BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708510.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP051114/SRP051114.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 = 3,067,162 number of mapped reads = 2,032,942 (66.28%) number of supplementary alignments = 381 (0.01%) number of secondary alignments = 0 number of mapped bases = 96,622,611 bp number of sequenced bases = 96,600,586 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 113,481 duplication rate = 4.19% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 40.5431 >>>>>>> ACTG content number of A's = 27,592,802 bp (28.56%) number of C's = 17,701,383 bp (18.32%) number of T's = 31,160,852 bp (32.26%) number of G's = 20,144,118 bp (20.85%) number of N's = 1,431 bp (0%) GC percentage = 39.18% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 493,520 number of insertions = 4,954 mapped reads with insertion percentage = 0.24% number of deletions = 14,577 mapped reads with deletion percentage = 0.72% homopolymer indels = 48.69% >>>>>>> Coverage mean coverageData = 0.0312X std coverageData = 0.3375X There is a 2.55% of reference with a coverageData >= 1X There is a 0.41% of reference with a coverageData >= 2X There is a 0.08% 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 7753941 0.031109013766509333 0.4898725678756982 chr2 243199373 8476223 0.0348529804803403 0.47404177622142124 chr3 198022430 6812543 0.03440288557210413 0.226364438014499 chr4 191154276 6676777 0.03492873473570636 0.23959253719873302 chr5 180915260 6177057 0.03414337187476612 0.22463419729104514 chr6 171115067 5867574 0.034290224133214406 0.2935830028295866 chr7 159138663 5442806 0.0342016572050753 0.40184660226313884 chr8 146364022 5176341 0.035366211786664346 0.7102270110304575 chr9 141213431 4086482 0.02893833802536814 0.2534748582482896 chr10 135534747 4494843 0.03316376869763146 0.25403112658885263 chr11 135006516 4442581 0.03290641912424434 0.291459104126799 chr12 133851895 4430128 0.03309723780899777 0.2230753876575745 chr13 115169878 3319619 0.028823673842912293 0.22909936962567704 chr14 107349540 2990396 0.027856626120614954 0.20766208440517336 chr15 102531392 2752202 0.026842530334514527 0.20078597238015478 chr16 90354753 2524577 0.027940721613172913 0.20748952007423113 chr17 81195210 2375888 0.029261430569611186 0.24971161629635555 chr18 78077248 2634297 0.03373962412199774 0.3783421483106265 chr19 59128983 1718716 0.029067234252955102 0.34037048427894545 chr20 63025520 1858769 0.029492323109749828 0.2094832281856207 chr21 48129895 1293336 0.02687178104169976 0.22279494223766255 chr22 51304566 959805 0.01870798400282735 0.1770366062904234 chrMT 16571 127499 7.6941041578661515 5.098671498793905 chrX 155270560 3438879 0.02214765632325922 0.19921426275555915 chrY 59373566 791332 0.013328018734801949 0.15447289875747472