BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124855.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 74,665,198 number of mapped reads = 68,450,221 (91.68%) number of supplementary alignments = 2,204,549 (2.95%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 35,253,107 number of mapped paired reads (second in pair) = 33,197,114 number of mapped paired reads (both in pair) = 65,604,178 number of mapped paired reads (singletons) = 2,846,043 number of mapped bases = 8,877,330,441 bp number of sequenced bases = 8,869,102,145 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 22,705,181 duplication rate = 20.37% >>>>>>> Insert size mean insert size = 186,412.4005 std insert size = 4,102,100.6301 median insert size = 258 >>>>>>> Mapping quality mean mapping quality = 53.0451 >>>>>>> ACTG content number of A's = 2,563,078,430 bp (28.9%) number of C's = 1,709,945,502 bp (19.28%) number of T's = 2,619,156,659 bp (29.53%) number of G's = 1,976,772,901 bp (22.29%) number of N's = 148,653 bp (0%) GC percentage = 41.57% >>>>>>> Mismatches and indels general error rate = 0.0141 number of mismatches = 118,536,678 number of insertions = 1,982,046 mapped reads with insertion percentage = 2.65% number of deletions = 3,603,291 mapped reads with deletion percentage = 5% homopolymer indels = 43.01% >>>>>>> Coverage mean coverageData = 2.8676X std coverageData = 39.2812X There is a 52.01% of reference with a coverageData >= 1X There is a 39.1% of reference with a coverageData >= 2X There is a 29.98% of reference with a coverageData >= 3X There is a 23.7% of reference with a coverageData >= 4X There is a 18.97% of reference with a coverageData >= 5X There is a 15.4% of reference with a coverageData >= 6X There is a 12.62% of reference with a coverageData >= 7X There is a 10.43% of reference with a coverageData >= 8X There is a 8.69% of reference with a coverageData >= 9X There is a 7.29% of reference with a coverageData >= 10X There is a 6.15% of reference with a coverageData >= 11X There is a 5.22% of reference with a coverageData >= 12X There is a 4.45% of reference with a coverageData >= 13X There is a 3.81% of reference with a coverageData >= 14X There is a 3.28% of reference with a coverageData >= 15X There is a 2.84% of reference with a coverageData >= 16X There is a 2.46% of reference with a coverageData >= 17X There is a 2.14% of reference with a coverageData >= 18X There is a 1.87% of reference with a coverageData >= 19X There is a 1.64% of reference with a coverageData >= 20X There is a 1.44% of reference with a coverageData >= 21X There is a 1.27% of reference with a coverageData >= 22X There is a 1.13% of reference with a coverageData >= 23X There is a 1% of reference with a coverageData >= 24X There is a 0.89% of reference with a coverageData >= 25X There is a 0.79% of reference with a coverageData >= 26X There is a 0.71% of reference with a coverageData >= 27X There is a 0.64% of reference with a coverageData >= 28X There is a 0.57% of reference with a coverageData >= 29X There is a 0.52% of reference with a coverageData >= 30X There is a 0.47% of reference with a coverageData >= 31X There is a 0.42% of reference with a coverageData >= 32X There is a 0.38% of reference with a coverageData >= 33X There is a 0.35% of reference with a coverageData >= 34X There is a 0.32% of reference with a coverageData >= 35X There is a 0.29% of reference with a coverageData >= 36X There is a 0.27% of reference with a coverageData >= 37X There is a 0.24% of reference with a coverageData >= 38X There is a 0.22% of reference with a coverageData >= 39X There is a 0.21% of reference with a coverageData >= 40X There is a 0.19% of reference with a coverageData >= 41X There is a 0.18% of reference with a coverageData >= 42X There is a 0.16% of reference with a coverageData >= 43X There is a 0.15% of reference with a coverageData >= 44X There is a 0.14% of reference with a coverageData >= 45X There is a 0.13% of reference with a coverageData >= 46X There is a 0.12% of reference with a coverageData >= 47X There is a 0.12% of reference with a coverageData >= 48X There is a 0.11% of reference with a coverageData >= 49X There is a 0.1% of reference with a coverageData >= 50X There is a 0.1% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 696310531 2.793616032756043 19.685814902000484 chr2 243199373 792573296 3.2589446519666807 48.44320486008733 chr3 198022430 627355279 3.168102113482801 6.386091344914395 chr4 191154276 460181747 2.407384007460027 60.199092617952765 chr5 180915260 470774700 2.602183475291139 6.681564321538952 chr6 171115067 522715860 3.0547623255174834 11.299357096222321 chr7 159138663 583704096 3.6678961918889565 22.024683385065472 chr8 146364022 533519786 3.6451566355562433 9.885200943278358 chr9 141213431 379258797 2.6857133511613354 33.42535144927847 chr10 135534747 450190689 3.3215887362079926 122.4445518254736 chr11 135006516 335126639 2.482299735814233 9.836025288351182 chr12 133851895 402784403 3.009179683261115 20.346133030889174 chr13 115169878 205534287 1.7846184312186213 3.9227195553435497 chr14 107349540 238418356 2.2209536808448362 6.080885079729196 chr15 102531392 242970231 2.369715520881644 9.44794784026776 chr16 90354753 363107463 4.018686908479513 58.81449545681662 chr17 81195210 233587612 2.876864435722255 22.822735858283824 chr18 78077248 175293896 2.2451341522693014 30.849040324597723 chr19 59128983 149428817 2.5271670409078406 12.39456841627002 chr20 63025520 209135792 3.318271582685871 21.85116950970036 chr21 48129895 127593842 2.6510309652659747 29.282633651887988 chr22 51304566 90609911 1.766117873407213 6.776637877631229 chrMT 16571 6742807 406.90404924265283 188.3610922690153 chrX 155270560 394705064 2.542047017799124 7.38996822647087 chrY 59373566 185706540 3.1277646351913577 90.79367400572612