BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124859.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 130,711,296 number of mapped reads = 128,339,290 (98.19%) number of supplementary alignments = 24,219,952 (18.53%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 64,243,533 number of mapped paired reads (second in pair) = 64,095,757 number of mapped paired reads (both in pair) = 127,768,872 number of mapped paired reads (singletons) = 570,418 number of mapped bases = 13,684,821,647 bp number of sequenced bases = 13,671,114,823 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 63,000,551 duplication rate = 39.22% >>>>>>> Insert size mean insert size = 781,230.5844 std insert size = 8,556,573.5122 median insert size = 110 >>>>>>> Mapping quality mean mapping quality = 46.5485 >>>>>>> ACTG content number of A's = 3,886,428,748 bp (28.43%) number of C's = 2,950,488,976 bp (21.58%) number of T's = 3,807,351,878 bp (27.85%) number of G's = 3,024,935,672 bp (22.13%) number of N's = 1,909,549 bp (0.01%) GC percentage = 43.71% >>>>>>> Mismatches and indels general error rate = 0.0156 number of mismatches = 200,356,931 number of insertions = 4,837,774 mapped reads with insertion percentage = 3.56% number of deletions = 5,379,960 mapped reads with deletion percentage = 3.97% homopolymer indels = 36.87% >>>>>>> Coverage mean coverageData = 4.4206X std coverageData = 168.0159X There is a 62.41% of reference with a coverageData >= 1X There is a 55.38% of reference with a coverageData >= 2X There is a 39.33% of reference with a coverageData >= 3X There is a 34.1% of reference with a coverageData >= 4X There is a 26.56% of reference with a coverageData >= 5X There is a 23.17% of reference with a coverageData >= 6X There is a 19.26% of reference with a coverageData >= 7X There is a 16.9% of reference with a coverageData >= 8X There is a 14.47% of reference with a coverageData >= 9X There is a 12.68% of reference with a coverageData >= 10X There is a 10.94% of reference with a coverageData >= 11X There is a 9.52% of reference with a coverageData >= 12X There is a 8.19% of reference with a coverageData >= 13X There is a 7.07% of reference with a coverageData >= 14X There is a 6.06% of reference with a coverageData >= 15X There is a 5.19% of reference with a coverageData >= 16X There is a 4.42% of reference with a coverageData >= 17X There is a 3.77% of reference with a coverageData >= 18X There is a 3.2% of reference with a coverageData >= 19X There is a 2.72% of reference with a coverageData >= 20X There is a 2.31% of reference with a coverageData >= 21X There is a 1.97% of reference with a coverageData >= 22X There is a 1.68% of reference with a coverageData >= 23X There is a 1.43% of reference with a coverageData >= 24X There is a 1.23% of reference with a coverageData >= 25X There is a 1.06% of reference with a coverageData >= 26X There is a 0.92% of reference with a coverageData >= 27X There is a 0.8% of reference with a coverageData >= 28X There is a 0.7% of reference with a coverageData >= 29X There is a 0.62% of reference with a coverageData >= 30X There is a 0.55% of reference with a coverageData >= 31X There is a 0.49% of reference with a coverageData >= 32X There is a 0.44% 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 0.33% of reference with a coverageData >= 36X There is a 0.3% of reference with a coverageData >= 37X There is a 0.28% of reference with a coverageData >= 38X There is a 0.26% of reference with a coverageData >= 39X There is a 0.24% of reference with a coverageData >= 40X There is a 0.23% of reference with a coverageData >= 41X There is a 0.21% of reference with a coverageData >= 42X There is a 0.2% of reference with a coverageData >= 43X There is a 0.19% of reference with a coverageData >= 44X There is a 0.18% of reference with a coverageData >= 45X There is a 0.17% of reference with a coverageData >= 46X There is a 0.16% of reference with a coverageData >= 47X There is a 0.15% of reference with a coverageData >= 48X There is a 0.15% of reference with a coverageData >= 49X There is a 0.14% of reference with a coverageData >= 50X There is a 0.14% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1221808439 4.901927361697526 485.41227833346073 chr2 243199373 1108266742 4.557029602210364 89.50161441819637 chr3 198022430 846629805 4.275423773963384 26.631422057665443 chr4 191154276 773697569 4.047503331811421 112.01679925677998 chr5 180915260 698502043 3.8609349095261507 12.301642689685936 chr6 171115067 667903520 3.903242021346957 42.693379646672135 chr7 159138663 938799694 5.899255883530955 139.56691365707096 chr8 146364022 771762932 5.272900549289361 46.40675406036488 chr9 141213431 692725886 4.905524078655096 137.314393876925 chr10 135534747 811391555 5.986594382324704 259.8109609636725 chr11 135006516 507381676 3.75820138933146 42.68025153550856 chr12 133851895 644017021 4.811415041976058 23.84194777328519 chr13 115169878 294808842 2.559773849895022 4.719443339143142 chr14 107349540 332063801 3.0932950527780556 11.303410495973008 chr15 102531392 308065289 3.004594817165849 19.382846962171293 chr16 90354753 509508935 5.638983208774861 54.91641006038591 chr17 81195210 400191877 4.928762140032645 54.68886099444603 chr18 78077248 303558525 3.887925519608478 177.94718261120488 chr19 59128983 451437633 7.634794479722406 250.8398948623325 chr20 63025520 244005245 3.871530849725635 35.285376497547766 chr21 48129895 160627354 3.337371793559907 60.60715455304516 chr22 51304566 157261626 3.065255946225137 21.25390277059292 chrMT 16571 33704660 2033.9544988232453 998.3440628009068 chrX 155270560 547007413 3.5229306379779914 27.862981020478713 chrY 59373566 259693565 4.373891994292544 132.03927850786425