BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2093989.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 = 273,378 number of mapped reads = 259,461 (94.91%) number of supplementary alignments = 14,930 (5.46%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 130,411 number of mapped paired reads (second in pair) = 129,050 number of mapped paired reads (both in pair) = 257,256 number of mapped paired reads (singletons) = 2,205 number of mapped bases = 33,159,240 bp number of sequenced bases = 32,575,630 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 241,156 duplication rate = 49.54% >>>>>>> Insert size mean insert size = 979,949.4413 std insert size = 9,117,961.6107 median insert size = 159 >>>>>>> Mapping quality mean mapping quality = 39.6925 >>>>>>> ACTG content number of A's = 8,674,339 bp (26.63%) number of C's = 7,618,524 bp (23.39%) number of T's = 8,183,904 bp (25.12%) number of G's = 8,098,468 bp (24.86%) number of N's = 395 bp (0%) GC percentage = 48.25% >>>>>>> Mismatches and indels general error rate = 0.0345 number of mismatches = 1,082,578 number of insertions = 18,061 mapped reads with insertion percentage = 6.85% number of deletions = 89,614 mapped reads with deletion percentage = 33.17% homopolymer indels = 29.43% >>>>>>> Coverage mean coverageData = 0.0107X std coverageData = 2.2324X 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 0.01% 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% 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 606567 0.002433562642959273 0.8242762182581578 chr2 243199373 1927217 0.007924432436756324 2.561546902850783 chr3 198022430 490773 0.0024783707583024813 0.8165277858603667 chr4 191154276 806850 0.004220936182458194 1.3741952345175368 chr5 180915260 360383 0.0019919989060071547 0.972969344717627 chr6 171115067 836019 0.00488571237271584 1.4664657184043814 chr7 159138663 702881 0.004416783368350908 1.4167824458225347 chr8 146364022 383949 0.002623247125581176 1.072374918587641 chr9 141213431 591220 0.004186712239857695 1.361238910852056 chr10 135534747 477297 0.0035215840259767484 0.9410002782892574 chr11 135006516 854421 0.006328738977309806 1.7032922081844795 chr12 133851895 959196 0.007166099516185407 1.6818280359077658 chr13 115169878 702665 0.006101117863474684 1.8130055264122862 chr14 107349540 107798 0.001004177567970948 0.3475902149384563 chr15 102531392 374413 0.003651691376627365 0.9434008117601914 chr16 90354753 244830 0.0027096526953042524 0.7578198957417808 chr17 81195210 786615 0.00968794834079498 2.526388032172653 chr18 78077248 192056 0.0024598203051419023 0.67406206648545 chr19 59128983 134254 0.0022705278052896666 0.5852289832868797 chr20 63025520 295230 0.004684292965770056 1.6680243179942056 chr21 48129895 125661 0.0026108720993469857 0.4851927313401751 chr22 51304566 95362 0.0018587429430745013 0.6026682565347289 chrMT 16571 1296568 78.24319594472271 337.69936249467025 chrX 155270560 19320171 0.1244290675579453 6.962592066444351 chrY 59373566 486844 0.008199675929857405 1.6267668807392026