BamQC report ----------------------------------- >>>>>>> Input bam file = SRR089600.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 10,620,644 number of mapped reads = 8,896,905 (83.77%) number of supplementary alignments = 393 (0%) number of secondary alignments = 0 number of mapped bases = 418,561,332 bp number of sequenced bases = 418,476,897 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,491,566 duplication rate = 20.76% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.9061 >>>>>>> ACTG content number of A's = 131,896,049 bp (31.52%) number of C's = 79,277,277 bp (18.94%) number of T's = 116,081,601 bp (27.74%) number of G's = 90,793,526 bp (21.7%) number of N's = 428,444 bp (0.1%) GC percentage = 40.64% >>>>>>> Mismatches and indels general error rate = 0.0058 number of mismatches = 2,389,386 number of insertions = 17,978 mapped reads with insertion percentage = 0.2% number of deletions = 56,261 mapped reads with deletion percentage = 0.63% homopolymer indels = 46.95% >>>>>>> Coverage mean coverageData = 0.1352X std coverageData = 1.0277X There is a 5.09% of reference with a coverageData >= 1X There is a 2.47% of reference with a coverageData >= 2X There is a 1.53% of reference with a coverageData >= 3X There is a 1.03% of reference with a coverageData >= 4X There is a 0.72% of reference with a coverageData >= 5X There is a 0.53% of reference with a coverageData >= 6X There is a 0.39% of reference with a coverageData >= 7X There is a 0.3% of reference with a coverageData >= 8X There is a 0.23% of reference with a coverageData >= 9X There is a 0.19% of reference with a coverageData >= 10X There is a 0.15% of reference with a coverageData >= 11X There is a 0.12% of reference with a coverageData >= 12X There is a 0.1% of reference with a coverageData >= 13X There is a 0.08% of reference with a coverageData >= 14X There is a 0.07% of reference with a coverageData >= 15X There is a 0.06% of reference with a coverageData >= 16X There is a 0.05% of reference with a coverageData >= 17X There is a 0.04% of reference with a coverageData >= 18X There is a 0.04% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% 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% 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 33365579 0.13386357420549816 1.101584988839943 chr2 243199373 35427842 0.14567406800016708 1.2064854122545738 chr3 198022430 28964801 0.1462703038236628 0.9987348674609529 chr4 191154276 27150777 0.14203593855258567 1.0109581634987095 chr5 180915260 26216867 0.14491241369025476 0.9983589349654297 chr6 171115067 24694929 0.1443176771803502 1.0316173391741847 chr7 159138663 22431118 0.14095328927075376 1.0696609418364955 chr8 146364022 21259163 0.14524855705318074 1.2452786260505266 chr9 141213431 17133856 0.12133304798748215 0.9214627747541245 chr10 135534747 19299453 0.1423948723643539 1.0384886038264596 chr11 135006516 19076811 0.1413028908915774 1.0487248529447868 chr12 133851895 19073755 0.14249895378769198 0.9909020682008907 chr13 115169878 13811640 0.11992406556165666 0.9018898866151263 chr14 107349540 12965997 0.12078297680642135 0.9697502481870905 chr15 102531392 12019296 0.11722552250144035 0.8726131502076541 chr16 90354753 11522037 0.1275199877974322 0.937370627531977 chr17 81195210 10952977 0.13489683689468873 0.9583273358971873 chr18 78077248 11062190 0.14168263205178544 1.0696348257433141 chr19 59128983 7383680 0.12487412475874987 0.9705029516407182 chr20 63025520 8498861 0.13484793144110513 0.9743490545374048 chr21 48129895 5398739 0.1121701803006219 0.9538815634991932 chr22 51304566 4489888 0.08751439394302643 0.7464282155678579 chrMT 16571 43856 2.646551203910446 5.4614509135808005 chrX 155270560 25277663 0.16279752581558282 1.1087128648606641 chrY 59373566 1039557 0.017508751285041563 0.32742309836676686