BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10174051.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 = 1,790,574 number of mapped reads = 1,747,286 (97.58%) number of supplementary alignments = 194,362 (10.85%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 873,111 number of mapped paired reads (second in pair) = 874,175 number of mapped paired reads (both in pair) = 1,718,202 number of mapped paired reads (singletons) = 29,084 number of mapped bases = 206,989,199 bp number of sequenced bases = 206,877,365 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,328,209 duplication rate = 62.7% >>>>>>> Insert size mean insert size = 1,178,673.2117 std insert size = 9,772,142.7551 median insert size = 199 >>>>>>> Mapping quality mean mapping quality = 52.6281 >>>>>>> ACTG content number of A's = 62,011,820 bp (29.98%) number of C's = 40,826,009 bp (19.73%) number of T's = 61,771,017 bp (29.86%) number of G's = 42,265,871 bp (20.43%) number of N's = 2,648 bp (0%) GC percentage = 40.16% >>>>>>> Mismatches and indels general error rate = 0.0103 number of mismatches = 2,078,597 number of insertions = 20,872 mapped reads with insertion percentage = 1.16% number of deletions = 47,692 mapped reads with deletion percentage = 2.66% homopolymer indels = 42.48% >>>>>>> Coverage mean coverageData = 0.0669X std coverageData = 1.1272X There is a 1.54% of reference with a coverageData >= 1X There is a 1.18% of reference with a coverageData >= 2X There is a 0.88% of reference with a coverageData >= 3X There is a 0.71% of reference with a coverageData >= 4X There is a 0.53% of reference with a coverageData >= 5X There is a 0.42% of reference with a coverageData >= 6X There is a 0.3% of reference with a coverageData >= 7X There is a 0.24% of reference with a coverageData >= 8X There is a 0.17% of reference with a coverageData >= 9X There is a 0.14% of reference with a coverageData >= 10X There is a 0.1% of reference with a coverageData >= 11X There is a 0.08% of reference with a coverageData >= 12X There is a 0.06% of reference with a coverageData >= 13X There is a 0.05% of reference with a coverageData >= 14X There is a 0.04% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% 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% 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 18012858 0.07226805665611562 1.0348832043265448 chr2 243199373 21337808 0.08773792356775525 2.946548195923391 chr3 198022430 15885241 0.0802194024182008 0.7913443757827752 chr4 191154276 11779109 0.061620954793603466 0.7260036382539806 chr5 180915260 14134260 0.07812641122700208 0.7775029864165505 chr6 171115067 11401212 0.06662891935752215 0.7216299297169033 chr7 159138663 14590173 0.09168213886527374 0.9977430127351005 chr8 146364022 8524972 0.058244996847654266 0.7235806934805564 chr9 141213431 8364936 0.05923612181053798 0.7301300672936537 chr10 135534747 10321276 0.07615225046312293 1.0435430526460387 chr11 135006516 9908076 0.07338961328355441 0.7457824633825603 chr12 133851895 6249736 0.0466914271180098 0.5917902808199544 chr13 115169878 6478809 0.056254370608953844 0.6661243215698507 chr14 107349540 5293073 0.04930689968489851 0.6133209483946318 chr15 102531392 6811766 0.06643590677087462 0.7028802486965109 chr16 90354753 8240215 0.09119846744531525 0.9328022846151295 chr17 81195210 4764195 0.058675813511659125 0.678574666209025 chr18 78077248 3186196 0.04080825184822088 0.848498280786093 chr19 59128983 3913897 0.0661925303196911 0.923511017377607 chr20 63025520 5115117 0.08115945731189525 0.7770106333537851 chr21 48129895 2994220 0.06221123067066737 0.6951240364392531 chr22 51304566 1993406 0.038854358499007674 0.5220232668526545 chrMT 16571 740622 44.693862772313075 37.79223816988223 chrX 155270560 6669924 0.0429567845958693 0.5700894441633619 chrY 59373566 278102 0.004683936282351644 0.24981708423134427