BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094078.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 = 429,258 number of mapped reads = 411,994 (95.98%) number of supplementary alignments = 14,654 (3.41%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 207,011 number of mapped paired reads (second in pair) = 204,983 number of mapped paired reads (both in pair) = 409,182 number of mapped paired reads (singletons) = 2,812 number of mapped bases = 54,541,007 bp number of sequenced bases = 53,325,698 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 393,090 duplication rate = 49.54% >>>>>>> Insert size mean insert size = 391,674.106 std insert size = 5,609,190.3424 median insert size = 166 >>>>>>> Mapping quality mean mapping quality = 39.381 >>>>>>> ACTG content number of A's = 14,133,495 bp (26.5%) number of C's = 12,499,207 bp (23.44%) number of T's = 13,524,501 bp (25.36%) number of G's = 13,167,806 bp (24.69%) number of N's = 689 bp (0%) GC percentage = 48.13% >>>>>>> Mismatches and indels general error rate = 0.0412 number of mismatches = 2,115,453 number of insertions = 35,515 mapped reads with insertion percentage = 8.46% number of deletions = 171,947 mapped reads with deletion percentage = 39.77% homopolymer indels = 27.49% >>>>>>> Coverage mean coverageData = 0.0176X std coverageData = 4.6772X There is a 0.02% 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 0.01% 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% 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 455836 0.0018288259350013815 0.7281707471023857 chr2 243199373 2111926 0.00868392863825352 3.4221021469891153 chr3 198022430 832485 0.004203993456700839 1.5555977514979047 chr4 191154276 745852 0.0039018326746716354 1.3881788433221365 chr5 180915260 433717 0.0023973489024640597 1.0721676510452716 chr6 171115067 1282247 0.007493478058247203 3.899423186140871 chr7 159138663 2016551 0.01267165980903082 4.7324575302706124 chr8 146364022 913621 0.006242114609285607 2.01494246199958 chr9 141213431 820446 0.005809971432533213 2.8512866596644755 chr10 135534747 1136750 0.00838714813109881 3.384437680553989 chr11 135006516 1628442 0.012061951143158157 3.3007674191327245 chr12 133851895 1103827 0.008246629605057142 2.453952560501257 chr13 115169878 1406636 0.012213575497579324 3.459529261377765 chr14 107349540 322170 0.003001130698836716 1.4853349193016194 chr15 102531392 957935 0.009342845945171601 3.1129726571394083 chr16 90354753 349403 0.0038670129506081434 1.4060008980085306 chr17 81195210 1066807 0.01313879230067882 3.89066612583104 chr18 78077248 118596 0.001518957225541556 0.5746682308139163 chr19 59128983 206605 0.0034941409359264645 0.8472938260402555 chr20 63025520 297004 0.004712440294026928 1.4522229487962652 chr21 48129895 643297 0.013365850891633984 5.629086274674359 chr22 51304566 81882 0.0015959982976953748 0.392005846047972 chrMT 16571 1139617 68.77176995956792 313.4604078809528 chrX 155270560 33878298 0.2181888053987826 16.865867760242157 chrY 59373566 591057 0.009954884636708532 2.3091349209693197