BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124849.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 78,608,894 number of mapped reads = 75,194,307 (95.66%) number of supplementary alignments = 1,583,212 (2.01%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 38,121,508 number of mapped paired reads (second in pair) = 37,072,799 number of mapped paired reads (both in pair) = 73,909,484 number of mapped paired reads (singletons) = 1,284,823 number of mapped bases = 9,144,937,670 bp number of sequenced bases = 9,138,363,025 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 32,235,030 duplication rate = 34.46% >>>>>>> Insert size mean insert size = 80,594.0624 std insert size = 2,696,717.0275 median insert size = 157 >>>>>>> Mapping quality mean mapping quality = 53.199 >>>>>>> ACTG content number of A's = 2,669,522,937 bp (29.21%) number of C's = 1,807,302,732 bp (19.78%) number of T's = 2,691,631,959 bp (29.45%) number of G's = 1,969,771,420 bp (21.55%) number of N's = 133,977 bp (0%) GC percentage = 41.33% >>>>>>> Mismatches and indels general error rate = 0.0118 number of mismatches = 103,543,204 number of insertions = 1,612,646 mapped reads with insertion percentage = 2% number of deletions = 3,026,570 mapped reads with deletion percentage = 3.86% homopolymer indels = 43.51% >>>>>>> Coverage mean coverageData = 2.9541X std coverageData = 37.3372X There is a 49.86% of reference with a coverageData >= 1X There is a 39.38% of reference with a coverageData >= 2X There is a 29.43% of reference with a coverageData >= 3X There is a 24.24% of reference with a coverageData >= 4X There is a 19.2% of reference with a coverageData >= 5X There is a 16.07% of reference with a coverageData >= 6X There is a 13.16% of reference with a coverageData >= 7X There is a 11.15% of reference with a coverageData >= 8X There is a 9.33% of reference with a coverageData >= 9X There is a 7.98% of reference with a coverageData >= 10X There is a 6.79% of reference with a coverageData >= 11X There is a 5.87% of reference with a coverageData >= 12X There is a 5.05% of reference with a coverageData >= 13X There is a 4.4% of reference with a coverageData >= 14X There is a 3.82% of reference with a coverageData >= 15X There is a 3.35% of reference with a coverageData >= 16X There is a 2.94% of reference with a coverageData >= 17X There is a 2.59% of reference with a coverageData >= 18X There is a 2.29% of reference with a coverageData >= 19X There is a 2.03% of reference with a coverageData >= 20X There is a 1.8% of reference with a coverageData >= 21X There is a 1.61% of reference with a coverageData >= 22X There is a 1.44% of reference with a coverageData >= 23X There is a 1.29% of reference with a coverageData >= 24X There is a 1.16% of reference with a coverageData >= 25X There is a 1.04% of reference with a coverageData >= 26X There is a 0.94% of reference with a coverageData >= 27X There is a 0.85% of reference with a coverageData >= 28X There is a 0.77% of reference with a coverageData >= 29X There is a 0.7% of reference with a coverageData >= 30X There is a 0.64% of reference with a coverageData >= 31X There is a 0.58% of reference with a coverageData >= 32X There is a 0.53% of reference with a coverageData >= 33X There is a 0.48% of reference with a coverageData >= 34X There is a 0.44% of reference with a coverageData >= 35X There is a 0.41% of reference with a coverageData >= 36X There is a 0.37% of reference with a coverageData >= 37X There is a 0.34% of reference with a coverageData >= 38X There is a 0.32% of reference with a coverageData >= 39X There is a 0.29% of reference with a coverageData >= 40X There is a 0.27% of reference with a coverageData >= 41X There is a 0.25% of reference with a coverageData >= 42X There is a 0.23% of reference with a coverageData >= 43X There is a 0.21% of reference with a coverageData >= 44X There is a 0.2% of reference with a coverageData >= 45X There is a 0.19% of reference with a coverageData >= 46X There is a 0.17% of reference with a coverageData >= 47X There is a 0.16% of reference with a coverageData >= 48X There is a 0.15% of reference with a coverageData >= 49X There is a 0.14% of reference with a coverageData >= 50X There is a 0.13% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 751396767 3.0146234500254265 26.430178374775643 chr2 243199373 806778079 3.3173526273852687 44.75165052628949 chr3 198022430 635421206 3.2088345042528768 7.452677664240963 chr4 191154276 532894974 2.7877742792423854 28.651829808251584 chr5 180915260 535658755 2.960826825774675 6.674032303873152 chr6 171115067 540387988 3.158038608020415 14.147072452292727 chr7 159138663 571270164 3.5897635007779347 25.70829136542436 chr8 146364022 556550759 3.802510694875548 11.21312758850012 chr9 141213431 367352579 2.601399713884156 37.14896784354244 chr10 135534747 493787239 3.6432520068082614 131.1853609666855 chr11 135006516 364581753 2.700475234839776 13.907287228040442 chr12 133851895 430886872 3.219131652936255 6.292439794459457 chr13 115169878 230926832 2.0050974787001166 4.4667995745395155 chr14 107349540 312243128 2.9086582765049576 7.3615727884279245 chr15 102531392 258747848 2.5235963635410315 5.93607614854991 chr16 90354753 316643210 3.504444420317324 58.44098407981741 chr17 81195210 210006671 2.586441626297906 25.494788387564498 chr18 78077248 188256461 2.4111564613547856 36.723501442010196 chr19 59128983 134179973 2.269275847345455 15.736470843225662 chr20 63025520 198447489 3.148684675667888 11.510964378492936 chr21 48129895 101400339 2.1068057389279575 16.328416380887987 chr22 51304566 80781752 1.574552877028528 6.100038527433243 chrMT 16571 2258948 136.31935308671777 74.96865969721907 chrX 155270560 377415456 2.4306955291460275 8.548078337508885 chrY 59373566 146662428 2.470163708880144 62.67688751411105