BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094014.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP024468/ERP024468.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 = 28,166 number of mapped reads = 8,617 (30.59%) number of supplementary alignments = 29 (0.1%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 4,248 number of mapped paired reads (second in pair) = 4,369 number of mapped paired reads (both in pair) = 8,336 number of mapped paired reads (singletons) = 281 number of mapped bases = 1,238,467 bp number of sequenced bases = 1,237,086 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 8,278 duplication rate = 32.61% >>>>>>> Insert size mean insert size = 73,787.9048 std insert size = 2,549,813.0499 median insert size = 237 >>>>>>> Mapping quality mean mapping quality = 5.0905 >>>>>>> ACTG content number of A's = 320,204 bp (25.88%) number of C's = 250,586 bp (20.26%) number of T's = 354,542 bp (28.66%) number of G's = 311,747 bp (25.2%) number of N's = 7 bp (0%) GC percentage = 45.46% >>>>>>> Mismatches and indels general error rate = 0.0272 number of mismatches = 33,324 number of insertions = 96 mapped reads with insertion percentage = 0.97% number of deletions = 1,081 mapped reads with deletion percentage = 12.34% homopolymer indels = 85.22% >>>>>>> Coverage mean coverageData = 0.0004X std coverageData = 0.9613X There is a 0% of reference with a coverageData >= 1X There is a 0% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% 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 570 2.286854884104782E-6 0.002008004250087913 chr2 243199373 35096 1.4430958257445836E-4 0.15404507192411307 chr3 198022430 13723 6.930023028199381E-5 0.07486696375057834 chr4 191154276 141 7.376240958376469E-7 8.588501334623755E-4 chr5 180915260 469 2.592373910304747E-6 0.001934444989073157 chr6 171115067 260 1.519445391679039E-6 0.0013802711514849999 chr7 159138663 1161 7.295524406912983E-6 0.003477975930455496 chr8 146364022 30 2.0496840405219255E-7 4.527343172768615E-4 chr9 141213431 286 2.0253031030738145E-6 0.0014231300015181871 chr10 135534747 119 8.780036310541089E-7 9.370180682162606E-4 chr11 135006516 918 6.799671802507665E-6 0.0029763712199437175 chr12 133851895 1560 1.165467250202173E-5 0.007087629559402441 chr13 115169878 194 1.6844682252767517E-6 0.0016772694343178867 chr14 107349540 257 2.394048451441897E-6 0.0018888564097448326 chr15 102531392 100 9.753110540038314E-7 0.0012647170344921553 chr16 90354753 7677 8.496509309255707E-5 0.04785937641762906 chr17 81195210 459 5.653042833438081E-6 0.0030086934374865685 chr18 78077248 99 1.2679750187916459E-6 0.0011260432545115652 chr19 59128983 84 1.4206231147253116E-6 0.0011847822435661918 chr20 63025520 1004 1.593005499994288E-5 0.009326328071510473 chr21 48129895 240 4.986505788138536E-6 0.002757607017265385 chr22 51304566 34 6.627090462084798E-7 8.140691659958629E-4 chrMT 16571 1164751 70.28851608231247 408.9605980244618 chrX 155270560 9115 5.87039809735986E-5 0.03042050346760022 chrY 59373566 120 2.0211014443700418E-6 0.0014216530376709338