BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081024.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 = 2,601,484 number of mapped reads = 1,809,678 (69.56%) number of supplementary alignments = 6,730 (0.26%) number of secondary alignments = 0 number of mapped bases = 112,288,910 bp number of sequenced bases = 112,250,253 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 51,959 duplication rate = 2.29% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8396 >>>>>>> ACTG content number of A's = 31,669,611 bp (28.21%) number of C's = 22,308,282 bp (19.87%) number of T's = 32,578,002 bp (29.02%) number of G's = 25,692,934 bp (22.89%) number of N's = 1,424 bp (0%) GC percentage = 42.76% >>>>>>> Mismatches and indels general error rate = 0.0077 number of mismatches = 849,733 number of insertions = 7,246 mapped reads with insertion percentage = 0.4% number of deletions = 22,236 mapped reads with deletion percentage = 1.22% homopolymer indels = 46.68% >>>>>>> Coverage mean coverageData = 0.0363X std coverageData = 0.2755X There is a 3.17% of reference with a coverageData >= 1X There is a 0.35% of reference with a coverageData >= 2X There is a 0.05% 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% 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 8413386 0.033754724326243504 0.3654309237551652 chr2 243199373 9683384 0.03981664870492902 0.3235262428676611 chr3 198022430 7493148 0.03783989520783075 0.216125343729586 chr4 191154276 7466004 0.03905747836893798 0.22823136837360952 chr5 180915260 7118202 0.03934550352468885 0.2221933337947535 chr6 171115067 6520234 0.03810438270757303 0.25493863914294507 chr7 159138663 6345495 0.039873999695473124 0.3910512289455708 chr8 146364022 5145496 0.03515547010589802 0.2602310458979399 chr9 141213431 4496243 0.03184005209816055 0.26838711096563095 chr10 135534747 5557585 0.04100487235203235 0.25847165239264697 chr11 135006516 5253915 0.03891601054278002 0.27816193209495527 chr12 133851895 4952197 0.03699758602595802 0.21621342299379176 chr13 115169878 3722661 0.03232321736070607 0.2004998704742757 chr14 107349540 3482743 0.032443017454942054 0.21273360937362062 chr15 102531392 3434500 0.03349705814976159 0.21405336273341463 chr16 90354753 3282767 0.03633197912676492 0.23174543332695124 chr17 81195210 3048867 0.037549838223215386 0.2370754663033608 chr18 78077248 3049475 0.03905715273161267 0.5112209905741658 chr19 59128983 2062921 0.03488849114824113 0.29363161919294284 chr20 63025520 2331926 0.03699971059342311 0.22016151286872615 chr21 48129895 1533897 0.03186994278711807 0.21178246190065 chr22 51304566 1283692 0.025021008851336936 0.17588309908222097 chrMT 16571 35357 2.1336672500150864 1.8815399459577444 chrX 155270560 6285205 0.040479051534302445 0.2538999965243737 chrY 59373566 289610 0.004877759910866732 0.09834374432040639