BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094087.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 = 400,164 number of mapped reads = 389,330 (97.29%) number of supplementary alignments = 13,633 (3.41%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 195,558 number of mapped paired reads (second in pair) = 193,772 number of mapped paired reads (both in pair) = 386,804 number of mapped paired reads (singletons) = 2,526 number of mapped bases = 52,020,089 bp number of sequenced bases = 50,869,635 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 372,433 duplication rate = 51.18% >>>>>>> Insert size mean insert size = 461,824.4228 std insert size = 6,160,640.7335 median insert size = 169 >>>>>>> Mapping quality mean mapping quality = 37.655 >>>>>>> ACTG content number of A's = 13,232,925 bp (26.01%) number of C's = 12,260,949 bp (24.1%) number of T's = 12,647,299 bp (24.86%) number of G's = 12,727,763 bp (25.02%) number of N's = 699 bp (0%) GC percentage = 49.12% >>>>>>> Mismatches and indels general error rate = 0.041 number of mismatches = 2,006,975 number of insertions = 31,008 mapped reads with insertion percentage = 7.86% number of deletions = 153,384 mapped reads with deletion percentage = 37.73% homopolymer indels = 26.68% >>>>>>> Coverage mean coverageData = 0.0168X std coverageData = 4.8989X There is a 0.01% 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% 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 453792 0.001820625353627504 0.6967962113056274 chr2 243199373 2368261 0.00973794040168023 4.592263116099304 chr3 198022430 1065809 0.0053822640192830685 2.1813594343891807 chr4 191154276 881361 0.004610731281784144 1.703775382313627 chr5 180915260 196406 0.0010856242861989641 0.5486906244885918 chr6 171115067 1206435 0.0070504311581165435 3.859307316803589 chr7 159138663 1746643 0.01097560433821164 4.194819056649006 chr8 146364022 796050 0.0054388366015249295 1.7733446137801223 chr9 141213431 424810 0.0030082832560027525 0.9797042227133634 chr10 135534747 854573 0.006305194932779858 2.3285784988405362 chr11 135006516 1682205 0.012460176366598484 3.81129093338291 chr12 133851895 1967047 0.014695697808387398 5.877554337068332 chr13 115169878 1011307 0.008781002615979154 3.160261875079509 chr14 107349540 248092 0.002311067192276744 0.9365160754247359 chr15 102531392 773392 0.007542977666781311 2.3979339194144296 chr16 90354753 323239 0.0035774432364393716 1.1073011108014639 chr17 81195210 1088607 0.013407281045273483 4.2584545907471485 chr18 78077248 130437 0.0016706147224861204 0.4909951046365757 chr19 59128983 204106 0.003451877398263386 0.9757255455881075 chr20 63025520 252364 0.004004155776897993 1.2833021317196542 chr21 48129895 853730 0.017738039943781304 8.192645619122535 chr22 51304566 54940 0.0010708598529027612 0.2792740373848732 chrMT 16571 1947642 117.53316034035363 581.1722883518084 chrX 155270560 30633241 0.1972894346487834 16.152462465618914 chrY 59373566 855600 0.014410453298358397 4.21972180119407