BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472399.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 32,608,772 number of mapped reads = 32,237,253 (98.86%) number of supplementary alignments = 48,630 (0.15%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 16,225,312 number of mapped paired reads (second in pair) = 16,011,941 number of mapped paired reads (both in pair) = 31,957,060 number of mapped paired reads (singletons) = 280,193 number of mapped bases = 3,174,756,617 bp number of sequenced bases = 3,174,305,600 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 20,285,849 duplication rate = 51.3% >>>>>>> Insert size mean insert size = 44,694.6653 std insert size = 2,081,458.7619 median insert size = 235 >>>>>>> Mapping quality mean mapping quality = 54.7562 >>>>>>> ACTG content number of A's = 893,629,043 bp (28.15%) number of C's = 694,077,500 bp (21.87%) number of T's = 898,096,794 bp (28.29%) number of G's = 688,065,451 bp (21.68%) number of N's = 436,812 bp (0.01%) GC percentage = 43.54% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 16,884,753 number of insertions = 156,192 mapped reads with insertion percentage = 0.48% number of deletions = 190,960 mapped reads with deletion percentage = 0.58% homopolymer indels = 45.72% >>>>>>> Coverage mean coverageData = 1.0255X std coverageData = 19.636X There is a 8.49% of reference with a coverageData >= 1X There is a 3.25% of reference with a coverageData >= 2X There is a 1.3% of reference with a coverageData >= 3X There is a 0.97% of reference with a coverageData >= 4X There is a 0.77% of reference with a coverageData >= 5X There is a 0.71% of reference with a coverageData >= 6X There is a 0.67% of reference with a coverageData >= 7X There is a 0.64% of reference with a coverageData >= 8X There is a 0.62% of reference with a coverageData >= 9X There is a 0.61% of reference with a coverageData >= 10X There is a 0.59% of reference with a coverageData >= 11X There is a 0.58% of reference with a coverageData >= 12X There is a 0.57% of reference with a coverageData >= 13X There is a 0.56% of reference with a coverageData >= 14X There is a 0.55% of reference with a coverageData >= 15X There is a 0.54% of reference with a coverageData >= 16X There is a 0.53% of reference with a coverageData >= 17X There is a 0.52% of reference with a coverageData >= 18X There is a 0.51% of reference with a coverageData >= 19X There is a 0.5% of reference with a coverageData >= 20X There is a 0.5% of reference with a coverageData >= 21X There is a 0.49% of reference with a coverageData >= 22X There is a 0.48% of reference with a coverageData >= 23X There is a 0.48% of reference with a coverageData >= 24X There is a 0.47% of reference with a coverageData >= 25X There is a 0.47% of reference with a coverageData >= 26X There is a 0.46% of reference with a coverageData >= 27X There is a 0.46% of reference with a coverageData >= 28X There is a 0.45% of reference with a coverageData >= 29X There is a 0.45% of reference with a coverageData >= 30X There is a 0.44% of reference with a coverageData >= 31X There is a 0.44% of reference with a coverageData >= 32X There is a 0.43% of reference with a coverageData >= 33X There is a 0.43% of reference with a coverageData >= 34X There is a 0.42% of reference with a coverageData >= 35X There is a 0.42% of reference with a coverageData >= 36X There is a 0.41% of reference with a coverageData >= 37X There is a 0.41% of reference with a coverageData >= 38X There is a 0.41% of reference with a coverageData >= 39X There is a 0.4% of reference with a coverageData >= 40X There is a 0.4% of reference with a coverageData >= 41X There is a 0.39% of reference with a coverageData >= 42X There is a 0.39% of reference with a coverageData >= 43X There is a 0.39% of reference with a coverageData >= 44X There is a 0.38% of reference with a coverageData >= 45X There is a 0.38% of reference with a coverageData >= 46X There is a 0.38% of reference with a coverageData >= 47X There is a 0.37% of reference with a coverageData >= 48X There is a 0.37% of reference with a coverageData >= 49X There is a 0.37% of reference with a coverageData >= 50X There is a 0.36% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 262864966 1.054621107644101 17.5512842014277 chr2 243199373 259666125 1.067708858772428 21.47993457601069 chr3 198022430 223058451 1.1264302281312273 16.676525793208903 chr4 191154276 91407026 0.47818457380466867 11.470181376981165 chr5 180915260 116329901 0.6430076766326953 12.90794924570198 chr6 171115067 245449840 1.434413954909067 21.836536810852465 chr7 159138663 261053215 1.6404135241478057 31.04198289803798 chr8 146364022 167047459 1.1413150357401356 20.49360018734851 chr9 141213431 118719686 0.8407110085725485 13.395264300664055 chr10 135534747 87417729 0.644983894794152 13.816513247561033 chr11 135006516 97823034 0.7245800936008155 14.514053475122282 chr12 133851895 150109712 1.121461238931283 17.57717592647383 chr13 115169878 128360577 1.1145325429623187 27.944309955686663 chr14 107349540 65296248 0.6082582934216579 12.06184880035883 chr15 102531392 67380116 0.6571657195486041 14.908090793968265 chr16 90354753 166200639 1.8394233117985503 30.177893145539965 chr17 81195210 168338409 2.073255417407012 30.365207212415633 chr18 78077248 39583232 0.5069752458488291 9.910791181962797 chr19 59128983 83336970 1.4094098320615458 18.35355761195455 chr20 63025520 115456008 1.8318929855715589 34.27637626536129 chr21 48129895 28500920 0.5921666772803057 21.970181139280303 chr22 51304566 37790378 0.7365889811834682 14.761748132253821 chrMT 16571 129924 7.8404441494176575 3.819628454355101 chrX 155270560 191280081 1.2319146720408556 18.755014718088017 chrY 59373566 2155971 0.03631196751766603 1.5765506283933268