BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3085011.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 = 2,444,583 number of mapped reads = 2,210,637 (90.43%) number of supplementary alignments = 18,848 (0.77%) number of secondary alignments = 0 number of mapped bases = 146,607,718 bp number of sequenced bases = 146,552,315 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 70,262 duplication rate = 2.3% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.6303 >>>>>>> ACTG content number of A's = 40,583,181 bp (27.69%) number of C's = 28,871,368 bp (19.7%) number of T's = 43,668,330 bp (29.8%) number of G's = 33,423,690 bp (22.81%) number of N's = 5,746 bp (0%) GC percentage = 42.51% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 1,281,526 number of insertions = 10,967 mapped reads with insertion percentage = 0.49% number of deletions = 31,745 mapped reads with deletion percentage = 1.42% homopolymer indels = 45.98% >>>>>>> Coverage mean coverageData = 0.0474X std coverageData = 0.3932X There is a 4.1% of reference with a coverageData >= 1X There is a 0.46% of reference with a coverageData >= 2X There is a 0.07% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% 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 10778887 0.04324517610730446 0.6374052102325574 chr2 243199373 15237780 0.06265550692846564 0.5210164510518728 chr3 198022430 8066773 0.04073666301337682 0.23119897683218 chr4 191154276 7958198 0.04163233052657425 0.2402366991470533 chr5 180915260 7540373 0.041679032492891975 0.22791857059395132 chr6 171115067 10030139 0.05861634031327002 0.3950638277182138 chr7 159138663 13256932 0.08330428162513845 0.4639000230257726 chr8 146364022 9099664 0.06217145358303969 0.5563885202827049 chr9 141213431 5113730 0.036212773556928875 0.37447544024981133 chr10 135534747 9632375 0.07106941366113297 0.4819390261548969 chr11 135006516 6159035 0.04562027954265556 0.37967892564924033 chr12 133851895 6213219 0.04641861065919164 0.24822917094137634 chr13 115169878 2841468 0.024671971954333405 0.17270957651548022 chr14 107349540 5040243 0.04695169629976989 0.26725890224689985 chr15 102531392 2873568 0.028026226348316818 0.19860383051745195 chr16 90354753 4197386 0.046454512470417576 0.26373134217739097 chr17 81195210 2863706 0.035269395817807477 0.23763750631502284 chr18 78077248 3626539 0.046448089461349866 0.6658805767272284 chr19 59128983 2870895 0.04855309282082528 0.46289348705088096 chr20 63025520 3638471 0.05773012265507686 0.2749619998784822 chr21 48129895 1383420 0.02874346598927756 0.2077173164894329 chr22 51304566 1061933 0.02069860604609734 0.15797675739886038 chrMT 16571 15102 0.9113511556333354 1.1929939570816988 chrX 155270560 6790622 0.04373412448567198 0.27802141412326836 chrY 59373566 317260 0.005343455368673662 0.11896457888866391