BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081177.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,817,408 number of mapped reads = 2,523,506 (89.57%) number of supplementary alignments = 26,842 (0.95%) number of secondary alignments = 0 number of mapped bases = 169,110,508 bp number of sequenced bases = 169,047,635 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 124,551 duplication rate = 3.78% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.7344 >>>>>>> ACTG content number of A's = 47,244,213 bp (27.95%) number of C's = 31,059,739 bp (18.37%) number of T's = 53,753,236 bp (31.8%) number of G's = 36,940,134 bp (21.85%) number of N's = 50,313 bp (0.03%) GC percentage = 40.23% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 1,401,944 number of insertions = 13,349 mapped reads with insertion percentage = 0.52% number of deletions = 39,123 mapped reads with deletion percentage = 1.54% homopolymer indels = 47.15% >>>>>>> Coverage mean coverageData = 0.0546X std coverageData = 0.4792X There is a 4.58% of reference with a coverageData >= 1X There is a 0.64% of reference with a coverageData >= 2X There is a 0.11% of reference with a coverageData >= 3X There is a 0.03% 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% 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 12057114 0.04837345620896166 0.7829080241439954 chr2 243199373 14844617 0.06103887858296411 0.5396826712845442 chr3 198022430 12011131 0.06065540656177182 0.28090255930979435 chr4 191154276 10315305 0.05396324485045786 0.279268211198807 chr5 180915260 11802966 0.06524030090109591 0.29409698641172793 chr6 171115067 10609053 0.06199952573434109 0.357963959210711 chr7 159138663 9047374 0.0568521428384754 0.8424289660938438 chr8 146364022 8153373 0.05570612838174124 0.5770720035282952 chr9 141213431 7891457 0.05588319003452299 0.471323182686768 chr10 135534747 9024687 0.06658578113551944 0.3936594089160292 chr11 135006516 6647729 0.04924006038345586 0.47242819246862433 chr12 133851895 7068183 0.05280599874958812 0.27309980548189494 chr13 115169878 5543803 0.04813587629223676 0.2511304149762368 chr14 107349540 5967128 0.055585967112667646 0.3065347403506156 chr15 102531392 4119090 0.040173940094366416 0.23985708961714325 chr16 90354753 3332528 0.036882708317513745 0.26887440412057384 chr17 81195210 4612292 0.056804976549725036 0.36676878887774916 chr18 78077248 4726316 0.06053384463550764 0.9329543135493122 chr19 59128983 2820638 0.04770313739372111 0.6085126409386918 chr20 63025520 3652594 0.0579542064865153 0.28532207412855104 chr21 48129895 2179278 0.045279093170679054 0.2676712672636601 chr22 51304566 1801791 0.0351195057375595 0.21243967610139633 chrMT 16571 197681 11.929334379337396 6.73642448165667 chrX 155270560 10295165 0.06630468132529438 0.3497764365894604 chrY 59373566 389215 0.006555358322254048 0.13263069948830214