BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818933.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 3,410,976 number of mapped reads = 3,261,067 (95.61%) number of supplementary alignments = 40,074 (1.17%) number of secondary alignments = 0 number of mapped bases = 302,522,292 bp number of sequenced bases = 302,360,486 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,757,701 duplication rate = 43.53% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.3757 >>>>>>> ACTG content number of A's = 88,093,622 bp (29.14%) number of C's = 63,347,249 bp (20.95%) number of T's = 86,869,271 bp (28.73%) number of G's = 64,036,720 bp (21.18%) number of N's = 13,624 bp (0%) GC percentage = 42.13% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 1,918,166 number of insertions = 41,712 mapped reads with insertion percentage = 1.25% number of deletions = 88,223 mapped reads with deletion percentage = 2.65% homopolymer indels = 41.17% >>>>>>> Coverage mean coverageData = 0.0977X std coverageData = 1.0065X There is a 3.51% of reference with a coverageData >= 1X There is a 1.99% of reference with a coverageData >= 2X There is a 1.28% of reference with a coverageData >= 3X There is a 0.85% of reference with a coverageData >= 4X There is a 0.58% of reference with a coverageData >= 5X There is a 0.4% of reference with a coverageData >= 6X There is a 0.28% of reference with a coverageData >= 7X There is a 0.19% of reference with a coverageData >= 8X There is a 0.14% of reference with a coverageData >= 9X There is a 0.1% of reference with a coverageData >= 10X There is a 0.07% of reference with a coverageData >= 11X There is a 0.05% of reference with a coverageData >= 12X There is a 0.04% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% 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% 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 34732005 0.13934571099824863 1.697672989012068 chr2 243199373 26419328 0.10863238533102633 1.372322899712839 chr3 198022430 20039974 0.10120052561722427 0.7089567709407325 chr4 191154276 19738166 0.1032577790726481 0.7708276782145239 chr5 180915260 15534426 0.08586575836665188 0.6698149613339417 chr6 171115067 16303843 0.09527999658849445 0.727221082551139 chr7 159138663 15468602 0.0972020356863247 0.8625184826690917 chr8 146364022 20410910 0.13945305493176458 0.9538524934850459 chr9 141213431 11679812 0.08271034785635936 1.1498383327406745 chr10 135534747 14772155 0.10899164477726143 1.2206575600089864 chr11 135006516 11616867 0.08604671347862942 0.746129793028202 chr12 133851895 13576199 0.10142702126107367 0.7225689538648116 chr13 115169878 4952547 0.043002103379843816 0.45118654940942043 chr14 107349540 7438051 0.06928814972099555 0.6608452830932401 chr15 102531392 9141755 0.08916054704494795 0.6765975127274284 chr16 90354753 9084208 0.10053934849448373 1.0647068017524084 chr17 81195210 6365638 0.07839918142954493 0.6848627161798162 chr18 78077248 7956648 0.10190738280119709 1.4095759129204848 chr19 59128983 4510010 0.07627410063859884 1.5277456021317717 chr20 63025520 6576623 0.10434857181662285 0.7719090081768175 chr21 48129895 3957698 0.08222951660293462 0.692961942750709 chr22 51304566 3908823 0.07618859888611083 0.6819189178990293 chrMT 16571 121940 7.358638585480659 7.061444252878555 chrX 155270560 17331961 0.11162425768284728 0.8697524594239262 chrY 59373566 884103 0.014890515418932392 0.7508661024238996