BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716252.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 3,895,609 number of mapped reads = 3,694,772 (94.84%) number of supplementary alignments = 75,664 (1.94%) number of secondary alignments = 0 number of mapped bases = 288,471,559 bp number of sequenced bases = 288,357,144 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 304,224 duplication rate = 6.24% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.6754 >>>>>>> ACTG content number of A's = 69,468,310 bp (24.09%) number of C's = 59,292,774 bp (20.56%) number of T's = 86,073,518 bp (29.85%) number of G's = 73,511,811 bp (25.49%) number of N's = 10,731 bp (0%) GC percentage = 46.06% >>>>>>> Mismatches and indels general error rate = 0.0068 number of mismatches = 1,899,541 number of insertions = 22,077 mapped reads with insertion percentage = 0.59% number of deletions = 55,269 mapped reads with deletion percentage = 1.47% homopolymer indels = 39.1% >>>>>>> Coverage mean coverageData = 0.0932X std coverageData = 0.6913X There is a 6.63% of reference with a coverageData >= 1X There is a 1.62% of reference with a coverageData >= 2X There is a 0.52% of reference with a coverageData >= 3X There is a 0.2% of reference with a coverageData >= 4X There is a 0.09% of reference with a coverageData >= 5X There is a 0.05% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% 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% 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 32838238 0.131747868343325 1.3668771335430432 chr2 243199373 27827943 0.11442440273067644 0.7487683008835307 chr3 198022430 19133154 0.09662114539246892 0.42020151733922356 chr4 191154276 13648729 0.07140164104934801 0.5837377625055944 chr5 180915260 17501251 0.09673728462706795 0.4325357489260644 chr6 171115067 17423316 0.10182222001526026 0.46511266458971506 chr7 159138663 17835426 0.1120747508102415 0.9222046490126448 chr8 146364022 17927130 0.12248317417787276 0.7812499816598851 chr9 141213431 8785275 0.062212743772226596 0.48394154603799583 chr10 135534747 15610838 0.11517960040165937 0.9613244387213934 chr11 135006516 8775834 0.0650030402976994 0.5300966607824712 chr12 133851895 10137332 0.07573543878478523 0.3721944531308288 chr13 115169878 5499159 0.04774824021260143 0.2848805872264697 chr14 107349540 5617923 0.052332995558248316 0.3522699597528964 chr15 102531392 5957151 0.05810075220669978 0.31984530341985123 chr16 90354753 8795547 0.09734459680278247 0.4665623966759052 chr17 81195210 5812943 0.07159219121423542 0.436417318441904 chr18 78077248 8535216 0.10931758250495714 0.7558043668378525 chr19 59128983 7358080 0.12444117295235739 0.9850882191378801 chr20 63025520 7636887 0.12117134456010835 0.5049332443165943 chr21 48129895 6059473 0.12589832161487158 0.6122237896030807 chr22 51304566 4622230 0.09009393043106534 0.4324555044785367 chrMT 16571 167867 10.130167159495505 8.276416811592734 chrX 155270560 14078140 0.09066844352206883 0.4540372568820679 chrY 59373566 886477 0.014930499542506845 0.5154056796887244