BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094075.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 = 426,792 number of mapped reads = 411,080 (96.32%) number of supplementary alignments = 17,954 (4.21%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 206,430 number of mapped paired reads (second in pair) = 204,650 number of mapped paired reads (both in pair) = 407,948 number of mapped paired reads (singletons) = 3,132 number of mapped bases = 54,848,258 bp number of sequenced bases = 53,662,583 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 393,314 duplication rate = 50.56% >>>>>>> Insert size mean insert size = 572,752.0917 std insert size = 6,833,088.2576 median insert size = 168 >>>>>>> Mapping quality mean mapping quality = 40.7904 >>>>>>> ACTG content number of A's = 14,080,823 bp (26.24%) number of C's = 12,708,791 bp (23.68%) number of T's = 13,499,669 bp (25.16%) number of G's = 13,372,640 bp (24.92%) number of N's = 660 bp (0%) GC percentage = 48.6% >>>>>>> Mismatches and indels general error rate = 0.0404 number of mismatches = 2,089,595 number of insertions = 34,563 mapped reads with insertion percentage = 8.26% number of deletions = 162,838 mapped reads with deletion percentage = 37.68% homopolymer indels = 28.22% >>>>>>> Coverage mean coverageData = 0.0177X std coverageData = 4.579X 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% 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 357801 0.0014355069550659213 0.5018932528535087 chr2 243199373 2470080 0.010156605132366029 4.057363681151089 chr3 198022430 1006969 0.005085125962750786 1.8449906178789608 chr4 191154276 707681 0.003702145799762282 1.5483197098842125 chr5 180915260 427565 0.00236334403189648 1.1335093953127482 chr6 171115067 1282714 0.0074962072159314875 3.730803808670719 chr7 159138663 1750660 0.011000846475629872 3.7143288401811216 chr8 146364022 764492 0.005223223505022293 1.7389257983617146 chr9 141213431 637332 0.004513253417091749 1.871319375172882 chr10 135534747 1132780 0.00835785674945776 2.7155458492807245 chr11 135006516 1892413 0.014017197510674225 3.9084236818020983 chr12 133851895 1364789 0.010196262070103677 3.486204850774192 chr13 115169878 1506009 0.013076413956086677 3.5312800895574443 chr14 107349540 279251 0.002601324607445919 1.0707644585976621 chr15 102531392 946448 0.009230811964398181 2.84493977011269 chr16 90354753 342878 0.0037947976018483497 1.2753438171125275 chr17 81195210 1023444 0.012604733702887153 3.913511340289121 chr18 78077248 158115 0.0020251097989519304 0.6248199716224622 chr19 59128983 233491 0.003948841805718187 0.9539657524972068 chr20 63025520 348708 0.005532806393346695 1.8706312410860266 chr21 48129895 703045 0.014607241507591072 6.36536613550596 chr22 51304566 71684 0.0013972245667179019 0.297088616558358 chrMT 16571 1362694 82.23366121537626 384.2186124673923 chrX 155270560 33571326 0.21621179185545542 16.138900446214496 chrY 59373566 505889 0.008520441571590967 1.9632257244562061