BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1548983.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 6,937,993 number of mapped reads = 3,076,419 (44.34%) number of secondary alignments = 0 number of mapped bases = 121,895,931 bp number of sequenced bases = 121,880,773 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 66,169 duplication rate = 1.52% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.9923 >>>>>>> ACTG content number of A's = 36,813,161 bp (30.2%) number of C's = 23,746,811 bp (19.48%) number of T's = 37,233,599 bp (30.55%) number of G's = 24,080,480 bp (19.76%) number of N's = 6,722 bp (0.01%) GC percentage = 39.24% >>>>>>> Mismatches and indels general error rate = 0.0028 number of mismatches = 339,188 number of insertions = 4,013 mapped reads with insertion percentage = 0.13% number of deletions = 11,992 mapped reads with deletion percentage = 0.39% homopolymer indels = 46.63% >>>>>>> Coverage mean coverageData = 0.0394X std coverageData = 0.2968X There is a 3.49% of reference with a coverageData >= 1X There is a 0.35% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% 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 9869230 0.03959560846991832 0.4902186536905464 chr2 243199373 10839082 0.044568708653702 0.28122498033331267 chr3 198022430 8271096 0.04176848046961145 0.22516654018830562 chr4 191154276 8629294 0.045143086414661214 0.23726934816313783 chr5 180915260 8023811 0.044351211721996256 0.2329471193536464 chr6 171115067 7274147 0.0425102659136381 0.25331802323748737 chr7 159138663 6735033 0.042321789520124345 0.4221776097884073 chr8 146364022 6579146 0.044950568521545546 0.43642719771993277 chr9 141213431 5346007 0.03785763834319697 0.25540507754555675 chr10 135534747 5768232 0.042559064208088276 0.25872908127424193 chr11 135006516 5440563 0.040298521591357855 0.273273213652547 chr12 133851895 5756341 0.043005300746769407 0.23187381578315813 chr13 115169878 3787998 0.03289052715676229 0.19859926042816156 chr14 107349540 3820607 0.03559034347049834 0.22951874278458578 chr15 102531392 3573850 0.034856154103515925 0.20415772697478185 chr16 90354753 3204782 0.03546888119986339 0.21199886771317064 chr17 81195210 3048459 0.03754481329625233 0.22144589817514318 chr18 78077248 3269885 0.04188012620526789 0.39436888469801323 chr19 59128983 2145882 0.03629154250801168 0.4067685757075124 chr20 63025520 2410485 0.03824617393081406 0.21845951494705312 chr21 48129895 1637043 0.03401301831221531 0.21944738956712018 chr22 51304566 1220680 0.023792814074287266 0.1843489440361593 chrMT 16571 1146 0.06915696095588679 0.26783676946231544 chrX 155270560 4244101 0.0273335846795426 0.20494933400387472 chrY 59373566 999031 0.016826191642253727 0.18473500587605393