BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094018.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 = 38,580 number of mapped reads = 6,319 (16.38%) number of supplementary alignments = 39 (0.1%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 3,031 number of mapped paired reads (second in pair) = 3,288 number of mapped paired reads (both in pair) = 5,884 number of mapped paired reads (singletons) = 435 number of mapped bases = 820,219 bp number of sequenced bases = 817,877 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 5,939 duplication rate = 28.4% >>>>>>> Insert size mean insert size = 47,799.5102 std insert size = 2,374,083.2175 median insert size = 237 >>>>>>> Mapping quality mean mapping quality = 5.696 >>>>>>> ACTG content number of A's = 210,553 bp (25.74%) number of C's = 154,963 bp (18.95%) number of T's = 241,313 bp (29.5%) number of G's = 211,011 bp (25.8%) number of N's = 37 bp (0%) GC percentage = 44.75% >>>>>>> Mismatches and indels general error rate = 0.0319 number of mismatches = 25,588 number of insertions = 116 mapped reads with insertion percentage = 1.39% number of deletions = 240 mapped reads with deletion percentage = 3.77% homopolymer indels = 45.22% >>>>>>> Coverage mean coverageData = 0.0003X std coverageData = 0.8667X There is a 0% 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 1581 6.343013283806422E-6 0.004804284128899011 chr2 243199373 37362 1.5362704080655669E-4 0.15497507939572805 chr3 198022430 721 3.6410016784462245E-6 0.001966783149523375 chr4 191154276 952 4.980270491045672E-6 0.0028217251147874827 chr5 180915260 534 2.9516581409439977E-6 0.002046899646279244 chr6 171115067 541 3.1616152188398466E-6 0.0019142077285783593 chr7 159138663 1499 9.419458299709354E-6 0.005354719304179852 chr8 146364022 616 4.20868456320502E-6 0.0032395006674557896 chr9 141213431 44146 3.126189887702679E-4 0.32661913650109553 chr10 135534747 1055 7.783981771109957E-6 0.00505329857894154 chr11 135006516 408 3.022076356670074E-6 0.0017384093947412295 chr12 133851895 828 6.18594155876538E-6 0.0038712627424008733 chr13 115169878 406 3.5252273168162947E-6 0.00241733933634439 chr14 107349540 361 3.362846268367801E-6 0.002358232553198398 chr15 102531392 107 1.0435828277840996E-6 0.0010215584852170635 chr16 90354753 60 6.640491839981014E-7 0.0011524313112003179 chr17 81195210 3233 3.981761978323598E-5 0.02496249799135662 chr18 78077248 128 1.6394020444982897E-6 0.0015517309899650133 chr19 59128983 507 8.574475228163489E-6 0.0029282079343069286 chr20 63025520 73 1.1582609711113848E-6 0.0010762247114533784 chr21 48129895 183 3.802210663455634E-6 0.002638241182897698 chr22 51304566 296 5.769466990520882E-6 0.0026415720964939092 chrMT 16571 698791 42.169513004646674 370.45047112470616 chrX 155270560 25707 1.6556261534704324E-4 0.08429137244101527 chrY 59373566 124 2.0884714925157096E-6 0.0020437560087540403