BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716506.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 = 675,105 number of mapped reads = 607,091 (89.93%) number of supplementary alignments = 1,836 (0.27%) number of secondary alignments = 0 number of mapped bases = 34,493,127 bp number of sequenced bases = 34,482,384 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 14,570 duplication rate = 1.69% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.8096 >>>>>>> ACTG content number of A's = 8,562,195 bp (24.83%) number of C's = 6,248,320 bp (18.12%) number of T's = 11,357,232 bp (32.94%) number of G's = 8,313,993 bp (24.11%) number of N's = 644 bp (0%) GC percentage = 42.23% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 179,343 number of insertions = 2,585 mapped reads with insertion percentage = 0.42% number of deletions = 6,750 mapped reads with deletion percentage = 1.1% homopolymer indels = 42.73% >>>>>>> Coverage mean coverageData = 0.0111X std coverageData = 0.1384X There is a 1.05% of reference with a coverageData >= 1X There is a 0.04% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% 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 2883106 0.011567096557003161 0.18043925376237296 chr2 243199373 2750305 0.011308849056942264 0.20812207418374196 chr3 198022430 1976274 0.009980051249749839 0.10443904715398322 chr4 191154276 2158625 0.011292580240266244 0.12095808954714747 chr5 180915260 1947709 0.010765863531909912 0.10814745422344231 chr6 171115067 1818606 0.010627971176845578 0.11711670850785193 chr7 159138663 1959841 0.012315303918319333 0.16409807054822886 chr8 146364022 1811550 0.012377017078691648 0.16974565809646688 chr9 141213431 1142634 0.008091539111460298 0.10259694147917202 chr10 135534747 1534987 0.011325413106057593 0.14184963885534707 chr11 135006516 1240110 0.009185556643799326 0.11468204534457539 chr12 133851895 1726849 0.012901192022720337 0.11892095284208261 chr13 115169878 1048619 0.009104976216090114 0.10017122696404927 chr14 107349540 1160652 0.010811895421256578 0.10955010645047943 chr15 102531392 1274277 0.012428164439628402 0.11689105188686953 chr16 90354753 1186371 0.013130144907816858 0.12318367160367887 chr17 81195210 1499876 0.018472469004021295 0.14354251873603102 chr18 78077248 649302 0.008316148642943973 0.143318518750402 chr19 59128983 869477 0.01470475147526214 0.15868363467511762 chr20 63025520 1099905 0.01745174018397627 0.13946118527398998 chr21 48129895 440946 0.00916158242190223 0.106780133303229 chr22 51304566 324675 0.006328384105227593 0.08349454175314339 chrMT 16571 5523 0.3332931024078209 0.6271771419823242 chrX 155270560 1857912 0.011965642424423535 0.11991329218638959 chrY 59373566 124996 0.0021052466345039813 0.09165189877190077