BamQC report ----------------------------------- >>>>>>> Input bam file = SRR8438276.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP178894/SRP178894.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 = 697,391,010 number of mapped reads = 695,071,512 (99.67%) number of supplementary alignments = 12,284,435 (1.76%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 347,777,449 number of mapped paired reads (second in pair) = 347,294,063 number of mapped paired reads (both in pair) = 693,425,402 number of mapped paired reads (singletons) = 1,646,110 number of mapped bases = 100,095,259,945 bp number of sequenced bases = 100,068,038,774 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 255,278,229 duplication rate = 33.89% >>>>>>> Insert size mean insert size = 39,845.4198 std insert size = 1,953,270.2214 median insert size = 266 >>>>>>> Mapping quality mean mapping quality = 55.1049 >>>>>>> ACTG content number of A's = 30,260,849,929 bp (30.24%) number of C's = 20,015,915,033 bp (20%) number of T's = 28,823,027,344 bp (28.8%) number of G's = 20,967,493,191 bp (20.95%) number of N's = 753,277 bp (0%) GC percentage = 40.96% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 511,906,824 number of insertions = 12,111,454 mapped reads with insertion percentage = 1.71% number of deletions = 10,826,043 mapped reads with deletion percentage = 1.53% homopolymer indels = 48.33% >>>>>>> Coverage mean coverageData = 32.3337X std coverageData = 69.3751X There is a 91.5% of reference with a coverageData >= 1X There is a 90.85% of reference with a coverageData >= 2X There is a 90.13% of reference with a coverageData >= 3X There is a 89.33% of reference with a coverageData >= 4X There is a 88.44% of reference with a coverageData >= 5X There is a 87.45% of reference with a coverageData >= 6X There is a 86.36% of reference with a coverageData >= 7X There is a 85.17% of reference with a coverageData >= 8X There is a 83.87% of reference with a coverageData >= 9X There is a 82.47% of reference with a coverageData >= 10X There is a 80.99% of reference with a coverageData >= 11X There is a 79.42% of reference with a coverageData >= 12X There is a 77.77% of reference with a coverageData >= 13X There is a 76.06% of reference with a coverageData >= 14X There is a 74.29% of reference with a coverageData >= 15X There is a 72.46% of reference with a coverageData >= 16X There is a 70.6% of reference with a coverageData >= 17X There is a 68.7% of reference with a coverageData >= 18X There is a 66.77% of reference with a coverageData >= 19X There is a 64.83% of reference with a coverageData >= 20X There is a 62.89% of reference with a coverageData >= 21X There is a 60.94% of reference with a coverageData >= 22X There is a 58.99% of reference with a coverageData >= 23X There is a 57.06% of reference with a coverageData >= 24X There is a 55.14% of reference with a coverageData >= 25X There is a 53.25% of reference with a coverageData >= 26X There is a 51.39% of reference with a coverageData >= 27X There is a 49.55% of reference with a coverageData >= 28X There is a 47.75% of reference with a coverageData >= 29X There is a 45.99% of reference with a coverageData >= 30X There is a 44.26% of reference with a coverageData >= 31X There is a 42.57% of reference with a coverageData >= 32X There is a 40.93% of reference with a coverageData >= 33X There is a 39.33% of reference with a coverageData >= 34X There is a 37.78% of reference with a coverageData >= 35X There is a 36.27% of reference with a coverageData >= 36X There is a 34.81% of reference with a coverageData >= 37X There is a 33.4% of reference with a coverageData >= 38X There is a 32.03% of reference with a coverageData >= 39X There is a 30.71% of reference with a coverageData >= 40X There is a 29.44% of reference with a coverageData >= 41X There is a 28.21% of reference with a coverageData >= 42X There is a 27.03% of reference with a coverageData >= 43X There is a 25.89% of reference with a coverageData >= 44X There is a 24.79% of reference with a coverageData >= 45X There is a 23.73% of reference with a coverageData >= 46X There is a 22.72% of reference with a coverageData >= 47X There is a 21.74% of reference with a coverageData >= 48X There is a 20.8% of reference with a coverageData >= 49X There is a 19.91% of reference with a coverageData >= 50X There is a 19.04% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 8204091786 32.915030474487764 29.437050228540194 chr2 243199373 8984548958 36.94314194634046 101.40753211859838 chr3 198022430 7123138820 35.97137364691464 50.74919856882016 chr4 191154276 6844667648 35.80703393734179 25.287688750235592 chr5 180915260 6441178706 35.60329131992514 26.19543469638888 chr6 171115067 6002436702 35.078364560380884 25.936820674653774 chr7 159138663 5472356091 34.387344896821205 25.668911562920954 chr8 146364022 5253568010 35.89384835297844 26.07988721047498 chr9 141213431 4314383666 30.5522189741286 30.539555707498604 chr10 135534747 4794970791 35.37816609492767 31.028359203805575 chr11 135006516 4706887130 34.86414781639132 26.57935987561786 chr12 133851895 4703894531 35.14253220695904 25.888341183631052 chr13 115169878 3491447168 30.315627910971653 26.206394417870516 chr14 107349540 3216745628 29.965155211657173 28.091365051700397 chr15 102531392 2937213092 28.646963965923725 28.16380978344727 chr16 90354753 2689587098 29.76696862864536 42.845454891873864 chr17 81195210 2375562848 29.25742599840557 34.61528250348649 chr18 78077248 2681572354 34.34511874701322 26.31953324836248 chr19 59128983 1483846732 25.095082930819224 61.92894942717104 chr20 63025520 2162689693 34.314507726394005 29.21228008102094 chr21 48129895 1276742447 26.52701500803191 37.62360460997559 chr22 51304566 1061119197 20.682743851687587 27.47779140082906 chrMT 16571 373612644 22546.173676905437 8278.381080521394 chrX 155270560 3014861182 19.416824296891825 17.07639694067358 chrY 59373566 484137023 8.1540836371526 24.038271120706842