BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1264613.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 = 1,138,187,484 number of mapped reads = 1,125,040,896 (98.84%) number of supplementary alignments = 9,704,839 (0.85%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 563,749,337 number of mapped paired reads (second in pair) = 561,291,559 number of mapped paired reads (both in pair) = 1,119,052,774 number of mapped paired reads (singletons) = 5,988,122 number of mapped bases = 111,164,185,247 bp number of sequenced bases = 111,129,814,649 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 339,834,217 duplication rate = 25.01% >>>>>>> Insert size mean insert size = 135,142.4943 std insert size = 3,539,910.4585 median insert size = 303 >>>>>>> Mapping quality mean mapping quality = 53.5466 >>>>>>> ACTG content number of A's = 33,095,889,398 bp (29.78%) number of C's = 22,393,090,466 bp (20.15%) number of T's = 33,150,978,695 bp (29.83%) number of G's = 22,430,084,221 bp (20.18%) number of N's = 59,771,869 bp (0.05%) GC percentage = 40.33% >>>>>>> Mismatches and indels general error rate = 0.0061 number of mismatches = 648,854,760 number of insertions = 11,292,782 mapped reads with insertion percentage = 0.98% number of deletions = 14,652,528 mapped reads with deletion percentage = 1.26% homopolymer indels = 42.78% >>>>>>> Coverage mean coverageData = 35.9093X std coverageData = 511.7754X There is a 92.37% of reference with a coverageData >= 1X There is a 92.35% of reference with a coverageData >= 2X There is a 92.33% of reference with a coverageData >= 3X There is a 92.31% of reference with a coverageData >= 4X There is a 92.29% of reference with a coverageData >= 5X There is a 92.26% of reference with a coverageData >= 6X There is a 92.22% of reference with a coverageData >= 7X There is a 92.17% of reference with a coverageData >= 8X There is a 92.1% of reference with a coverageData >= 9X There is a 92% of reference with a coverageData >= 10X There is a 91.85% of reference with a coverageData >= 11X There is a 91.66% of reference with a coverageData >= 12X There is a 91.4% of reference with a coverageData >= 13X There is a 91.08% of reference with a coverageData >= 14X There is a 90.69% of reference with a coverageData >= 15X There is a 90.23% of reference with a coverageData >= 16X There is a 89.71% of reference with a coverageData >= 17X There is a 89.13% of reference with a coverageData >= 18X There is a 88.49% of reference with a coverageData >= 19X There is a 87.79% of reference with a coverageData >= 20X There is a 87.03% of reference with a coverageData >= 21X There is a 86.17% of reference with a coverageData >= 22X There is a 85.2% of reference with a coverageData >= 23X There is a 84.08% of reference with a coverageData >= 24X There is a 82.77% of reference with a coverageData >= 25X There is a 81.23% of reference with a coverageData >= 26X There is a 79.41% of reference with a coverageData >= 27X There is a 77.28% of reference with a coverageData >= 28X There is a 74.81% of reference with a coverageData >= 29X There is a 71.99% of reference with a coverageData >= 30X There is a 68.82% of reference with a coverageData >= 31X There is a 65.31% of reference with a coverageData >= 32X There is a 61.51% of reference with a coverageData >= 33X There is a 57.46% of reference with a coverageData >= 34X There is a 53.21% of reference with a coverageData >= 35X There is a 48.84% of reference with a coverageData >= 36X There is a 44.43% of reference with a coverageData >= 37X There is a 40.04% of reference with a coverageData >= 38X There is a 35.76% of reference with a coverageData >= 39X There is a 31.63% of reference with a coverageData >= 40X There is a 27.73% of reference with a coverageData >= 41X There is a 24.09% of reference with a coverageData >= 42X There is a 20.75% of reference with a coverageData >= 43X There is a 17.71% of reference with a coverageData >= 44X There is a 15.01% of reference with a coverageData >= 45X There is a 12.62% of reference with a coverageData >= 46X There is a 10.54% of reference with a coverageData >= 47X There is a 8.75% of reference with a coverageData >= 48X There is a 7.23% of reference with a coverageData >= 49X There is a 5.95% of reference with a coverageData >= 50X There is a 4.89% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 9026541162 36.214718847179924 976.2760328353329 chr2 243199373 9387207281 38.59881366141516 216.43244198709354 chr3 198022430 7312676270 36.92852506657958 31.549616459591647 chr4 191154276 7490041662 39.1832284306316 278.64041832482826 chr5 180915260 6712526008 37.10314988354216 31.595602239681167 chr6 171115067 6427438604 37.56208448902983 216.74774324427236 chr7 159138663 6010318554 37.76780853060202 342.85548242153 chr8 146364022 5610576354 38.33302936974498 629.7451643083483 chr9 141213431 4655816817 32.97007079305367 322.5775645517482 chr10 135534747 5815980211 42.91135918820876 794.1458773199303 chr11 135006516 4989155882 36.954926545915754 160.37807875890164 chr12 133851895 4861897579 36.32296411642136 22.99265508568578 chr13 115169878 3574243933 31.034537806838696 18.056672172851282 chr14 107349540 3295256183 30.6965095798268 26.552201762247 chr15 102531392 3074719267 29.988076890636577 19.141304587293234 chr16 90354753 3319393123 36.73733824495099 234.8897315733732 chr17 81195210 2949336421 36.32401986521126 137.25694812988453 chr18 78077248 3075138258 39.38584333812585 479.14240469642834 chr19 59128983 2149668451 36.355579648647094 414.48429901999816 chr20 63025520 2221895175 35.25389675483836 53.04540121691345 chr21 48129895 1537050145 31.93545601959032 106.55334208432201 chr22 51304566 1286011143 25.066212293853145 109.96816884470606 chrMT 16571 2273176894 137178.0154486754 16592.920530774594 chrX 155270560 2962555633 19.079957159940687 65.17874130572568 chrY 59373566 1145564237 19.294179450161373 292.9051155295752