BamQC report ----------------------------------- >>>>>>> Input bam file = SRR926909.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 = 33,595,756 number of mapped reads = 32,608,521 (97.06%) number of supplementary alignments = 1,243,771 (3.7%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 16,383,621 number of mapped paired reads (second in pair) = 16,224,900 number of mapped paired reads (both in pair) = 32,089,492 number of mapped paired reads (singletons) = 519,029 number of mapped bases = 2,914,272,556 bp number of sequenced bases = 2,912,053,834 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,588,383 duplication rate = 8.58% >>>>>>> Insert size mean insert size = 435,865.3906 std insert size = 6,498,383.9464 median insert size = 176 >>>>>>> Mapping quality mean mapping quality = 52.3451 >>>>>>> ACTG content number of A's = 822,038,297 bp (28.23%) number of C's = 567,794,195 bp (19.5%) number of T's = 828,925,316 bp (28.47%) number of G's = 693,053,242 bp (23.8%) number of N's = 242,784 bp (0.01%) GC percentage = 43.3% >>>>>>> Mismatches and indels general error rate = 0.0096 number of mismatches = 27,077,751 number of insertions = 483,621 mapped reads with insertion percentage = 1.46% number of deletions = 1,491,560 mapped reads with deletion percentage = 4.46% homopolymer indels = 51.61% >>>>>>> Coverage mean coverageData = 0.9414X std coverageData = 2.9997X There is a 35.87% of reference with a coverageData >= 1X There is a 20.02% of reference with a coverageData >= 2X There is a 11.77% of reference with a coverageData >= 3X There is a 7.47% of reference with a coverageData >= 4X There is a 4.94% of reference with a coverageData >= 5X There is a 3.39% of reference with a coverageData >= 6X There is a 2.38% of reference with a coverageData >= 7X There is a 1.72% of reference with a coverageData >= 8X There is a 1.26% of reference with a coverageData >= 9X There is a 0.93% of reference with a coverageData >= 10X There is a 0.71% of reference with a coverageData >= 11X There is a 0.54% of reference with a coverageData >= 12X There is a 0.42% of reference with a coverageData >= 13X There is a 0.33% of reference with a coverageData >= 14X There is a 0.26% of reference with a coverageData >= 15X There is a 0.21% of reference with a coverageData >= 16X There is a 0.17% of reference with a coverageData >= 17X There is a 0.13% of reference with a coverageData >= 18X There is a 0.11% of reference with a coverageData >= 19X There is a 0.09% of reference with a coverageData >= 20X There is a 0.08% of reference with a coverageData >= 21X There is a 0.06% of reference with a coverageData >= 22X There is a 0.05% of reference with a coverageData >= 23X There is a 0.05% of reference with a coverageData >= 24X There is a 0.04% of reference with a coverageData >= 25X There is a 0.04% of reference with a coverageData >= 26X There is a 0.03% of reference with a coverageData >= 27X There is a 0.03% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 242851581 0.974326884425295 2.8419424584760353 chr2 243199373 249786069 1.0270835237720781 4.838498419838696 chr3 198022430 196965091 0.9946605089130559 2.06736771336139 chr4 191154276 172666088 0.9032813265448479 2.328403648381351 chr5 180915260 175168394 0.9682344872400482 2.0130125058153543 chr6 171115067 166825945 0.9749342820875031 2.1955152838887817 chr7 159138663 150252241 0.9441592518594931 2.3806241296835324 chr8 146364022 146596402 1.0015876852577883 2.178188875751863 chr9 141213431 122880776 0.8701776816116025 2.871597351136123 chr10 135534747 142097463 1.0484209115762764 6.340411185095085 chr11 135006516 140290093 1.0391357184567298 2.4361128447909906 chr12 133851895 131805594 0.9847122000028464 2.3870123841630897 chr13 115169878 86886622 0.754421412168206 1.8368923181635113 chr14 107349540 87470250 0.814817185057337 1.9251116242192994 chr15 102531392 87210170 0.8505704282255331 2.01593440110416 chr16 90354753 92808951 1.0271618029878296 4.824501155791219 chr17 81195210 77935865 0.9598579152637206 2.1981152790932845 chr18 78077248 76613208 0.9812488268029119 2.9179675610722198 chr19 59128983 49801700 0.8422553115787565 2.197766590945272 chr20 63025520 70054293 1.111522649872623 2.3369681906867417 chr21 48129895 36588824 0.7602099277382591 2.6959512433536466 chr22 51304566 38147093 0.7435418711075346 1.973700930556146 chrMT 16571 2046890 123.52241868324181 84.81165047990015 chrX 155270560 165942139 1.0687289271063363 2.2030754185124315 chrY 59373566 4580814 0.07715241493158757 1.8534380288633159