BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094061.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 = 642,056 number of mapped reads = 601,500 (93.68%) number of supplementary alignments = 37,511 (5.84%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 302,276 number of mapped paired reads (second in pair) = 299,224 number of mapped paired reads (both in pair) = 596,240 number of mapped paired reads (singletons) = 5,260 number of mapped bases = 76,795,192 bp number of sequenced bases = 75,276,955 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 568,965 duplication rate = 50.93% >>>>>>> Insert size mean insert size = 1,294,257.5649 std insert size = 10,245,046.7427 median insert size = 156 >>>>>>> Mapping quality mean mapping quality = 46.7658 >>>>>>> ACTG content number of A's = 20,882,527 bp (27.74%) number of C's = 16,887,239 bp (22.43%) number of T's = 19,746,936 bp (26.23%) number of G's = 17,759,427 bp (23.59%) number of N's = 826 bp (0%) GC percentage = 46.03% >>>>>>> Mismatches and indels general error rate = 0.0364 number of mismatches = 2,668,741 number of insertions = 41,430 mapped reads with insertion percentage = 6.8% number of deletions = 212,341 mapped reads with deletion percentage = 34.01% homopolymer indels = 29% >>>>>>> Coverage mean coverageData = 0.0248X std coverageData = 4.7879X There is a 0.03% of reference with a coverageData >= 1X There is a 0.02% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.02% 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 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1321214 0.005300745068153712 1.5039635737312267 chr2 243199373 3972485 0.016334273197324403 4.101443955753332 chr3 198022430 1192749 0.006023302511740715 1.39129160212477 chr4 191154276 1813160 0.009485322734815517 2.1720170805778243 chr5 180915260 1391930 0.0076938230639029565 2.5580233698778825 chr6 171115067 1876390 0.010965662071125508 3.50689030985645 chr7 159138663 1916353 0.012042032802550314 3.1308906318429153 chr8 146364022 1429335 0.009765617126864688 2.513675666302512 chr9 141213431 1127937 0.0079874626089922 2.6231571930386326 chr10 135534747 1304102 0.009621901607268283 2.1768463296211635 chr11 135006516 1881619 0.013937245814120557 3.162996944708783 chr12 133851895 2111963 0.015778357116273924 3.1039350821168328 chr13 115169878 1931170 0.016768012900039715 3.8033774484348157 chr14 107349540 334455 0.0031155699409610885 0.9253763505545917 chr15 102531392 1048339 0.010224566150433226 2.5412807436743634 chr16 90354753 489512 0.00541766740262131 1.6395524305299969 chr17 81195210 1123658 0.013838969072190342 2.5974692335940057 chr18 78077248 376199 0.004818292263579782 1.2306467903780616 chr19 59128983 205219 0.0034707006545334966 0.7604459355215644 chr20 63025520 606129 0.009617199509024281 2.8688685450612903 chr21 48129895 371262 0.007713750466316205 2.061036852046361 chr22 51304566 235601 0.00459220335281659 1.2911698248505348 chrMT 16571 5314524 320.71232876712327 1293.7415321766111 chrX 155270560 42298669 0.272419117957712 11.552244116305248 chrY 59373566 1121218 0.018884127660447413 3.3271489737336317