BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2093985.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 = 360,064 number of mapped reads = 343,151 (95.3%) number of supplementary alignments = 21,095 (5.86%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 172,576 number of mapped paired reads (second in pair) = 170,575 number of mapped paired reads (both in pair) = 339,800 number of mapped paired reads (singletons) = 3,351 number of mapped bases = 43,887,305 bp number of sequenced bases = 43,143,603 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 323,021 duplication rate = 49.44% >>>>>>> Insert size mean insert size = 1,030,877.3101 std insert size = 9,162,734.3483 median insert size = 163 >>>>>>> Mapping quality mean mapping quality = 40.5092 >>>>>>> ACTG content number of A's = 11,297,824 bp (26.19%) number of C's = 10,284,784 bp (23.84%) number of T's = 10,601,846 bp (24.57%) number of G's = 10,958,632 bp (25.4%) number of N's = 517 bp (0%) GC percentage = 49.24% >>>>>>> Mismatches and indels general error rate = 0.0337 number of mismatches = 1,400,062 number of insertions = 23,269 mapped reads with insertion percentage = 6.67% number of deletions = 112,956 mapped reads with deletion percentage = 31.6% homopolymer indels = 29.83% >>>>>>> Coverage mean coverageData = 0.0142X std coverageData = 2.847X There is a 0.02% of reference with a coverageData >= 1X There is a 0.01% of reference with a coverageData >= 2X There is a 0.01% 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% 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 843581 0.003384468999978941 1.1318500516359482 chr2 243199373 2419411 0.009948261667598953 3.2213324783982142 chr3 198022430 810215 0.004091531449240371 1.4609520850451747 chr4 191154276 1117611 0.005846643995554669 2.035156946755919 chr5 180915260 419396 0.0023181902952796795 1.3297805798289757 chr6 171115067 782155 0.0045709300397258415 1.358796308740035 chr7 159138663 847988 0.005328610810309498 1.5183858783815667 chr8 146364022 446747 0.0030523006535034957 0.9764222878137877 chr9 141213431 504915 0.003575545161847955 1.0825046319749618 chr10 135534747 631657 0.004660480164544078 1.3577596500983762 chr11 135006516 1119156 0.008289644330944737 2.1880879112337053 chr12 133851895 1011383 0.007555985666097592 1.8293728155497 chr13 115169878 860285 0.007469704882382527 2.2475146721400265 chr14 107349540 179711 0.0016740733122843376 0.5679978197537608 chr15 102531392 658229 0.006419780197658879 1.7092236446261553 chr16 90354753 260148 0.002879184451978968 0.8498521127849337 chr17 81195210 1211666 0.014922875376515437 3.5244223682617717 chr18 78077248 208163 0.0026661159983507616 0.7064772762263924 chr19 59128983 146769 0.002482183737203801 0.6762189882407756 chr20 63025520 426459 0.006766449527112192 2.4611983355203564 chr21 48129895 87566 0.001819368191017246 0.3409168940036052 chr22 51304566 163654 0.0031898525367118394 0.9457179377259638 chrMT 16571 1274325 76.90091123046285 355.69894928365886 chrX 155270560 26869704 0.1730508603820325 9.346998925344426 chrY 59373566 586411 0.009876634325787339 1.4818196271444697