BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2093974.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 = 480,768 number of mapped reads = 188,447 (39.2%) number of supplementary alignments = 6,573 (1.37%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 93,299 number of mapped paired reads (second in pair) = 95,148 number of mapped paired reads (both in pair) = 184,468 number of mapped paired reads (singletons) = 3,979 number of mapped bases = 24,734,769 bp number of sequenced bases = 24,697,241 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 188,359 duplication rate = 36.72% >>>>>>> Insert size mean insert size = 120,761.1315 std insert size = 3,645,639.0817 median insert size = 208 >>>>>>> Mapping quality mean mapping quality = 22.6919 >>>>>>> ACTG content number of A's = 6,361,332 bp (25.76%) number of C's = 5,176,405 bp (20.96%) number of T's = 6,930,832 bp (28.06%) number of G's = 6,228,335 bp (25.22%) number of N's = 337 bp (0%) GC percentage = 46.18% >>>>>>> Mismatches and indels general error rate = 0.0225 number of mismatches = 545,915 number of insertions = 3,687 mapped reads with insertion percentage = 1.81% number of deletions = 12,865 mapped reads with deletion percentage = 6.68% homopolymer indels = 35.23% >>>>>>> Coverage mean coverageData = 0.008X std coverageData = 16.4362X 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 357575 0.0014346002371645045 1.5310653458192578 chr2 243199373 775178 0.0031874177570350892 2.0179297802780507 chr3 198022430 586478 0.002961674594135624 1.9398323586632031 chr4 191154276 77802 4.0701155960539434E-4 0.3135058579627277 chr5 180915260 796278 0.004401386593922481 3.1677055103563574 chr6 171115067 55032 3.2160814921108026E-4 0.1425437722544927 chr7 159138663 396264 0.0024900548523522532 1.5409871630627257 chr8 146364022 37081 2.533477796886451E-4 0.07671751227290188 chr9 141213431 116536 8.252472811881471E-4 0.48459972605339574 chr10 135534747 97069 7.161927265780781E-4 0.34176815165444996 chr11 135006516 64287 4.761770165226692E-4 0.20160403314388722 chr12 133851895 29869 2.2314962369415837E-4 0.06445544972155645 chr13 115169878 60504 5.253456984646628E-4 0.2938283441285662 chr14 107349540 31849 2.966850160699338E-4 0.1338996566440117 chr15 102531392 295463 0.00288168329949134 2.571678834986377 chr16 90354753 181850 0.0020126224018342455 1.0510194212847197 chr17 81195210 986128 0.012145149941726859 6.337811157145121 chr18 78077248 2010456 0.02574957559979573 13.377986669627587 chr19 59128983 30546 5.165994483618973E-4 0.17131745870568393 chr20 63025520 1248888 0.01981559216012815 11.959939499523449 chr21 48129895 3441 7.149402673743627E-5 0.01608644671277149 chr22 51304566 17540 3.418799020734334E-4 0.07775936998832175 chrMT 16571 12972009 782.8138917385794 6814.719691630245 chrX 155270560 3503462 0.022563594798653396 12.675965679117942 chrY 59373566 3184 5.362655832395177E-5 0.02380150959601439