BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094136.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 = 471,618 number of mapped reads = 438,770 (93.04%) number of supplementary alignments = 8,648 (1.83%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 220,716 number of mapped paired reads (second in pair) = 218,054 number of mapped paired reads (both in pair) = 433,612 number of mapped paired reads (singletons) = 5,158 number of mapped bases = 56,774,930 bp number of sequenced bases = 56,592,944 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 422,809 duplication rate = 53.92% >>>>>>> Insert size mean insert size = 37,288.0762 std insert size = 1,695,031.7528 median insert size = 212 >>>>>>> Mapping quality mean mapping quality = 35.0674 >>>>>>> ACTG content number of A's = 14,848,450 bp (26.24%) number of C's = 13,001,991 bp (22.97%) number of T's = 14,929,402 bp (26.38%) number of G's = 13,812,497 bp (24.41%) number of N's = 604 bp (0%) GC percentage = 47.38% >>>>>>> Mismatches and indels general error rate = 0.016 number of mismatches = 877,372 number of insertions = 16,258 mapped reads with insertion percentage = 3.62% number of deletions = 39,990 mapped reads with deletion percentage = 8.94% homopolymer indels = 53.71% >>>>>>> Coverage mean coverageData = 0.0183X std coverageData = 17.519X There is a 0.02% of reference with a coverageData >= 1X There is a 0.02% 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% 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 1278885 0.005130920014839201 0.8897548787345761 chr2 243199373 1006828 0.004139928436410895 1.434237354832599 chr3 198022430 5562260 0.02808904021630277 7.646336606265193 chr4 191154276 61115 3.1971557884480703E-4 0.07292792057630237 chr5 180915260 296636 0.0016396405698446885 0.34665600193473434 chr6 171115067 237364 0.001387160138271167 0.2715799719438881 chr7 159138663 527517 0.0033148261400185322 1.7211853304338522 chr8 146364022 7179986 0.04905567571790286 12.284639547527213 chr9 141213431 1329051 0.009411647253298449 2.430564233677072 chr10 135534747 765996 0.0056516577258228845 0.6933572228886804 chr11 135006516 1106856 0.008198537617251008 1.5496692701125092 chr12 133851895 228440 0.0017066624271550284 0.2945226907666762 chr13 115169878 341692 0.002966852148614762 0.6447822645592762 chr14 107349540 124045 0.0011555242807747476 0.2575980662060742 chr15 102531392 290632 0.002834566022472415 0.5096820464200357 chr16 90354753 178875 0.0019796966297943395 0.49938664104060837 chr17 81195210 451304 0.0055582589169976895 0.7185753750638293 chr18 78077248 384667 0.004926748955086122 1.2859293765940603 chr19 59128983 74534 0.0012605324194397188 0.19145871905500755 chr20 63025520 239792 0.003804681024448509 0.528096434652813 chr21 48129895 27905 5.797851834083577E-4 0.11866494776168211 chr22 51304566 167533 0.0032654598423072128 1.3496111048527841 chrMT 16571 32760834 1976.998008569187 7141.86141569435 chrX 155270560 2148411 0.013836563737517273 4.896774077349036 chrY 59373566 3772 6.352995540136498E-5 0.017781937401658687