BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094079.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP024468/ERP024468.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 = 424,002 number of mapped reads = 403,845 (95.25%) number of supplementary alignments = 13,395 (3.16%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 202,892 number of mapped paired reads (second in pair) = 200,953 number of mapped paired reads (both in pair) = 400,994 number of mapped paired reads (singletons) = 2,851 number of mapped bases = 53,714,731 bp number of sequenced bases = 52,401,841 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 387,163 duplication rate = 50.03% >>>>>>> Insert size mean insert size = 383,473.1123 std insert size = 5,776,752.9484 median insert size = 168 >>>>>>> Mapping quality mean mapping quality = 37.5536 >>>>>>> ACTG content number of A's = 14,356,107 bp (27.4%) number of C's = 11,976,796 bp (22.86%) number of T's = 13,585,929 bp (25.93%) number of G's = 12,482,556 bp (23.82%) number of N's = 453 bp (0%) GC percentage = 46.68% >>>>>>> Mismatches and indels general error rate = 0.0435 number of mismatches = 2,206,196 number of insertions = 37,824 mapped reads with insertion percentage = 9.2% number of deletions = 174,819 mapped reads with deletion percentage = 41.21% homopolymer indels = 27.27% >>>>>>> Coverage mean coverageData = 0.0174X std coverageData = 5.0113X There is a 0.01% of reference with a coverageData >= 1X There is a 0.01% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 522755 0.0020973067104213955 1.0010910915633704 chr2 243199373 2229051 0.009165529386459396 3.5197731189937294 chr3 198022430 940888 0.004751421341511666 2.0639185761771226 chr4 191154276 982955 0.00514220775265315 2.1447215998463878 chr5 180915260 403493 0.00223028726266651 1.0126040363590703 chr6 171115067 1458897 0.008525824321478366 4.98868199525354 chr7 159138663 1592692 0.010008202720667573 3.7059083004109183 chr8 146364022 556153 0.0037997930939613015 0.9992739243857297 chr9 141213431 326307 0.0023107362924989763 0.8210307544331734 chr10 135534747 1089190 0.008036241805948108 2.3936526090143895 chr11 135006516 1385322 0.010261149172977695 2.9675241113893027 chr12 133851895 1662636 0.012421460301327823 3.813011301293207 chr13 115169878 1375605 0.011944138726968175 4.127273953033054 chr14 107349540 235841 0.002196944672515597 0.9232772761962814 chr15 102531392 946879 0.009235015555040938 3.2498058308179054 chr16 90354753 450738 0.004988536684948937 1.553103578300082 chr17 81195210 769878 0.009481815491332556 2.861508490737055 chr18 78077248 275045 0.0035227291822580633 1.2632959316181376 chr19 59128983 178776 0.003023491880453956 0.6571410789758666 chr20 63025520 297705 0.004723562772667326 1.4733622762307972 chr21 48129895 768418 0.01596550335295766 6.7244865637939135 chr22 51304566 113305 0.0022084778964897587 0.6105606561004917 chrMT 16571 2077248 125.35441433830185 608.8523689251386 chrX 155270560 32076480 0.2065844291409782 17.568825523430665 chrY 59373566 998474 0.016816810363049443 4.380670888443195