BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1781858.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 = 163,177,316 number of mapped reads = 158,468,042 (97.11%) number of supplementary alignments = 486,956 (0.3%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 79,747,060 number of mapped paired reads (second in pair) = 78,720,982 number of mapped paired reads (both in pair) = 156,670,264 number of mapped paired reads (singletons) = 1,797,778 number of mapped bases = 15,735,971,741 bp number of sequenced bases = 15,732,745,779 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 10,621,494 duplication rate = 6.47% >>>>>>> Insert size mean insert size = 33,060.7308 std insert size = 1,778,518.3984 median insert size = 193 >>>>>>> Mapping quality mean mapping quality = 53.8655 >>>>>>> ACTG content number of A's = 4,686,923,859 bp (29.79%) number of C's = 3,167,989,761 bp (20.14%) number of T's = 4,667,951,802 bp (29.67%) number of G's = 3,208,297,429 bp (20.39%) number of N's = 1,582,928 bp (0.01%) GC percentage = 40.53% >>>>>>> Mismatches and indels general error rate = 0.0043 number of mismatches = 64,659,712 number of insertions = 1,750,556 mapped reads with insertion percentage = 1.09% number of deletions = 1,440,784 mapped reads with deletion percentage = 0.89% homopolymer indels = 47.08% >>>>>>> Coverage mean coverageData = 5.0832X std coverageData = 6.4505X There is a 82.46% of reference with a coverageData >= 1X There is a 71.78% of reference with a coverageData >= 2X There is a 60.71% of reference with a coverageData >= 3X There is a 50.48% of reference with a coverageData >= 4X There is a 41.54% of reference with a coverageData >= 5X There is a 33.99% of reference with a coverageData >= 6X There is a 27.75% of reference with a coverageData >= 7X There is a 22.66% of reference with a coverageData >= 8X There is a 18.54% of reference with a coverageData >= 9X There is a 15.21% of reference with a coverageData >= 10X There is a 12.53% of reference with a coverageData >= 11X There is a 10.36% of reference with a coverageData >= 12X There is a 8.61% of reference with a coverageData >= 13X There is a 7.18% of reference with a coverageData >= 14X There is a 6.01% of reference with a coverageData >= 15X There is a 5.05% of reference with a coverageData >= 16X There is a 4.27% of reference with a coverageData >= 17X There is a 3.62% of reference with a coverageData >= 18X There is a 3.08% of reference with a coverageData >= 19X There is a 2.63% of reference with a coverageData >= 20X There is a 2.26% of reference with a coverageData >= 21X There is a 1.94% of reference with a coverageData >= 22X There is a 1.68% of reference with a coverageData >= 23X There is a 1.45% of reference with a coverageData >= 24X There is a 1.26% of reference with a coverageData >= 25X There is a 1.1% of reference with a coverageData >= 26X There is a 0.96% of reference with a coverageData >= 27X There is a 0.84% of reference with a coverageData >= 28X There is a 0.74% of reference with a coverageData >= 29X There is a 0.65% of reference with a coverageData >= 30X There is a 0.58% of reference with a coverageData >= 31X There is a 0.51% of reference with a coverageData >= 32X There is a 0.45% of reference with a coverageData >= 33X There is a 0.4% of reference with a coverageData >= 34X There is a 0.36% of reference with a coverageData >= 35X There is a 0.32% of reference with a coverageData >= 36X There is a 0.29% of reference with a coverageData >= 37X There is a 0.26% of reference with a coverageData >= 38X There is a 0.24% of reference with a coverageData >= 39X There is a 0.21% of reference with a coverageData >= 40X There is a 0.19% of reference with a coverageData >= 41X There is a 0.17% of reference with a coverageData >= 42X There is a 0.16% of reference with a coverageData >= 43X There is a 0.14% of reference with a coverageData >= 44X There is a 0.13% of reference with a coverageData >= 45X There is a 0.12% of reference with a coverageData >= 46X There is a 0.11% of reference with a coverageData >= 47X There is a 0.1% of reference with a coverageData >= 48X There is a 0.09% of reference with a coverageData >= 49X There is a 0.09% of reference with a coverageData >= 50X There is a 0.08% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1270751718 5.098289075075163 7.342372925143345 chr2 243199373 1353782194 5.566552977914133 9.109139684012561 chr3 198022430 1118430042 5.64799675471107 5.616969419270116 chr4 191154276 1063058418 5.561258896452832 5.683025498837834 chr5 180915260 1012107749 5.594374675745982 5.355930046967478 chr6 171115067 965062025 5.639842486810352 5.790934006662576 chr7 159138663 847419943 5.325041237778905 6.03117236636718 chr8 146364022 808745478 5.525575663669587 5.5149871222590985 chr9 141213431 335374523 2.374947769663638 4.395149716917129 chr10 135534747 874892249 6.455114045404165 8.145574404775727 chr11 135006516 738346453 5.468969016280666 5.76341581195937 chr12 133851895 1073713196 8.02165106440966 7.956546432296876 chr13 115169878 505569559 4.389772462900412 5.023643497939979 chr14 107349540 469273172 4.371450236302829 5.306269162992434 chr15 102531392 436741419 4.259587336920189 5.329902959287219 chr16 90354753 366918256 4.060862808180108 5.2488609201891 chr17 81195210 334399549 4.11846399559777 5.205028276737646 chr18 78077248 208851767 2.6749376079443783 4.215488751442639 chr19 59128983 216973235 3.6694903918777024 5.399510832386888 chr20 63025520 296805103 4.709284477145131 6.0799646355804 chr21 48129895 190608094 3.960284849987726 6.983178957600646 chr22 51304566 135887469 2.648642793313952 4.243894508392697 chrMT 16571 528330 31.88280731398226 10.906028892283228 chrX 155270560 1097442176 7.067934681242858 7.288028517648143 chrY 59373566 14289624 0.24067316421587345 2.439381774088682