BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094120.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 = 970,798 number of mapped reads = 906,544 (93.38%) number of supplementary alignments = 14,159 (1.46%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 454,681 number of mapped paired reads (second in pair) = 451,863 number of mapped paired reads (both in pair) = 902,182 number of mapped paired reads (singletons) = 4,362 number of mapped bases = 131,724,790 bp number of sequenced bases = 131,315,980 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 912,568 duplication rate = 42.72% >>>>>>> Insert size mean insert size = 33,446.734 std insert size = 1,816,527.5027 median insert size = 237 >>>>>>> Mapping quality mean mapping quality = 14.7988 >>>>>>> ACTG content number of A's = 36,871,048 bp (28.08%) number of C's = 27,350,610 bp (20.83%) number of T's = 38,006,833 bp (28.94%) number of G's = 29,085,909 bp (22.15%) number of N's = 1,580 bp (0%) GC percentage = 42.98% >>>>>>> Mismatches and indels general error rate = 0.0203 number of mismatches = 2,596,293 number of insertions = 43,053 mapped reads with insertion percentage = 4.69% number of deletions = 118,911 mapped reads with deletion percentage = 12.83% homopolymer indels = 57.77% >>>>>>> Coverage mean coverageData = 0.0426X std coverageData = 66.1078X There is a 0.01% of reference with a coverageData >= 1X There is a 0% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% 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 53326 2.1394530447328353E-4 0.1076580724797681 chr2 243199373 441955 0.001817253862739194 1.636593903440429 chr3 198022430 26253 1.3257589051906898E-4 0.06669585675459251 chr4 191154276 104395 5.461295566310011E-4 0.5810012718422318 chr5 180915260 18902 1.044798542698941E-4 0.04285319286395923 chr6 171115067 333565 0.0019493607772131487 0.7506499196804731 chr7 159138663 44230 2.779337162082353E-4 0.14699847032042135 chr8 146364022 20105 1.373629921156444E-4 0.08366588390686128 chr9 141213431 15706 1.1122171516390676E-4 0.051893133798004844 chr10 135534747 32259 2.3801276583339918E-4 0.16227256916036095 chr11 135006516 26362 1.952646493003345E-4 0.13168227587059272 chr12 133851895 22240 1.6615379259292518E-4 0.059070422077341 chr13 115169878 16007 1.38985994237139E-4 0.09435333416175605 chr14 107349540 60591 5.644271973592062E-4 0.3269426765709135 chr15 102531392 15983 1.5588396576143236E-4 0.09593085042292879 chr16 90354753 12227 1.353221562124131E-4 0.0314317367139086 chr17 81195210 28160 3.468184884305367E-4 0.13486968960581325 chr18 78077248 5783 7.406767205729383E-5 0.018897491872659763 chr19 59128983 5659 9.570602626464926E-5 0.017388122282497965 chr20 63025520 12144 1.9268385250926926E-4 0.10867815057665882 chr21 48129895 3868 8.036585161883274E-5 0.02160250406395443 chr22 51304566 5266 1.0264193639217218E-4 0.05523042898136783 chrMT 16571 109692409 6619.540703638887 27249.563311230442 chrX 155270560 20467199 0.1318163533383276 56.63914266519765 chrY 59373566 260196 0.004382354261827561 2.770243533156934