BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716313.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 = 1,650,750 number of mapped reads = 1,506,259 (91.25%) number of supplementary alignments = 28,351 (1.72%) number of secondary alignments = 0 number of mapped bases = 118,879,015 bp number of sequenced bases = 118,823,659 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 54,095 duplication rate = 2.5% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.3691 >>>>>>> ACTG content number of A's = 31,189,037 bp (26.25%) number of C's = 22,790,056 bp (19.18%) number of T's = 36,966,366 bp (31.11%) number of G's = 27,869,789 bp (23.45%) number of N's = 8,411 bp (0.01%) GC percentage = 42.63% >>>>>>> Mismatches and indels general error rate = 0.0071 number of mismatches = 820,543 number of insertions = 10,054 mapped reads with insertion percentage = 0.66% number of deletions = 28,957 mapped reads with deletion percentage = 1.89% homopolymer indels = 43.46% >>>>>>> Coverage mean coverageData = 0.0384X std coverageData = 0.3759X There is a 3.35% of reference with a coverageData >= 1X There is a 0.34% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.02% 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% 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 11501560 0.04614455905407754 0.7900186686725486 chr2 243199373 9730180 0.040009066964165244 0.40476889071885963 chr3 198022430 7658479 0.03867480567731645 0.21681965192959748 chr4 191154276 7568766 0.039595065087636334 0.274067587652417 chr5 180915260 6969782 0.038525119439896886 0.2186469553817793 chr6 171115067 6615203 0.038659383512966744 0.23813410223548515 chr7 159138663 6260192 0.03933797030832162 0.4444882823308217 chr8 146364022 5847828 0.03995399907772417 0.4188027129291675 chr9 141213431 4800921 0.03399762307311972 0.2986296611146791 chr10 135534747 5463857 0.04031333013075975 0.35703658813616085 chr11 135006516 6722490 0.04979381884056618 0.42067758238262126 chr12 133851895 5092480 0.038045632450702326 0.21530828887958228 chr13 115169878 4160583 0.03612561784601352 0.21023829519591922 chr14 107349540 3464277 0.03227099995025596 0.21357172009262784 chr15 102531392 3303534 0.032219732274774926 0.19799084607645637 chr16 90354753 2643708 0.029259202335487542 0.2037652156508487 chr17 81195210 3728754 0.045923324787262694 0.27906192082036685 chr18 78077248 2980685 0.03817610221097957 0.5314660626055869 chr19 59128983 2200811 0.037220511639782475 0.5254275276852801 chr20 63025520 2445406 0.03880025107289872 0.22910044776712163 chr21 48129895 1542656 0.032051929471277676 0.22942580465123572 chr22 51304566 1293340 0.02520906228891986 0.17445002623468908 chrMT 16571 17010 1.0264920644499427 1.1055970406815427 chrX 155270560 6515999 0.041965450501369995 0.26520869373632916 chrY 59373566 350514 0.0059035362639326735 0.18598280777367882