with a coverageData >= 14X There is a 60.62% of reference with a coverageData >= 15X There is a 58.51% of reference with a coverageData >= 16X There is a 56.45% of reference with a coverageData >= 17X There is a 54.44% of reference with a coverageData >= 18X There is a 52.48% of reference with a coverageData >= 19X There is a 50.57% of reference with a coverageData >= 20X There is a 48.71% of reference with a coverageData >= 21X There is a 46.9% of reference with a coverageData >= 22X There is a 45.15% of reference with a coverageData >= 23X There is a 43.45% of reference with a coverageData >= 24X There is a 41.81% of reference with a coverageData >= 25X There is a 40.22% of reference with a coverageData >= 26X There is a 38.68% of reference with a coverageData >= 27X There is a 37.2% of reference with a coverageData >= 28X There is a 35.77% of reference with a coverageData >= 29X There is a 34.38% of reference with a coverageData >= 30X There is a 33.05% of reference with a coverageData >= 31X There is a 31.77% of reference with a coverageData >= 32X There is a 30.54% of reference with a coverageData >= 33X There is a 29.35% of reference with a coverageData >= 34X There is a 28.21% of reference with a coverageData >= 35X There is a 27.12% of reference with a coverageData >= 36X There is a 26.07% of reference with a coverageData >= 37X There is a 25.06% of reference with a coverageData >= 38X There is a 24.09% of reference with a coverageData >= 39X There is a 23.16% of reference with a coverageData >= 40X There is a 22.27% of reference with a coverageData >= 41X There is a 21.41% of reference with a coverageData >= 42X There is a 20.59% of reference with a coverageData >= 43X There is a 19.8% of reference with a coverageData >= 44X There is a 19.04% of reference with a coverageData >= 45X There is a 18.31% of reference with a coverageData >= 46X There is a 17.62% of reference with a coverageData >= 47X There is a 16.95% of reference with a coverageData >= 48X There is a 16.31% of reference with a coverageData >= 49X There is a 15.69% of reference with a coverageData >= 50X There is a 15.1% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 7875813248 31.597968407870084 77.46669630934917 chr2 243199373 7147815522 29.390764597078135 35.679900255300346 chr3 198022430 5888793988 29.73801497133431 28.88446054154802 chr4 191154276 4892727561 25.59570030753589 25.142586630776343 chr5 180915260 5119443075 28.297464100043303 28.26553354002641 chr6 171115067 4947415261 28.91279738095769 37.71314781779478 chr7 159138663 4437770741 27.886188417958493 30.08190802967213 chr8 146364022 4352352704 29.73649292037083 32.49094641573171 chr9 141213431 3715667689 26.31242412770213 87.05274127319804 chr10 135534747 4209657033 31.059614793835856 71.8758491719091 chr11 135006516 4311974255 31.939008447562635 42.96450374240796 chr12 133851895 4072800427 30.42766355306363 30.958741409270846 chr13 115169878 2422451339 21.033723236209383 23.105727332590092 chr14 107349540 2747493612 25.59390205118718 29.80985271943066 chr15 102531392 2605402463 25.41077822292708 30.374005458914823 chr16 90354753 2832924452 31.35335284464781 35.24587201629661 chr17 81195210 2891594099 35.61286557421306 88.02283037492609 chr18 78077248 2253519617 28.862692714271898 76.40562802921384 chr19 59128983 2041895493 34.53290399058614 65.56107912346982 chr20 63025520 2144517961 34.02618432977626 35.53588326083102 chr21 48129895 1085756696 22.55888353797572 32.11952989556001 chr22 51304566 1217108010 23.72319083646473 33.19004221878824 chrMT 16571 310046 18.710156297145616 9.9550569516937 chrX 155270560 2189834069 14.103343666693801 21.00057943743501 chrY 59373566 464788338 7.828203177151259 29.89469553396512