BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173871.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 2,599,832 number of mapped reads = 2,542,400 (97.79%) number of supplementary alignments = 238,646 (9.18%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,269,062 number of mapped paired reads (second in pair) = 1,273,338 number of mapped paired reads (both in pair) = 2,504,246 number of mapped paired reads (singletons) = 38,154 number of mapped bases = 301,304,161 bp number of sequenced bases = 301,151,862 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,972,747 duplication rate = 66.03% >>>>>>> Insert size mean insert size = 800,803.7627 std insert size = 7,871,968.1975 median insert size = 197 >>>>>>> Mapping quality mean mapping quality = 52.8738 >>>>>>> ACTG content number of A's = 91,103,290 bp (30.25%) number of C's = 58,723,908 bp (19.5%) number of T's = 90,794,531 bp (30.15%) number of G's = 60,526,646 bp (20.1%) number of N's = 3,487 bp (0%) GC percentage = 39.6% >>>>>>> Mismatches and indels general error rate = 0.01 number of mismatches = 2,911,216 number of insertions = 31,603 mapped reads with insertion percentage = 1.2% number of deletions = 60,325 mapped reads with deletion percentage = 2.31% homopolymer indels = 44.25% >>>>>>> Coverage mean coverageData = 0.0973X std coverageData = 1.5593X There is a 2.04% of reference with a coverageData >= 1X There is a 1.62% of reference with a coverageData >= 2X There is a 1.24% of reference with a coverageData >= 3X There is a 1.03% of reference with a coverageData >= 4X There is a 0.78% of reference with a coverageData >= 5X There is a 0.63% of reference with a coverageData >= 6X There is a 0.46% of reference with a coverageData >= 7X There is a 0.38% of reference with a coverageData >= 8X There is a 0.28% of reference with a coverageData >= 9X There is a 0.23% of reference with a coverageData >= 10X There is a 0.17% of reference with a coverageData >= 11X There is a 0.15% of reference with a coverageData >= 12X There is a 0.11% of reference with a coverageData >= 13X There is a 0.09% of reference with a coverageData >= 14X There is a 0.07% of reference with a coverageData >= 15X There is a 0.06% of reference with a coverageData >= 16X There is a 0.04% of reference with a coverageData >= 17X There is a 0.04% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.03% 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 0.01% 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% 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 26974069 0.10822066918742 1.0255043649369475 chr2 243199373 22939961 0.09432574071644502 4.1537950594940725 chr3 198022430 18681656 0.09434111075194866 0.8877739263454081 chr4 191154276 19887127 0.10403705015732946 1.0858238921701866 chr5 180915260 14938722 0.08257303446928689 0.8221745194672555 chr6 171115067 14659239 0.08566889670796786 0.862001060537831 chr7 159138663 27458849 0.1725466865333662 1.8307150027770178 chr8 146364022 28951989 0.1978080993155545 1.4473000834569558 chr9 141213431 10293503 0.07289322925664203 0.9128660709237157 chr10 135534747 13793314 0.10176957795184434 1.9566008998918025 chr11 135006516 12179144 0.09021152727176517 0.8716913077108923 chr12 133851895 11329576 0.0846426268376701 0.8362369261374993 chr13 115169878 7755777 0.06734206143727964 0.7461333709235507 chr14 107349540 10268840 0.09565797859962884 0.896204775221515 chr15 102531392 7072105 0.06897502181575765 0.7480110214323223 chr16 90354753 6681230 0.07394442216006057 0.934324697517821 chr17 81195210 7436874 0.09159252128296731 0.9020778065518886 chr18 78077248 5189324 0.06646397168096908 0.9519811708259786 chr19 59128983 3881210 0.06563972189408365 0.8046737701130484 chr20 63025520 11806619 0.18733076696550857 1.2450958597032848 chr21 48129895 3594686 0.07468717727308567 0.828319348486735 chr22 51304566 3076140 0.059958406041286855 0.6693314881544693 chrMT 16571 565086 34.100899161185204 35.86151295357172 chrX 155270560 11346679 0.07307682151722773 0.7762324094129076 chrY 59373566 542442 0.009136085914058118 0.4426731608658757