BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234047.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 3,009,227 number of mapped reads = 2,762,971 (91.82%) number of supplementary alignments = 18,129 (0.6%) number of secondary alignments = 0 number of mapped bases = 179,645,480 bp number of sequenced bases = 179,568,493 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 180,203 duplication rate = 4.87% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.2133 >>>>>>> ACTG content number of A's = 46,317,008 bp (25.79%) number of C's = 33,531,564 bp (18.67%) number of T's = 56,565,394 bp (31.5%) number of G's = 43,086,298 bp (23.99%) number of N's = 68,229 bp (0.04%) GC percentage = 42.67% >>>>>>> Mismatches and indels general error rate = 0.0068 number of mismatches = 1,202,183 number of insertions = 13,170 mapped reads with insertion percentage = 0.47% number of deletions = 43,017 mapped reads with deletion percentage = 1.54% homopolymer indels = 43.88% >>>>>>> Coverage mean coverageData = 0.058X std coverageData = 0.7228X There is a 4.89% of reference with a coverageData >= 1X There is a 0.62% of reference with a coverageData >= 2X There is a 0.1% of reference with a coverageData >= 3X There is a 0.03% 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% 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 15403003 0.0617972502463695 1.6764063527813302 chr2 243199373 13935982 0.05730270529932657 0.7719964476943647 chr3 198022430 19142269 0.09666717553157993 0.36132992015957527 chr4 191154276 6733169 0.035223742523028886 0.25298822160625206 chr5 180915260 8726116 0.04823316728505932 0.2584165118567572 chr6 171115067 10913380 0.0637780190332392 0.3901162999384799 chr7 159138663 13439043 0.08444863584156165 1.3178504617409155 chr8 146364022 8418894 0.057520242235485984 0.5955937213876831 chr9 141213431 7821967 0.055391098032311105 0.4776495022789944 chr10 135534747 7182733 0.05299550970497625 0.6490968944475077 chr11 135006516 8271518 0.06126754652345817 0.43768564384397224 chr12 133851895 6436130 0.0480839662374597 0.2660113488093284 chr13 115169878 8885121 0.07714795877442884 0.3286415466940155 chr14 107349540 7033556 0.06552013171178936 0.35085992555361156 chr15 102531392 3123675 0.030465547566154178 0.2349329650395473 chr16 90354753 5831361 0.06453850856080587 0.37221297563430783 chr17 81195210 4650105 0.057270681361622194 0.30102333616323146 chr18 78077248 3479172 0.044560638202821905 1.1573803544030317 chr19 59128983 6128776 0.1036509625068302 0.9839650793760907 chr20 63025520 4020761 0.06379576082831209 0.34819144286667947 chr21 48129895 2837448 0.058953961981425475 0.3014583733147733 chr22 51304566 1555674 0.030322330375039133 0.19600443471390344 chrMT 16571 68569 4.137891497193893 3.1629713479544925 chrX 155270560 5193505 0.033448098596411326 0.28548257568602764 chrY 59373566 413553 0.006965271380196365 0.1591719033285531