BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5365339.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 = 114,630,740 number of mapped reads = 111,368,544 (97.15%) number of supplementary alignments = 913,788 (0.8%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 55,970,528 number of mapped paired reads (second in pair) = 55,398,016 number of mapped paired reads (both in pair) = 110,622,546 number of mapped paired reads (singletons) = 745,998 number of mapped bases = 14,670,441,295 bp number of sequenced bases = 14,664,808,217 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 47,729,748 duplication rate = 30.11% >>>>>>> Insert size mean insert size = 73,268.3006 std insert size = 2,655,252.5617 median insert size = 203 >>>>>>> Mapping quality mean mapping quality = 54.2316 >>>>>>> ACTG content number of A's = 4,380,875,607 bp (29.87%) number of C's = 2,906,227,013 bp (19.82%) number of T's = 4,325,434,774 bp (29.5%) number of G's = 3,051,404,524 bp (20.81%) number of N's = 866,299 bp (0.01%) GC percentage = 40.63% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 112,852,929 number of insertions = 4,451,521 mapped reads with insertion percentage = 3.87% number of deletions = 2,300,908 mapped reads with deletion percentage = 2% homopolymer indels = 49.96% >>>>>>> Coverage mean coverageData = 4.739X std coverageData = 53.0095X There is a 74.55% of reference with a coverageData >= 1X There is a 65.89% of reference with a coverageData >= 2X There is a 55.37% of reference with a coverageData >= 3X There is a 47.27% of reference with a coverageData >= 4X There is a 39.07% of reference with a coverageData >= 5X There is a 32.61% of reference with a coverageData >= 6X There is a 26.61% of reference with a coverageData >= 7X There is a 21.88% of reference with a coverageData >= 8X There is a 17.69% of reference with a coverageData >= 9X There is a 14.4% of reference with a coverageData >= 10X There is a 11.57% of reference with a coverageData >= 11X There is a 9.36% of reference with a coverageData >= 12X There is a 7.49% of reference with a coverageData >= 13X There is a 6.04% of reference with a coverageData >= 14X There is a 4.83% of reference with a coverageData >= 15X There is a 3.89% of reference with a coverageData >= 16X There is a 3.11% of reference with a coverageData >= 17X There is a 2.51% of reference with a coverageData >= 18X There is a 2.01% of reference with a coverageData >= 19X There is a 1.63% of reference with a coverageData >= 20X There is a 1.32% of reference with a coverageData >= 21X There is a 1.07% of reference with a coverageData >= 22X There is a 0.87% of reference with a coverageData >= 23X There is a 0.72% of reference with a coverageData >= 24X There is a 0.59% of reference with a coverageData >= 25X There is a 0.5% of reference with a coverageData >= 26X There is a 0.41% of reference with a coverageData >= 27X There is a 0.35% of reference with a coverageData >= 28X There is a 0.3% of reference with a coverageData >= 29X There is a 0.25% of reference with a coverageData >= 30X There is a 0.22% of reference with a coverageData >= 31X There is a 0.19% of reference with a coverageData >= 32X There is a 0.17% of reference with a coverageData >= 33X There is a 0.15% of reference with a coverageData >= 34X There is a 0.13% of reference with a coverageData >= 35X There is a 0.12% of reference with a coverageData >= 36X There is a 0.11% of reference with a coverageData >= 37X There is a 0.1% of reference with a coverageData >= 38X There is a 0.09% of reference with a coverageData >= 39X There is a 0.08% of reference with a coverageData >= 40X There is a 0.08% of reference with a coverageData >= 41X There is a 0.07% of reference with a coverageData >= 42X There is a 0.07% of reference with a coverageData >= 43X There is a 0.06% of reference with a coverageData >= 44X There is a 0.06% of reference with a coverageData >= 45X There is a 0.06% of reference with a coverageData >= 46X There is a 0.05% of reference with a coverageData >= 47X There is a 0.05% of reference with a coverageData >= 48X There is a 0.05% of reference with a coverageData >= 49X There is a 0.05% of reference with a coverageData >= 50X There is a 0.05% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1232772955 4.9459172862000615 143.45130102402533 chr2 243199373 1261600543 5.187515606793937 31.044666831938574 chr3 198022430 1018413300 5.142918910751676 6.883228812441928 chr4 191154276 965365824 5.050192149507553 25.121605486202256 chr5 180915260 917993248 5.074161505226259 6.393672341556286 chr6 171115067 882967079 5.160077919964816 20.412597544447337 chr7 159138663 806246742 5.06631592097767 33.779858744392875 chr8 146364022 748864835 5.116454336025283 19.532725649847205 chr9 141213431 629285066 4.4562692198874485 52.77642014596154 chr10 135534747 755121601 5.571424433322623 104.33556734784645 chr11 135006516 695096597 5.148615174989035 32.04009306000058 chr12 133851895 680363305 5.082956091133413 25.576986298622096 chr13 115169878 479024294 4.1592845483434475 4.938263595398136 chr14 107349540 450112601 4.192962550188851 5.5598119714465195 chr15 102531392 427175455 4.166289432606162 12.885156579219009 chr16 90354753 417245179 4.617855344034862 16.977050577775305 chr17 81195210 422186195 5.199644104621442 25.735768362353173 chr18 78077248 404993878 5.187092121894461 50.99780299060897 chr19 59128983 280529545 4.744366142742553 72.02308695579333 chr20 63025520 299539246 4.7526659994237255 10.316741997946265 chr21 48129895 201195342 4.180257239289634 18.60215786644162 chr22 51304566 178577105 3.4807253802712217 15.8740775218373 chrMT 16571 10028462 605.1814615895239 144.47284244747877 chrX 155270560 380357463 2.449643145487464 10.654759445447898 chrY 59373566 125385435 2.111805698178883 44.87203445899065