BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5365359.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP102259/SRP102259.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 = 572,714,332 number of mapped reads = 456,903,566 (79.78%) number of supplementary alignments = 12,128,619 (2.12%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 225,430,078 number of mapped paired reads (second in pair) = 231,473,488 number of mapped paired reads (both in pair) = 441,043,066 number of mapped paired reads (singletons) = 15,860,500 number of mapped bases = 55,511,476,305 bp number of sequenced bases = 55,483,175,741 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 275,890,720 duplication rate = 47.73% >>>>>>> Insert size mean insert size = 122,773.4987 std insert size = 3,517,023.4434 median insert size = 140 >>>>>>> Mapping quality mean mapping quality = 52.5951 >>>>>>> ACTG content number of A's = 14,497,304,006 bp (26.13%) number of C's = 12,929,910,506 bp (23.3%) number of T's = 14,238,431,914 bp (25.66%) number of G's = 13,816,337,545 bp (24.9%) number of N's = 1,191,770 bp (0%) GC percentage = 48.21% >>>>>>> Mismatches and indels general error rate = 0.0115 number of mismatches = 619,075,600 number of insertions = 6,788,694 mapped reads with insertion percentage = 1.4% number of deletions = 15,299,017 mapped reads with deletion percentage = 3.24% homopolymer indels = 39.87% >>>>>>> Coverage mean coverageData = 17.9318X std coverageData = 139.65X There is a 49.69% of reference with a coverageData >= 1X There is a 45.83% of reference with a coverageData >= 2X There is a 39.37% of reference with a coverageData >= 3X There is a 37.26% of reference with a coverageData >= 4X There is a 34.05% of reference with a coverageData >= 5X There is a 32.46% of reference with a coverageData >= 6X There is a 30.35% of reference with a coverageData >= 7X There is a 29.06% of reference with a coverageData >= 8X There is a 27.51% of reference with a coverageData >= 9X There is a 26.42% of reference with a coverageData >= 10X There is a 25.21% of reference with a coverageData >= 11X There is a 24.28% of reference with a coverageData >= 12X There is a 23.29% of reference with a coverageData >= 13X There is a 22.49% of reference with a coverageData >= 14X There is a 21.65% of reference with a coverageData >= 15X There is a 20.95% of reference with a coverageData >= 16X There is a 20.23% of reference with a coverageData >= 17X There is a 19.61% of reference with a coverageData >= 18X There is a 18.98% of reference with a coverageData >= 19X There is a 18.42% of reference with a coverageData >= 20X There is a 17.87% of reference with a coverageData >= 21X There is a 17.37% of reference with a coverageData >= 22X There is a 16.87% of reference with a coverageData >= 23X There is a 16.42% of reference with a coverageData >= 24X There is a 15.97% of reference with a coverageData >= 25X There is a 15.56% of reference with a coverageData >= 26X There is a 15.16% of reference with a coverageData >= 27X There is a 14.78% of reference with a coverageData >= 28X There is a 14.41% of reference with a coverageData >= 29X There is a 14.06% of reference with a coverageData >= 30X There is a 13.73% of reference with a coverageData >= 31X There is a 13.41% of reference with a coverageData >= 32X There is a 13.1% of reference with a coverageData >= 33X There is a 12.8% of reference with a coverageData >= 34X There is a 12.51% of reference with a coverageData >= 35X There is a 12.24% of reference with a coverageData >= 36X There is a 11.97% of reference with a coverageData >= 37X There is a 11.72% of reference with a coverageData >= 38X There is a 11.47% of reference with a coverageData >= 39X There is a 11.23% of reference with a coverageData >= 40X There is a 11% of reference with a coverageData >= 41X There is a 10.78% of reference with a coverageData >= 42X There is a 10.56% of reference with a coverageData >= 43X There is a 10.35% of reference with a coverageData >= 44X There is a 10.15% of reference with a coverageData >= 45X There is a 9.95% of reference with a coverageData >= 46X There is a 9.76% of reference with a coverageData >= 47X There is a 9.57% of reference with a coverageData >= 48X There is a 9.39% of reference with a coverageData >= 49X There is a 9.22% of reference with a coverageData >= 50X There is a 9.05% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 4640131937 18.616330496524622 126.00739944295665 chr2 243199373 4721546140 19.414302272892783 260.91032694804335 chr3 198022430 3500063544 17.675086322291875 64.72898968630345 chr4 191154276 3000817342 15.698405522458728 111.23294387166985 chr5 180915260 3027881258 16.736461357654406 76.8031670435873 chr6 171115067 3041882011 17.77682155248199 139.3809283641248 chr7 159138663 2970351708 18.6651794856414 118.75982518183768 chr8 146364022 2676666743 18.287737016409675 95.87952408335448 chr9 141213431 2398642423 16.985936861770607 169.49114870209334 chr10 135534747 2820846359 20.812717191998004 78.5024270555035 chr11 135006516 2685832171 19.894092896968026 223.8331908178676 chr12 133851895 2465949616 18.42297126985016 60.209560184506465 chr13 115169878 1481904521 12.867118961435384 48.95454412914445 chr14 107349540 1674451954 15.598128822908789 64.39782884179236 chr15 102531392 1706800856 16.646617418400016 58.625731835844284 chr16 90354753 2113027915 23.385907712015992 119.18454668902018 chr17 81195210 2112085680 26.012441866952496 240.0556182379649 chr18 78077248 1453741142 18.619267190359988 247.31821328224737 chr19 59128983 1698247112 28.721060735984583 102.34533719711395 chr20 63025520 1570902357 24.924861500547713 93.18978300999532 chr21 48129895 802152491 16.666408497255187 168.66683627771545 chr22 51304566 1086666339 21.180694501927956 104.18651815927223 chrMT 16571 13757940 830.2419890169573 2550.0564954436622 chrX 155270560 1475824224 9.504855421401198 70.90437209179312 chrY 59373566 371302522 6.253667195936993 108.03924509203415