BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094144.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 = 429,402 number of mapped reads = 393,441 (91.63%) number of supplementary alignments = 22,415 (5.22%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 197,616 number of mapped paired reads (second in pair) = 195,825 number of mapped paired reads (both in pair) = 390,006 number of mapped paired reads (singletons) = 3,435 number of mapped bases = 49,811,403 bp number of sequenced bases = 48,690,462 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 364,525 duplication rate = 47.89% >>>>>>> Insert size mean insert size = 1,078,563.5137 std insert size = 9,408,547.2375 median insert size = 157 >>>>>>> Mapping quality mean mapping quality = 44.4672 >>>>>>> ACTG content number of A's = 13,381,312 bp (27.48%) number of C's = 10,860,469 bp (22.31%) number of T's = 12,763,515 bp (26.21%) number of G's = 11,684,590 bp (24%) number of N's = 576 bp (0%) GC percentage = 46.3% >>>>>>> Mismatches and indels general error rate = 0.0399 number of mismatches = 1,872,197 number of insertions = 32,112 mapped reads with insertion percentage = 8.01% number of deletions = 148,708 mapped reads with deletion percentage = 36.58% homopolymer indels = 28.98% >>>>>>> Coverage mean coverageData = 0.0161X std coverageData = 2.853X There is a 0.03% of reference with a coverageData >= 1X There is a 0.02% of reference with a coverageData >= 2X There is a 0.02% 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 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 838850 0.003365488104440871 1.0451455002784 chr2 243199373 2228062 0.009161462764133032 2.5900958234217923 chr3 198022430 725839 0.0036654383041355466 0.9914505306395208 chr4 191154276 1129914 0.005911005621448928 1.5606718606946486 chr5 180915260 1052537 0.005817845327143769 1.8258070421510586 chr6 171115067 629746 0.0036802486831858 1.1278071592949312 chr7 159138663 1086626 0.006828170976904588 1.73747009806582 chr8 146364022 1096783 0.007493528703385864 2.2350870182323335 chr9 141213431 818391 0.005795418992404483 2.132964849407304 chr10 135534747 736001 0.0054303491635248335 1.2084130564509694 chr11 135006516 852694 0.006315947002143215 1.4257081623915024 chr12 133851895 1140246 0.008518713911371968 2.01462109260531 chr13 115169878 889030 0.007719292712978301 1.5587013276645114 chr14 107349540 205822 0.0019173067718781095 0.5771235139886961 chr15 102531392 520317 0.005074709216861115 1.228012910592332 chr16 90354753 235074 0.0026016782979861614 0.752853524032943 chr17 81195210 762662 0.00939294325367223 1.8297197341934437 chr18 78077248 213444 0.0027337541405147887 0.6950080329709675 chr19 59128983 171463 0.002899813108573168 0.7338770666799856 chr20 63025520 270518 0.004292197827165885 1.4675979333925664 chr21 48129895 294631 0.0061215799452710214 1.7541577036572644 chr22 51304566 117699 0.002294123294990937 0.4531149826394621 chrMT 16571 2550057 153.88672982921972 612.86680481966 chrX 155270560 31239706 0.20119529420129612 8.479699329679203 chrY 59373566 5291 8.911373118468242E-5 0.03197656922627539