BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094090.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 = 431,074 number of mapped reads = 413,768 (95.99%) number of supplementary alignments = 23,971 (5.56%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 207,905 number of mapped paired reads (second in pair) = 205,863 number of mapped paired reads (both in pair) = 410,384 number of mapped paired reads (singletons) = 3,384 number of mapped bases = 49,514,328 bp number of sequenced bases = 48,490,861 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 401,792 duplication rate = 53.84% >>>>>>> Insert size mean insert size = 1,348,639.1097 std insert size = 10,360,852.6314 median insert size = 134 >>>>>>> Mapping quality mean mapping quality = 38.5816 >>>>>>> ACTG content number of A's = 13,869,490 bp (28.6%) number of C's = 10,446,821 bp (21.54%) number of T's = 13,048,071 bp (26.91%) number of G's = 11,126,066 bp (22.94%) number of N's = 413 bp (0%) GC percentage = 44.49% >>>>>>> Mismatches and indels general error rate = 0.0369 number of mismatches = 1,732,695 number of insertions = 33,918 mapped reads with insertion percentage = 8.12% number of deletions = 143,595 mapped reads with deletion percentage = 33.6% homopolymer indels = 26.83% >>>>>>> Coverage mean coverageData = 0.016X std coverageData = 4.1517X 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 0.01% of reference with a coverageData >= 16X There is a 0.01% 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 1502716 0.006028935831618249 3.155928419916823 chr2 243199373 2294156 0.009433231556892213 3.6895099322548828 chr3 198022430 565217 0.002854307969051789 1.1638118772192165 chr4 191154276 2654132 0.013884763948466421 4.761712670078166 chr5 180915260 1121371 0.006198321799941033 3.043194470048138 chr6 171115067 1521466 0.008891478854985925 3.6751860827383322 chr7 159138663 1384075 0.008697289357018162 2.9781033143688886 chr8 146364022 1096883 0.007494211931399371 2.404649544138626 chr9 141213431 785570 0.005562997757628309 2.1049349858235833 chr10 135534747 302105 0.0022289856047025343 0.5892227272507631 chr11 135006516 2200526 0.01629940587460238 4.719599537197213 chr12 133851895 1537582 0.01148718888141255 3.712141437666908 chr13 115169878 610251 0.005298703190429706 1.638009006582378 chr14 107349540 235389 0.002192734128157419 0.9066133525581597 chr15 102531392 432642 0.004219605250263256 1.4945283574528394 chr16 90354753 358942 0.003972585703377441 1.9096784578207433 chr17 81195210 401046 0.004939281516729867 1.6961498942115754 chr18 78077248 242660 0.003107947657171523 1.2827981553585006 chr19 59128983 108055 0.0018274456031148042 0.7445969536435644 chr20 63025520 240077 0.003809203002212437 1.46064527031648 chr21 48129895 95814 0.001990737773269607 0.5515811089706841 chr22 51304566 45723 8.912072270526565E-4 0.2161773437526665 chrMT 16571 6264 0.3780097761148995 2.679570610293227 chrX 155270560 28606459 0.18423620678639918 13.56715320235569 chrY 59373566 1165207 0.01962501292241736 4.318767369758034