BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094104.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 = 469,218 number of mapped reads = 437,446 (93.23%) number of supplementary alignments = 29,433 (6.27%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 219,705 number of mapped paired reads (second in pair) = 217,741 number of mapped paired reads (both in pair) = 433,906 number of mapped paired reads (singletons) = 3,540 number of mapped bases = 53,885,129 bp number of sequenced bases = 52,847,868 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 420,348 duplication rate = 52.36% >>>>>>> Insert size mean insert size = 1,663,545.7463 std insert size = 11,539,229.4062 median insert size = 145 >>>>>>> Mapping quality mean mapping quality = 41.8516 >>>>>>> ACTG content number of A's = 15,376,872 bp (29.1%) number of C's = 11,231,427 bp (21.25%) number of T's = 14,413,406 bp (27.27%) number of G's = 11,825,591 bp (22.38%) number of N's = 572 bp (0%) GC percentage = 43.63% >>>>>>> Mismatches and indels general error rate = 0.0349 number of mismatches = 1,778,601 number of insertions = 35,116 mapped reads with insertion percentage = 7.94% number of deletions = 139,727 mapped reads with deletion percentage = 30.99% homopolymer indels = 26.36% >>>>>>> Coverage mean coverageData = 0.0174X std coverageData = 3.6281X 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 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% 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 1368137 0.005489001369428885 2.3386833984929942 chr2 243199373 2556651 0.010512572332988704 3.4410871869559565 chr3 198022430 947573 0.004785180143481726 1.5733721317658365 chr4 191154276 2779562 0.014540935511167953 4.175108407009748 chr5 180915260 1245552 0.006884726031402768 3.0202759654809697 chr6 171115067 1292297 0.007552210466656334 2.9169566198200645 chr7 159138663 1673927 0.0105186694951685 2.926667121684001 chr8 146364022 1123600 0.007676749959768118 2.6298137106470216 chr9 141213431 922933 0.0065357310098923945 2.754238567103176 chr10 135534747 1110144 0.008190844226831367 2.5944390695261457 chr11 135006516 1678703 0.0124342368778704 3.3279057289396943 chr12 133851895 1653996 0.012356911345932009 2.9373208728645976 chr13 115169878 1712582 0.01487005135144799 4.0424538632665366 chr14 107349540 269561 0.0025110587339265728 0.8338527897718699 chr15 102531392 458943 0.004476121810576804 1.0066518318848718 chr16 90354753 247828 0.0027428330195313575 0.9547253808262024 chr17 81195210 435735 0.005366511152566759 2.0818199133939594 chr18 78077248 212537 0.0027221374400901014 0.7644562283836206 chr19 59128983 116610 0.0019721293024776024 0.6567460418433702 chr20 63025520 303123 0.004809527949947894 1.9010345015227057 chr21 48129895 116061 0.0024114118678214445 0.6063675121357397 chr22 51304566 77370 0.0015080529089750024 0.4386281616751696 chrMT 16571 188802 11.393518797899945 51.47812939948526 chrX 155270560 30595857 0.19704866782215508 11.143674167753504 chrY 59373566 797045 0.013424240006065999 2.6385805556889217