BamQC report ----------------------------------- >>>>>>> Input bam file = SRR926904.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 23,046,832 number of mapped reads = 20,085,920 (87.15%) number of supplementary alignments = 353,579 (1.53%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 10,084,420 number of mapped paired reads (second in pair) = 10,001,500 number of mapped paired reads (both in pair) = 19,768,300 number of mapped paired reads (singletons) = 317,620 number of mapped bases = 1,852,479,194 bp number of sequenced bases = 1,851,034,046 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,632,415 duplication rate = 6.52% >>>>>>> Insert size mean insert size = 295,889.8271 std insert size = 5,449,860.0058 median insert size = 187 >>>>>>> Mapping quality mean mapping quality = 49.0728 >>>>>>> ACTG content number of A's = 528,954,651 bp (28.58%) number of C's = 364,422,385 bp (19.69%) number of T's = 535,623,715 bp (28.94%) number of G's = 421,877,277 bp (22.79%) number of N's = 156,018 bp (0.01%) GC percentage = 42.48% >>>>>>> Mismatches and indels general error rate = 0.0107 number of mismatches = 19,255,507 number of insertions = 310,269 mapped reads with insertion percentage = 1.52% number of deletions = 1,010,044 mapped reads with deletion percentage = 4.89% homopolymer indels = 52.64% >>>>>>> Coverage mean coverageData = 0.5984X std coverageData = 2.7678X There is a 23.06% of reference with a coverageData >= 1X There is a 12.89% of reference with a coverageData >= 2X There is a 7.62% of reference with a coverageData >= 3X There is a 4.84% of reference with a coverageData >= 4X There is a 3.18% of reference with a coverageData >= 5X There is a 2.16% of reference with a coverageData >= 6X There is a 1.49% of reference with a coverageData >= 7X There is a 1.05% of reference with a coverageData >= 8X There is a 0.75% of reference with a coverageData >= 9X There is a 0.55% of reference with a coverageData >= 10X There is a 0.4% of reference with a coverageData >= 11X There is a 0.3% of reference with a coverageData >= 12X There is a 0.22% of reference with a coverageData >= 13X There is a 0.17% of reference with a coverageData >= 14X There is a 0.13% of reference with a coverageData >= 15X There is a 0.1% of reference with a coverageData >= 16X There is a 0.08% of reference with a coverageData >= 17X There is a 0.06% of reference with a coverageData >= 18X There is a 0.05% of reference with a coverageData >= 19X There is a 0.04% of reference with a coverageData >= 20X There is a 0.03% 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 0.02% 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 0.01% 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 206489138 0.8284398135962919 2.2761110938247078 chr2 243199373 190269570 0.7823604462993414 3.0109679734472854 chr3 198022430 20191382 0.10196512586983202 0.7522574413322717 chr4 191154276 191823261 1.0034997124521556 2.004380587925245 chr5 180915260 201228082 1.11227810191357 2.1165304875891913 chr6 171115067 180533111 1.055039244440117 2.556886028060147 chr7 159138663 115084225 0.7231694852180579 1.7196324175668551 chr8 146364022 7200392 0.049195095226339164 0.5597035928059019 chr9 141213431 17974233 0.1272841603855656 1.6038397053732325 chr10 135534747 18884483 0.1393331482737781 9.640069792838744 chr11 135006516 29415835 0.21788455751276478 0.9196649791655528 chr12 133851895 152829116 1.1417777536881342 2.219328892111239 chr13 115169878 34263769 0.2975063410243432 1.0023022869550198 chr14 107349540 8896229 0.0828716080199319 0.5558642456920249 chr15 102531392 102435565 0.9990653886762797 2.1280930918007788 chr16 90354753 14063340 0.15564582418813097 1.397634541945872 chr17 81195210 89312270 1.0999696903302547 2.4242170261544227 chr18 78077248 86473374 1.1075361416426972 2.442040491336605 chr19 59128983 8344239 0.1411192714070526 1.1156309069731642 chr20 63025520 80818543 1.282314576698455 2.4220238109212144 chr21 48129895 37493720 0.7790110491618567 1.946102190276038 chr22 51304566 2861536 0.05577546450738907 0.484396478465124 chrMT 16571 32404 1.9554643654577273 2.243609895869087 chrX 155270560 53234788 0.342851780788322 1.135927102848098 chrY 59373566 2326589 0.03918560323629543 0.8283558584628095