BamQC report ----------------------------------- >>>>>>> Input bam file = SRR21672008.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP398595/SRP398595.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 = 162,789,502 number of mapped reads = 161,118,315 (98.97%) number of supplementary alignments = 1,085,669 (0.67%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 80,539,458 number of mapped paired reads (second in pair) = 80,578,857 number of mapped paired reads (both in pair) = 160,448,500 number of mapped paired reads (singletons) = 669,815 number of mapped bases = 22,085,847,975 bp number of sequenced bases = 22,073,034,958 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 68,846,636 duplication rate = 31.83% >>>>>>> Insert size mean insert size = 118,940.673 std insert size = 3,457,762.4846 median insert size = 307 >>>>>>> Mapping quality mean mapping quality = 54.0943 >>>>>>> ACTG content number of A's = 5,595,367,389 bp (25.35%) number of C's = 4,799,270,256 bp (21.74%) number of T's = 5,999,380,657 bp (27.18%) number of G's = 5,678,828,860 bp (25.73%) number of N's = 187,796 bp (0%) GC percentage = 47.47% >>>>>>> Mismatches and indels general error rate = 0.0099 number of mismatches = 209,808,950 number of insertions = 3,305,516 mapped reads with insertion percentage = 1.95% number of deletions = 6,685,186 mapped reads with deletion percentage = 4.02% homopolymer indels = 45.94% >>>>>>> Coverage mean coverageData = 7.1344X std coverageData = 59.9049X There is a 43.28% of reference with a coverageData >= 1X There is a 36.71% of reference with a coverageData >= 2X There is a 32.13% of reference with a coverageData >= 3X There is a 28.82% of reference with a coverageData >= 4X There is a 26.15% of reference with a coverageData >= 5X There is a 23.96% of reference with a coverageData >= 6X There is a 22.09% of reference with a coverageData >= 7X There is a 20.47% of reference with a coverageData >= 8X There is a 19.06% of reference with a coverageData >= 9X There is a 17.8% of reference with a coverageData >= 10X There is a 16.67% of reference with a coverageData >= 11X There is a 15.66% of reference with a coverageData >= 12X There is a 14.74% of reference with a coverageData >= 13X There is a 13.91% of reference with a coverageData >= 14X There is a 13.14% of reference with a coverageData >= 15X There is a 12.44% of reference with a coverageData >= 16X There is a 11.79% of reference with a coverageData >= 17X There is a 11.19% of reference with a coverageData >= 18X There is a 10.63% of reference with a coverageData >= 19X There is a 10.12% of reference with a coverageData >= 20X There is a 9.64% of reference with a coverageData >= 21X There is a 9.19% of reference with a coverageData >= 22X There is a 8.77% of reference with a coverageData >= 23X There is a 8.38% of reference with a coverageData >= 24X There is a 8.01% of reference with a coverageData >= 25X There is a 7.66% of reference with a coverageData >= 26X There is a 7.34% of reference with a coverageData >= 27X There is a 7.03% of reference with a coverageData >= 28X There is a 6.74% of reference with a coverageData >= 29X There is a 6.47% of reference with a coverageData >= 30X There is a 6.21% of reference with a coverageData >= 31X There is a 5.96% of reference with a coverageData >= 32X There is a 5.73% of reference with a coverageData >= 33X There is a 5.51% of reference with a coverageData >= 34X There is a 5.3% of reference with a coverageData >= 35X There is a 5.11% of reference with a coverageData >= 36X There is a 4.92% of reference with a coverageData >= 37X There is a 4.74% of reference with a coverageData >= 38X There is a 4.57% of reference with a coverageData >= 39X There is a 4.41% of reference with a coverageData >= 40X There is a 4.25% of reference with a coverageData >= 41X There is a 4.1% of reference with a coverageData >= 42X There is a 3.96% of reference with a coverageData >= 43X There is a 3.83% of reference with a coverageData >= 44X There is a 3.7% of reference with a coverageData >= 45X There is a 3.58% of reference with a coverageData >= 46X There is a 3.46% of reference with a coverageData >= 47X There is a 3.35% of reference with a coverageData >= 48X There is a 3.24% of reference with a coverageData >= 49X There is a 3.13% of reference with a coverageData >= 50X There is a 3.03% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1912024141 7.671090781354563 54.872243257550984 chr2 243199373 1831399149 7.530443546826085 106.25240605669438 chr3 198022430 1287157611 6.500059670008089 18.090332948636693 chr4 191154276 1105429227 5.782916553747404 30.63034498403428 chr5 180915260 1182565234 6.536569850437161 19.55393083485191 chr6 171115067 1155375431 6.752037978046667 124.75637299069976 chr7 159138663 1169355073 7.348026249284248 31.789544980971332 chr8 146364022 1039123106 7.099580155019244 23.306100960421368 chr9 141213431 1011187655 7.160704529585433 92.69901654804274 chr10 135534747 1102494404 8.13440411704904 22.816467715798904 chr11 135006516 1133678055 8.397209916890233 49.79498633196544 chr12 133851895 1005255149 7.510204834978242 21.106575581941385 chr13 115169878 538665576 4.677139416610305 15.423968042282487 chr14 107349540 671594536 6.256147310924667 20.191595069900046 chr15 102531392 686217932 6.692759345352495 19.65718914637308 chr16 90354753 869783064 9.626312231742807 60.83995260036558 chr17 81195210 931956584 11.477974919949096 97.08980205639827 chr18 78077248 573636863 7.3470425468889475 103.08230095913686 chr19 59128983 717540291 12.13517051358722 33.91475812287807 chr20 63025520 631800008 10.024510833072064 25.67390448357564 chr21 48129895 319313970 6.634420665160396 88.64249868306972 chr22 51304566 494103213 9.630784382816922 32.10466510837171 chrMT 16571 310382 18.730432683603887 65.24969411664046 chrX 155270560 570508524 3.6742865099475392 19.682063482321386 chrY 59373566 145372797 2.4484430832401074 33.67227996592688