BamQC report ----------------------------------- >>>>>>> Input bam file = SRR926947.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 14,473,910 number of mapped reads = 14,197,289 (98.09%) number of supplementary alignments = 229,334 (1.58%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,104,445 number of mapped paired reads (second in pair) = 7,092,844 number of mapped paired reads (both in pair) = 14,030,220 number of mapped paired reads (singletons) = 167,069 number of mapped bases = 1,328,871,771 bp number of sequenced bases = 1,327,926,690 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 767,543 duplication rate = 4.26% >>>>>>> Insert size mean insert size = 166,280.0423 std insert size = 4,079,014.9787 median insert size = 185 >>>>>>> Mapping quality mean mapping quality = 53.5226 >>>>>>> ACTG content number of A's = 375,492,865 bp (28.28%) number of C's = 270,743,472 bp (20.39%) number of T's = 380,771,963 bp (28.67%) number of G's = 300,865,291 bp (22.66%) number of N's = 53,099 bp (0%) GC percentage = 43.05% >>>>>>> Mismatches and indels general error rate = 0.0092 number of mismatches = 11,881,178 number of insertions = 215,760 mapped reads with insertion percentage = 1.49% number of deletions = 644,795 mapped reads with deletion percentage = 4.43% homopolymer indels = 51.83% >>>>>>> Coverage mean coverageData = 0.4293X std coverageData = 1.9146X There is a 22.29% of reference with a coverageData >= 1X There is a 9.52% of reference with a coverageData >= 2X There is a 4.22% of reference with a coverageData >= 3X There is a 2.15% of reference with a coverageData >= 4X There is a 1.19% of reference with a coverageData >= 5X There is a 0.71% of reference with a coverageData >= 6X There is a 0.46% of reference with a coverageData >= 7X There is a 0.32% of reference with a coverageData >= 8X There is a 0.24% of reference with a coverageData >= 9X There is a 0.18% of reference with a coverageData >= 10X There is a 0.14% 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 0.05% of reference with a coverageData >= 18X There is a 0.04% of reference with a coverageData >= 19X There is a 0.04% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% 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 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 114168948 0.4580488006086051 2.3802955807104147 chr2 243199373 114479220 0.4707216905530427 3.0892375951500983 chr3 198022430 87480135 0.4417688188151211 1.180565136220823 chr4 191154276 71777112 0.3754931017080675 1.596870025491905 chr5 180915260 78520833 0.4340199549778167 1.1395253447800586 chr6 171115067 73450518 0.4292463503520704 1.3647289909340896 chr7 159138663 72736730 0.4570651067993452 1.5163814157000866 chr8 146364022 60503128 0.41337431954418413 1.1688093857821098 chr9 141213431 56275373 0.3985128935787985 1.9716077201842166 chr10 135534747 65379609 0.482382639486537 3.3487857657395996 chr11 135006516 66812813 0.49488583943607584 1.6132148587147033 chr12 133851895 56454530 0.42176862718305186 1.2694817257820723 chr13 115169878 37191770 0.32292966395258316 0.9559081462816199 chr14 107349540 41124590 0.383090509749739 1.090515043370444 chr15 102531392 44507165 0.4340833000687243 1.21786251457686 chr16 90354753 47008860 0.5202699187280164 2.716536876618121 chr17 81195210 40692456 0.5011681846749334 1.5471922033819614 chr18 78077248 31863591 0.4081034080504477 1.941179511713196 chr19 59128983 30337935 0.5130806156432625 1.908724289873674 chr20 63025520 33372708 0.5295110298177627 1.615543185897137 chr21 48129895 16672095 0.3463979092412315 1.3337428702685712 chr22 51304566 18961406 0.3695851554421102 1.1210047672423062 chrMT 16571 2545775 153.62832659465332 123.22660698972084 chrX 155270560 62950849 0.40542681754995924 1.2208359410011718 chrY 59373566 3603622 0.06069404690969715 1.535513232479059