BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094107.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 = 325,580 number of mapped reads = 311,761 (95.76%) number of supplementary alignments = 17,992 (5.53%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 156,609 number of mapped paired reads (second in pair) = 155,152 number of mapped paired reads (both in pair) = 309,562 number of mapped paired reads (singletons) = 2,199 number of mapped bases = 40,763,010 bp number of sequenced bases = 40,030,670 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 301,706 duplication rate = 50.42% >>>>>>> Insert size mean insert size = 1,130,520.5757 std insert size = 9,303,378.1878 median insert size = 165 >>>>>>> Mapping quality mean mapping quality = 35.5417 >>>>>>> ACTG content number of A's = 11,726,938 bp (29.29%) number of C's = 8,493,900 bp (21.22%) number of T's = 10,962,353 bp (27.38%) number of G's = 8,847,010 bp (22.1%) number of N's = 469 bp (0%) GC percentage = 43.32% >>>>>>> Mismatches and indels general error rate = 0.0351 number of mismatches = 1,341,875 number of insertions = 31,003 mapped reads with insertion percentage = 9.54% number of deletions = 90,792 mapped reads with deletion percentage = 28.19% homopolymer indels = 33.04% >>>>>>> Coverage mean coverageData = 0.0132X std coverageData = 4.3022X 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% 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 959588 0.0038498921132076136 1.7542767530241072 chr2 243199373 1000141 0.004112432477364981 1.2941998942149953 chr3 198022430 806804 0.004074306127846225 1.8673641906621756 chr4 191154276 1621717 0.00848381231084781 3.6394356861230066 chr5 180915260 938530 0.00518767736895163 2.2048832016806794 chr6 171115067 293695 0.0017163596704199051 0.6331235037026351 chr7 159138663 447404 0.0028114098206291956 1.0591046456374378 chr8 146364022 1369022 0.009353541815078026 4.153599490477647 chr9 141213431 396757 0.002809626514916984 0.8850951448070337 chr10 135534747 1048563 0.007736488415033526 4.8997539387881455 chr11 135006516 765373 0.005669155998366775 1.6500752200428588 chr12 133851895 1383209 0.010333876856954471 4.841903439039201 chr13 115169878 1188165 0.010316629839618308 3.467274772437881 chr14 107349540 185676 0.001729639456303213 0.8332788578683258 chr15 102531392 219505 0.00214085652909111 0.716597508447375 chr16 90354753 234637 0.002596841806429375 0.9321134653601966 chr17 81195210 499902 0.006156791761484452 2.0566426988436053 chr18 78077248 385366 0.004935701627188499 1.6078326373475884 chr19 59128983 56774 9.601721037549386E-4 0.38934008954477095 chr20 63025520 93031 0.0014760846082666197 0.49373100177268 chr21 48129895 465468 0.009671078650805284 3.5166145665039985 chr22 51304566 33371 6.504489288536229E-4 0.16766425415687813 chrMT 16571 2831682 170.8817814253817 771.0549960800884 chrX 155270560 22881936 0.14736815530258923 13.644792232659547 chrY 59373566 656694 0.011060376599242834 2.5196943639655243