BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094148.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 = 313,628 number of mapped reads = 292,214 (93.17%) number of supplementary alignments = 20,839 (6.64%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 146,878 number of mapped paired reads (second in pair) = 145,336 number of mapped paired reads (both in pair) = 289,462 number of mapped paired reads (singletons) = 2,752 number of mapped bases = 37,259,203 bp number of sequenced bases = 36,444,467 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 265,859 duplication rate = 48.38% >>>>>>> Insert size mean insert size = 1,594,094.4706 std insert size = 11,331,283.0827 median insert size = 156 >>>>>>> Mapping quality mean mapping quality = 46.7123 >>>>>>> ACTG content number of A's = 10,028,674 bp (27.52%) number of C's = 8,208,312 bp (22.52%) number of T's = 9,507,239 bp (26.09%) number of G's = 8,699,849 bp (23.87%) number of N's = 393 bp (0%) GC percentage = 46.39% >>>>>>> Mismatches and indels general error rate = 0.0385 number of mismatches = 1,361,305 number of insertions = 22,027 mapped reads with insertion percentage = 7.4% number of deletions = 106,587 mapped reads with deletion percentage = 35.33% homopolymer indels = 29.43% >>>>>>> Coverage mean coverageData = 0.012X std coverageData = 2.2588X There is a 0.03% of reference with a coverageData >= 1X There is a 0.02% of reference with a coverageData >= 2X There is a 0.02% 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 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 642661 0.0025783727134625675 0.672726659991859 chr2 243199373 1716332 0.007057304378823378 1.8169396985420583 chr3 198022430 613114 0.003096184608985962 0.7837200304584017 chr4 191154276 661110 0.0034585153616966432 0.7987896041665371 chr5 180915260 798894 0.004415846402343285 1.2858413095248378 chr6 171115067 529175 0.0030925096736221366 0.9523172398442243 chr7 159138663 817178 0.005135006067004597 1.199735057456717 chr8 146364022 668361 0.004566429583357582 1.2163933221402508 chr9 141213431 602425 0.004266060216326023 1.409934357260083 chr10 135534747 473599 0.003494299509778109 0.7383825246420762 chr11 135006516 687548 0.005092702340381852 1.1904564927041028 chr12 133851895 844934 0.0063124545229636085 1.2824677928897308 chr13 115169878 714488 0.006203774914131628 1.3162900082559754 chr14 107349540 165898 0.0015454001945420538 0.41702413245772935 chr15 102531392 439331 0.004284843806665572 0.9355450640967266 chr16 90354753 199411 0.00220697853050409 0.5027895013908553 chr17 81195210 461959 0.005689485869917696 1.0842981326661976 chr18 78077248 169079 0.002165534830325987 0.48853933139315775 chr19 59128983 130790 0.0022119440139871847 0.4946989054185787 chr20 63025520 222101 0.00352398520472342 1.1084182518094818 chr21 48129895 212418 0.004413431610436715 1.346746807560319 chr22 51304566 143512 0.002797255901160922 0.6149903372245128 chrMT 16571 2578000 155.57298895661094 619.7301923939029 chrX 155270560 22760285 0.14658467773929584 5.983127634531077 chrY 59373566 6600 1.111605794403523E-4 0.03549234429500452