BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5038413.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP093555/SRP093555.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 = 78,434,548 number of mapped reads = 77,983,729 (99.43%) number of supplementary alignments = 187,407 (0.24%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 39,134,592 number of mapped paired reads (second in pair) = 38,849,137 number of mapped paired reads (both in pair) = 77,656,418 number of mapped paired reads (singletons) = 327,311 number of mapped bases = 11,568,047,193 bp number of sequenced bases = 11,566,087,461 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 31,963,442 duplication rate = 38.28% >>>>>>> Insert size mean insert size = 22,738.2766 std insert size = 1,571,271.5776 median insert size = 222 >>>>>>> Mapping quality mean mapping quality = 55.8107 >>>>>>> ACTG content number of A's = 2,845,889,718 bp (24.61%) number of C's = 2,937,351,526 bp (25.4%) number of T's = 2,862,829,572 bp (24.75%) number of G's = 2,919,577,177 bp (25.24%) number of N's = 439,468 bp (0%) GC percentage = 50.64% >>>>>>> Mismatches and indels general error rate = 0.0056 number of mismatches = 62,801,048 number of insertions = 598,549 mapped reads with insertion percentage = 0.73% number of deletions = 699,630 mapped reads with deletion percentage = 0.87% homopolymer indels = 45.76% >>>>>>> Coverage mean coverageData = 3.7368X std coverageData = 24.9346X There is a 21.45% of reference with a coverageData >= 1X There is a 14.22% of reference with a coverageData >= 2X There is a 9.24% of reference with a coverageData >= 3X There is a 7.29% of reference with a coverageData >= 4X There is a 5.8% of reference with a coverageData >= 5X There is a 5.02% of reference with a coverageData >= 6X There is a 4.46% of reference with a coverageData >= 7X There is a 4.12% of reference with a coverageData >= 8X There is a 3.86% of reference with a coverageData >= 9X There is a 3.68% of reference with a coverageData >= 10X There is a 3.54% of reference with a coverageData >= 11X There is a 3.43% of reference with a coverageData >= 12X There is a 3.34% of reference with a coverageData >= 13X There is a 3.26% of reference with a coverageData >= 14X There is a 3.19% of reference with a coverageData >= 15X There is a 3.13% of reference with a coverageData >= 16X There is a 3.07% of reference with a coverageData >= 17X There is a 3.02% of reference with a coverageData >= 18X There is a 2.97% of reference with a coverageData >= 19X There is a 2.93% of reference with a coverageData >= 20X There is a 2.88% of reference with a coverageData >= 21X There is a 2.84% of reference with a coverageData >= 22X There is a 2.8% of reference with a coverageData >= 23X There is a 2.76% of reference with a coverageData >= 24X There is a 2.72% of reference with a coverageData >= 25X There is a 2.69% of reference with a coverageData >= 26X There is a 2.65% of reference with a coverageData >= 27X There is a 2.62% of reference with a coverageData >= 28X There is a 2.59% of reference with a coverageData >= 29X There is a 2.55% of reference with a coverageData >= 30X There is a 2.52% of reference with a coverageData >= 31X There is a 2.49% of reference with a coverageData >= 32X There is a 2.46% of reference with a coverageData >= 33X There is a 2.43% of reference with a coverageData >= 34X There is a 2.41% of reference with a coverageData >= 35X There is a 2.38% of reference with a coverageData >= 36X There is a 2.35% of reference with a coverageData >= 37X There is a 2.32% of reference with a coverageData >= 38X There is a 2.3% of reference with a coverageData >= 39X There is a 2.27% of reference with a coverageData >= 40X There is a 2.25% of reference with a coverageData >= 41X There is a 2.22% of reference with a coverageData >= 42X There is a 2.2% of reference with a coverageData >= 43X There is a 2.17% of reference with a coverageData >= 44X There is a 2.15% of reference with a coverageData >= 45X There is a 2.13% of reference with a coverageData >= 46X There is a 2.1% of reference with a coverageData >= 47X There is a 2.08% of reference with a coverageData >= 48X There is a 2.06% of reference with a coverageData >= 49X There is a 2.04% of reference with a coverageData >= 50X There is a 2.02% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1006932913 4.039841140455975 24.46715867761911 chr2 243199373 919359828 3.780272196672152 25.516386400776295 chr3 198022430 636036504 3.2119417179154905 21.326591998869993 chr4 191154276 389585920 2.0380706524189915 15.725685408773506 chr5 180915260 518957736 2.8685127832776516 22.146121445203402 chr6 171115067 684658318 4.001157408307008 27.148163263263594 chr7 159138663 725330271 4.557850727952892 31.627781228256353 chr8 146364022 358364939 2.448449653836378 17.86818294240933 chr9 141213431 455814344 3.227839878771871 21.947902448766992 chr10 135534747 364420744 2.688762491289411 17.102343904115934 chr11 135006516 668018734 4.948048092730576 29.40163417272743 chr12 133851895 522607203 3.904369101386275 22.434443910727072 chr13 115169878 377168038 3.274884410314301 27.80738698885854 chr14 107349540 279522710 2.603855684896274 16.99587386213915 chr15 102531392 347382971 3.3880645158899236 20.35754758652645 chr16 90354753 573649245 6.348855217389615 34.14447703733123 chr17 81195210 714753280 8.802899579913642 38.7589721740751 chr18 78077248 112191319 1.436927169871561 11.010064183359097 chr19 59128983 790116722 13.362596173859442 47.91646289987427 chr20 63025520 450830662 7.153144662669979 41.49926335610253 chr21 48129895 97531500 2.0264224553159735 29.302070851029814 chr22 51304566 202833082 3.953509362110187 21.380026975542727 chrMT 16571 1126170 67.96029207651922 25.453714518619424 chrX 155270560 350295028 2.2560299132044093 17.02772706043296 chrY 59373566 20559012 0.34626540706684183 5.211207543345533