BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124842.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 = 100,518,680 number of mapped reads = 97,267,480 (96.77%) number of supplementary alignments = 1,877,039 (1.87%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 49,938,052 number of mapped paired reads (second in pair) = 47,329,428 number of mapped paired reads (both in pair) = 94,504,170 number of mapped paired reads (singletons) = 2,763,310 number of mapped bases = 13,078,050,586 bp number of sequenced bases = 13,069,215,809 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 30,562,085 duplication rate = 19.56% >>>>>>> Insert size mean insert size = 115,403.4614 std insert size = 3,230,025.5526 median insert size = 267 >>>>>>> Mapping quality mean mapping quality = 53.4907 >>>>>>> ACTG content number of A's = 3,775,779,421 bp (28.89%) number of C's = 2,525,710,371 bp (19.33%) number of T's = 3,884,284,131 bp (29.72%) number of G's = 2,883,206,317 bp (22.06%) number of N's = 235,569 bp (0%) GC percentage = 41.39% >>>>>>> Mismatches and indels general error rate = 0.0129 number of mismatches = 163,502,894 number of insertions = 2,095,678 mapped reads with insertion percentage = 2.03% number of deletions = 4,562,272 mapped reads with deletion percentage = 4.51% homopolymer indels = 46.02% >>>>>>> Coverage mean coverageData = 4.2246X std coverageData = 44.7641X There is a 56.18% of reference with a coverageData >= 1X There is a 45.64% of reference with a coverageData >= 2X There is a 37.63% of reference with a coverageData >= 3X There is a 31.67% of reference with a coverageData >= 4X There is a 26.86% of reference with a coverageData >= 5X There is a 22.99% of reference with a coverageData >= 6X There is a 19.79% of reference with a coverageData >= 7X There is a 17.14% of reference with a coverageData >= 8X There is a 14.91% of reference with a coverageData >= 9X There is a 13.02% of reference with a coverageData >= 10X There is a 11.42% of reference with a coverageData >= 11X There is a 10.05% of reference with a coverageData >= 12X There is a 8.87% of reference with a coverageData >= 13X There is a 7.85% of reference with a coverageData >= 14X There is a 6.97% of reference with a coverageData >= 15X There is a 6.21% of reference with a coverageData >= 16X There is a 5.54% of reference with a coverageData >= 17X There is a 4.95% of reference with a coverageData >= 18X There is a 4.44% of reference with a coverageData >= 19X There is a 3.99% of reference with a coverageData >= 20X There is a 3.59% of reference with a coverageData >= 21X There is a 3.24% of reference with a coverageData >= 22X There is a 2.93% of reference with a coverageData >= 23X There is a 2.65% of reference with a coverageData >= 24X There is a 2.4% of reference with a coverageData >= 25X There is a 2.18% of reference with a coverageData >= 26X There is a 1.99% of reference with a coverageData >= 27X There is a 1.81% of reference with a coverageData >= 28X There is a 1.65% of reference with a coverageData >= 29X There is a 1.51% of reference with a coverageData >= 30X There is a 1.38% of reference with a coverageData >= 31X There is a 1.27% of reference with a coverageData >= 32X There is a 1.16% of reference with a coverageData >= 33X There is a 1.07% of reference with a coverageData >= 34X There is a 0.99% of reference with a coverageData >= 35X There is a 0.91% of reference with a coverageData >= 36X There is a 0.84% of reference with a coverageData >= 37X There is a 0.78% of reference with a coverageData >= 38X There is a 0.72% of reference with a coverageData >= 39X There is a 0.67% of reference with a coverageData >= 40X There is a 0.62% of reference with a coverageData >= 41X There is a 0.58% of reference with a coverageData >= 42X There is a 0.54% of reference with a coverageData >= 43X There is a 0.5% of reference with a coverageData >= 44X There is a 0.47% of reference with a coverageData >= 45X There is a 0.44% of reference with a coverageData >= 46X There is a 0.41% of reference with a coverageData >= 47X There is a 0.38% of reference with a coverageData >= 48X There is a 0.36% of reference with a coverageData >= 49X There is a 0.34% of reference with a coverageData >= 50X There is a 0.32% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1076499872 4.3189455965287245 56.67223816716113 chr2 243199373 1080128270 4.441328349970705 43.53821495618517 chr3 198022430 632772977 3.1954611252876757 6.317853386194729 chr4 191154276 705664453 3.691596483041792 31.866584712396634 chr5 180915260 840107514 4.643652028026823 8.60047525662966 chr6 171115067 603891388 3.5291537945048406 22.4052290812409 chr7 159138663 1137916135 7.150469367711101 67.8279911169744 chr8 146364022 1124269545 7.681324478771156 27.520963451476998 chr9 141213431 581390263 4.1171031599678365 75.63229066649868 chr10 135534747 642600092 4.741220286484912 110.84603525825646 chr11 135006516 592177118 4.386285458992217 25.3016209300706 chr12 133851895 622674771 4.65196828927973 18.039288700836593 chr13 115169878 334929828 2.908137386409318 5.615827685600052 chr14 107349540 320299015 2.9837017932261283 6.7294163901469215 chr15 102531392 311986077 3.0428346959339048 9.608882801983313 chr16 90354753 489009442 5.412105348791115 50.06312735462834 chr17 81195210 318460045 3.9221531048444853 75.28986281893701 chr18 78077248 250871031 3.2131131338030765 53.651322702746896 chr19 59128983 153909567 2.6029462911614765 31.97416730613813 chr20 63025520 229217184 3.6368947689761226 11.437136397794733 chr21 48129895 112811651 2.343899794504019 15.98231123023196 chr22 51304566 112737473 2.1974159765818895 5.9509446667252375 chrMT 16571 6772199 408.67775028664533 222.40824101650813 chrX 155270560 650572353 4.189927266315006 14.52931589294996 chrY 59373566 146382323 2.465446037046183 48.695073275375265