BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1264627.sorted.bam outfile = /home/yangyx/scDNA/SRP041470/SRP041470.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 = 1,440,914,148 number of mapped reads = 1,433,354,639 (99.48%) number of supplementary alignments = 7,975,327 (0.55%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 718,714,019 number of mapped paired reads (second in pair) = 714,640,620 number of mapped paired reads (both in pair) = 1,427,920,234 number of mapped paired reads (singletons) = 5,434,405 number of mapped bases = 143,931,001,380 bp number of sequenced bases = 143,897,676,638 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 537,461,986 duplication rate = 37.25% >>>>>>> Insert size mean insert size = 64,967.5019 std insert size = 2,449,130.862 median insert size = 307 >>>>>>> Mapping quality mean mapping quality = 54.5115 >>>>>>> ACTG content number of A's = 44,491,082,206 bp (30.92%) number of C's = 27,408,871,596 bp (19.05%) number of T's = 44,293,049,284 bp (30.78%) number of G's = 27,689,656,783 bp (19.24%) number of N's = 15,016,769 bp (0.01%) GC percentage = 38.29% >>>>>>> Mismatches and indels general error rate = 0.0039 number of mismatches = 537,571,743 number of insertions = 15,888,566 mapped reads with insertion percentage = 1.09% number of deletions = 14,911,058 mapped reads with deletion percentage = 1.02% homopolymer indels = 48.58% >>>>>>> Coverage mean coverageData = 46.4939X std coverageData = 46.435X There is a 90.8% of reference with a coverageData >= 1X There is a 89.55% of reference with a coverageData >= 2X There is a 88.3% of reference with a coverageData >= 3X There is a 87.05% of reference with a coverageData >= 4X There is a 85.8% of reference with a coverageData >= 5X There is a 84.54% of reference with a coverageData >= 6X There is a 83.27% of reference with a coverageData >= 7X There is a 82.01% of reference with a coverageData >= 8X There is a 80.74% of reference with a coverageData >= 9X There is a 79.48% of reference with a coverageData >= 10X There is a 78.23% of reference with a coverageData >= 11X There is a 76.97% of reference with a coverageData >= 12X There is a 75.72% of reference with a coverageData >= 13X There is a 74.48% of reference with a coverageData >= 14X There is a 73.24% of reference with a coverageData >= 15X There is a 72.01% of reference with a coverageData >= 16X There is a 70.79% of reference with a coverageData >= 17X There is a 69.57% of reference with a coverageData >= 18X There is a 68.36% of reference with a coverageData >= 19X There is a 67.16% of reference with a coverageData >= 20X There is a 65.96% of reference with a coverageData >= 21X There is a 64.78% of reference with a coverageData >= 22X There is a 63.6% of reference with a coverageData >= 23X There is a 62.44% of reference with a coverageData >= 24X There is a 61.28% of reference with a coverageData >= 25X There is a 60.14% of reference with a coverageData >= 26X There is a 59% of reference with a coverageData >= 27X There is a 57.88% of reference with a coverageData >= 28X There is a 56.78% of reference with a coverageData >= 29X There is a 55.68% of reference with a coverageData >= 30X There is a 54.6% of reference with a coverageData >= 31X There is a 53.53% of reference with a coverageData >= 32X There is a 52.47% of reference with a coverageData >= 33X There is a 51.43% of reference with a coverageData >= 34X There is a 50.4% of reference with a coverageData >= 35X There is a 49.38% of reference with a coverageData >= 36X There is a 48.38% of reference with a coverageData >= 37X There is a 47.39% of reference with a coverageData >= 38X There is a 46.42% of reference with a coverageData >= 39X There is a 45.46% of reference with a coverageData >= 40X There is a 44.51% of reference with a coverageData >= 41X There is a 43.58% of reference with a coverageData >= 42X There is a 42.66% of reference with a coverageData >= 43X There is a 41.76% of reference with a coverageData >= 44X There is a 40.87% of reference with a coverageData >= 45X There is a 40% of reference with a coverageData >= 46X There is a 39.14% of reference with a coverageData >= 47X There is a 38.3% of reference with a coverageData >= 48X There is a 37.47% of reference with a coverageData >= 49X There is a 36.65% of reference with a coverageData >= 50X There is a 35.85% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 11065745851 44.39606130810804 46.845304035924336 chr2 243199373 13006821145 53.482132723261586 47.17069452315201 chr3 198022430 10822179040 54.651278847552774 45.94879582430973 chr4 191154276 12115124974 63.378780885864145 48.44540990922883 chr5 180915260 10440011985 57.70664113685048 46.45466577939018 chr6 171115067 9905684130 57.88902347214112 48.843398652327586 chr7 159138663 8155734641 51.24923439252471 47.510252412231104 chr8 146364022 7804529678 53.32273308258774 45.14536728951829 chr9 141213431 6209288676 43.97094973211153 49.02675181889586 chr10 135534747 6098776396 44.99788084600918 42.384563096074814 chr11 135006516 6772243349 50.16234437899279 47.154715001069206 chr12 133851895 6961534955 52.009237187116405 51.036252852605124 chr13 115169878 5721547869 49.679204045002116 47.47542333298569 chr14 107349540 4439139277 41.35219654411188 44.84171086658866 chr15 102531392 3751942994 36.593114760404305 43.435866393633894 chr16 90354753 2641542192 29.2352322849026 37.17019604718256 chr17 81195210 2389198678 29.425364846029712 37.216220093595034 chr18 78077248 4357323225 55.807848465663135 48.580831305775035 chr19 59128983 1109173716 18.758545466611526 26.791311672537155 chr20 63025520 2183135224 34.63890855640699 43.795555780724655 chr21 48129895 1632403262 33.91661797724678 47.105148405614045 chr22 51304566 757810978 14.770829130491036 25.908084180084867 chrMT 16571 38366 2.315249532315491 7.8004646008378895 chrX 155270560 4914442875 31.650835000530687 32.707907505185254 chrY 59373566 675627904 11.3792711052592 24.533901745046844