BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238643.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 3,798,311 number of mapped reads = 2,778,199 (73.14%) number of supplementary alignments = 24,620 (0.65%) number of secondary alignments = 0 number of mapped bases = 173,653,207 bp number of sequenced bases = 173,579,351 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,113,670 duplication rate = 20.62% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.2027 >>>>>>> ACTG content number of A's = 43,795,625 bp (25.23%) number of C's = 30,914,725 bp (17.81%) number of T's = 57,601,643 bp (33.18%) number of G's = 41,262,995 bp (23.77%) number of N's = 4,363 bp (0%) GC percentage = 41.58% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 933,685 number of insertions = 12,583 mapped reads with insertion percentage = 0.45% number of deletions = 41,787 mapped reads with deletion percentage = 1.49% homopolymer indels = 43.95% >>>>>>> Coverage mean coverageData = 0.0561X std coverageData = 0.9659X There is a 1.32% of reference with a coverageData >= 1X There is a 0.79% of reference with a coverageData >= 2X There is a 0.62% of reference with a coverageData >= 3X There is a 0.5% of reference with a coverageData >= 4X There is a 0.41% of reference with a coverageData >= 5X There is a 0.33% of reference with a coverageData >= 6X There is a 0.27% of reference with a coverageData >= 7X There is a 0.22% of reference with a coverageData >= 8X There is a 0.18% of reference with a coverageData >= 9X There is a 0.15% of reference with a coverageData >= 10X There is a 0.12% of reference with a coverageData >= 11X There is a 0.1% of reference with a coverageData >= 12X There is a 0.08% of reference with a coverageData >= 13X There is a 0.07% of reference with a coverageData >= 14X There is a 0.06% of reference with a coverageData >= 15X There is a 0.05% of reference with a coverageData >= 16X There is a 0.04% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% 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 21141165 0.08481890602792119 1.2899025138436198 chr2 243199373 15244837 0.06268452427301283 1.504979500985666 chr3 198022430 14491946 0.07318335604709023 0.8822681832178634 chr4 191154276 7454160 0.03899551794488761 0.6324746222364743 chr5 180915260 14171604 0.07833282830867888 0.8978442025479452 chr6 171115067 8460101 0.0494410056830355 0.833619423630233 chr7 159138663 10625816 0.06677080100892892 0.9293718573165799 chr8 146364022 6914525 0.047241971800966225 0.9432444086286594 chr9 141213431 6060894 0.042920095893711416 0.6936841250891355 chr10 135534747 5992611 0.04421457325625878 0.9088109059323878 chr11 135006516 9856712 0.0730091575728093 0.885445549359849 chr12 133851895 9264952 0.06921793673522515 0.859702175901627 chr13 115169878 3316346 0.028795254953730177 0.6696640019531713 chr14 107349540 4408708 0.04106871813330546 1.0099774127063181 chr15 102531392 3690337 0.03599226469099337 1.2910582643950725 chr16 90354753 4569457 0.0505724032027402 0.7309099494093332 chr17 81195210 4900549 0.060355149029111446 0.7985206000297238 chr18 78077248 6626453 0.08487047340602988 1.3526222798442702 chr19 59128983 2415036 0.04084352338683045 0.8479935151321208 chr20 63025520 1915876 0.030398416387520485 0.5401033627409536 chr21 48129895 4508945 0.09368283475374296 0.9984633965910564 chr22 51304566 2126085 0.04144046360318105 0.6283712069553042 chrMT 16571 114863 6.931567195703337 9.784088754340344 chrX 155270560 4597531 0.029609804975263825 0.6234172932878982 chrY 59373566 783698 0.013199442997915941 0.34464578770948573