BamQC report ----------------------------------- >>>>>>> Input bam file = SRR927063.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 = 21,039,588 number of mapped reads = 20,405,798 (96.99%) number of supplementary alignments = 361,664 (1.72%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 10,235,023 number of mapped paired reads (second in pair) = 10,170,775 number of mapped paired reads (both in pair) = 20,030,588 number of mapped paired reads (singletons) = 375,210 number of mapped bases = 1,842,578,503 bp number of sequenced bases = 1,841,294,224 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,593,765 duplication rate = 6.25% >>>>>>> Insert size mean insert size = 178,594.7275 std insert size = 4,123,275.5112 median insert size = 183 >>>>>>> Mapping quality mean mapping quality = 53.0888 >>>>>>> ACTG content number of A's = 520,246,617 bp (28.25%) number of C's = 361,188,527 bp (19.62%) number of T's = 531,918,002 bp (28.89%) number of G's = 427,691,643 bp (23.23%) number of N's = 249,435 bp (0.01%) GC percentage = 42.84% >>>>>>> Mismatches and indels general error rate = 0.0108 number of mismatches = 19,322,710 number of insertions = 290,849 mapped reads with insertion percentage = 1.4% number of deletions = 884,047 mapped reads with deletion percentage = 4.23% homopolymer indels = 51.64% >>>>>>> Coverage mean coverageData = 0.5952X std coverageData = 2.259X There is a 29.17% of reference with a coverageData >= 1X There is a 13.76% of reference with a coverageData >= 2X There is a 6.73% of reference with a coverageData >= 3X There is a 3.63% of reference with a coverageData >= 4X There is a 2.05% of reference with a coverageData >= 5X There is a 1.2% of reference with a coverageData >= 6X There is a 0.73% of reference with a coverageData >= 7X There is a 0.46% of reference with a coverageData >= 8X There is a 0.3% of reference with a coverageData >= 9X There is a 0.2% of reference with a coverageData >= 10X There is a 0.13% of reference with a coverageData >= 11X There is a 0.09% of reference with a coverageData >= 12X There is a 0.07% of reference with a coverageData >= 13X There is a 0.05% of reference with a coverageData >= 14X There is a 0.04% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% 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 0.01% 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% 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 146866691 0.5892329993432595 3.398662490538062 chr2 243199373 160933725 0.661735772649381 3.6117146008456373 chr3 198022430 123301817 0.6226659121393471 1.2969729732238575 chr4 191154276 116773838 0.6108879196612897 2.0648314565686303 chr5 180915260 117858329 0.6514559855260413 1.3367858503155519 chr6 171115067 105733565 0.6179091464809466 1.3744837600427975 chr7 159138663 97328614 0.6115962781464364 1.8109691202187237 chr8 146364022 93007563 0.6354537250964585 1.5273210645909956 chr9 141213431 75524084 0.5348222436433826 2.486050393044183 chr10 135534747 84755382 0.6253406146838493 3.797348579703381 chr11 135006516 85991898 0.6369462789484917 1.8513391519946547 chr12 133851895 81682199 0.6102431273012608 1.2953424011170833 chr13 115169878 56946908 0.4944600879059714 1.1555171818543801 chr14 107349540 54769813 0.5102007237292306 1.2263374045680089 chr15 102531392 56496082 0.5510125328250688 1.2697421765621144 chr16 90354753 58357064 0.645866012162083 3.059980331197395 chr17 81195210 49747254 0.6126870538298995 1.758671105428812 chr18 78077248 46824873 0.5997249416372872 2.6640787947166586 chr19 59128983 30558616 0.516812812423985 2.044995579269575 chr20 63025520 44537636 0.7066603496488406 1.5084893234161025 chr21 48129895 22830034 0.4743420695183316 1.8612429341331387 chr22 51304566 21727597 0.4235022083609478 1.1575723672459712 chrMT 16571 123522 7.454106571721683 4.461090480634714 chrX 155270560 105582000 0.6799872429132735 1.5527568402099832 chrY 59373566 4319399 0.07274952964758762 2.6383834988690578