BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9717083.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 = 1,100,840 number of mapped reads = 1,006,537 (91.43%) number of supplementary alignments = 16,589 (1.51%) number of secondary alignments = 0 number of mapped bases = 80,325,690 bp number of sequenced bases = 80,289,234 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 34,059 duplication rate = 2.01% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4318 >>>>>>> ACTG content number of A's = 20,792,347 bp (25.9%) number of C's = 15,403,557 bp (19.19%) number of T's = 24,294,747 bp (30.26%) number of G's = 19,793,125 bp (24.65%) number of N's = 5,458 bp (0.01%) GC percentage = 43.84% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 652,576 number of insertions = 7,467 mapped reads with insertion percentage = 0.73% number of deletions = 21,081 mapped reads with deletion percentage = 2.06% homopolymer indels = 43.58% >>>>>>> Coverage mean coverageData = 0.0259X std coverageData = 0.3134X There is a 2.34% of reference with a coverageData >= 1X There is a 0.17% of reference with a coverageData >= 2X There is a 0.02% 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 6008217 0.024105123493353302 0.5434638982191053 chr2 243199373 6924241 0.02847145909376995 0.4031266799479601 chr3 198022430 5345419 0.026994007699026823 0.17849991971268578 chr4 191154276 5354424 0.02801100823922976 0.18833042660037425 chr5 180915260 4836756 0.026734925511535067 0.17961484609150946 chr6 171115067 4619287 0.026995209019203433 0.20742699905989195 chr7 159138663 4533944 0.02849052464390756 0.4008111498451654 chr8 146364022 4205187 0.028731015604367582 0.3928164465815963 chr9 141213431 3342996 0.0236733572460257 0.346594248882961 chr10 135534747 3898865 0.028766534680586375 0.2920653240577726 chr11 135006516 3670437 0.027187109991046655 0.2957600595605971 chr12 133851895 3745085 0.02797931997899619 0.1832274126511254 chr13 115169878 2460029 0.02136000352453269 0.15588974992580149 chr14 107349540 2372985 0.022105218149979962 0.20636570341937388 chr15 102531392 2206158 0.021516902842789846 0.15822816915988636 chr16 90354753 2336110 0.025854865653830075 0.19528573843368105 chr17 81195210 2175800 0.026797147270140688 0.19242922891264766 chr18 78077248 2301100 0.02947209409839855 0.6320166377698337 chr19 59128983 1667285 0.028197423926604657 0.3930257179766816 chr20 63025520 1612572 0.02558601658502778 0.183939844324097 chr21 48129895 1034241 0.02148853638679245 0.16614728825576097 chr22 51304566 875688 0.017068422331065036 0.14052018230207589 chrMT 16571 14244 0.8595739544988232 1.1627469116971245 chrX 155270560 4577134 0.029478440729524 0.24852432250126183 chrY 59373566 207486 0.0034945854523880204 0.1105126628722181