BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549000.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 9,038,593 number of mapped reads = 7,812,070 (86.43%) number of secondary alignments = 0 number of mapped bases = 310,244,106 bp number of sequenced bases = 310,209,604 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 689,628 duplication rate = 8.12% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7697 >>>>>>> ACTG content number of A's = 93,308,077 bp (30.08%) number of C's = 61,431,156 bp (19.8%) number of T's = 93,476,821 bp (30.13%) number of G's = 61,990,381 bp (19.98%) number of N's = 3,169 bp (0%) GC percentage = 39.79% >>>>>>> Mismatches and indels general error rate = 0.0029 number of mismatches = 888,740 number of insertions = 9,377 mapped reads with insertion percentage = 0.12% number of deletions = 26,783 mapped reads with deletion percentage = 0.34% homopolymer indels = 44.11% >>>>>>> Coverage mean coverageData = 0.1002X std coverageData = 0.8526X There is a 7.39% of reference with a coverageData >= 1X There is a 1.83% of reference with a coverageData >= 2X There is a 0.47% of reference with a coverageData >= 3X There is a 0.13% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% 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 25051408 0.10050690305000283 1.254771742802041 chr2 243199373 27095576 0.11141301749984364 0.5518763328966945 chr3 198022430 22045327 0.11132742386809413 0.4251007762289666 chr4 191154276 21583027 0.1129089416759895 0.4700757850051208 chr5 180915260 20124566 0.11123752634244342 0.43193314731695276 chr6 171115067 18898184 0.11044137919193288 0.4894518867324162 chr7 159138663 17453237 0.1096731408381884 0.809495697631379 chr8 146364022 16737616 0.11435608130528144 2.7246672686467925 chr9 141213431 12979132 0.09191145564617009 0.5080627519929546 chr10 135534747 14794138 0.1091538393471897 0.6172374499289113 chr11 135006516 14413220 0.1067594396703045 0.5327340327126602 chr12 133851895 14279640 0.10668238951716 0.4339385095499963 chr13 115169878 10461854 0.09083845690971384 0.380886803543613 chr14 107349540 9769971 0.09101083246374414 0.4498398770004536 chr15 102531392 8788997 0.08572005927706512 0.369090569357444 chr16 90354753 8021937 0.08878267864890295 0.4117621995863408 chr17 81195210 7416327 0.09133946448318811 0.41360916213339044 chr18 78077248 8630998 0.11054434193172383 1.0117157221626192 chr19 59128983 5164338 0.08734021351255103 0.9698404642230474 chr20 63025520 6140994 0.09743662567163269 0.4209519769400317 chr21 48129895 4091153 0.08500232547775141 0.44693338915107284 chr22 51304566 3062032 0.0596834207699954 0.3292544421813319 chrMT 16571 5562 0.33564661155029873 0.7691447869225208 chrX 155270560 10283647 0.06623050113299005 0.407036150302433 chrY 59373566 2951225 0.0497060425846748 0.5645096846849317