BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094132.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP024468/ERP024468.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 = 478,504 number of mapped reads = 430,132 (89.89%) number of supplementary alignments = 6,043 (1.26%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 215,731 number of mapped paired reads (second in pair) = 214,401 number of mapped paired reads (both in pair) = 426,836 number of mapped paired reads (singletons) = 3,296 number of mapped bases = 60,820,590 bp number of sequenced bases = 60,482,901 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 426,612 duplication rate = 42.32% >>>>>>> Insert size mean insert size = 92,114.0055 std insert size = 3,329,713.0662 median insert size = 231 >>>>>>> Mapping quality mean mapping quality = 26.4467 >>>>>>> ACTG content number of A's = 16,748,112 bp (27.69%) number of C's = 12,963,644 bp (21.43%) number of T's = 17,213,830 bp (28.46%) number of G's = 13,556,644 bp (22.41%) number of N's = 671 bp (0%) GC percentage = 43.85% >>>>>>> Mismatches and indels general error rate = 0.0204 number of mismatches = 1,208,806 number of insertions = 20,524 mapped reads with insertion percentage = 4.65% number of deletions = 61,607 mapped reads with deletion percentage = 13.89% homopolymer indels = 50.13% >>>>>>> Coverage mean coverageData = 0.0196X std coverageData = 26.8588X There is a 0.01% of reference with a coverageData >= 1X There is a 0% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% 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 319387 0.0012813889839817089 0.5902587129596758 chr2 243199373 1470265 0.006045513118983247 4.094261765861563 chr3 198022430 1355212 0.006843729773440312 6.062547627174708 chr4 191154276 93078 4.8692606803103897E-4 0.1566181281004839 chr5 180915260 290729 0.001606989924454134 1.0270713608087734 chr6 171115067 229532 0.0013413897678572046 0.5200099838695234 chr7 159138663 154165 9.68746356754298E-4 0.4366709722950319 chr8 146364022 708684 0.0048419276152441345 3.4116111648226446 chr9 141213431 508765 0.0036028088574662563 1.6666449102270429 chr10 135534747 108394 7.997506351636898E-4 0.4335951843364796 chr11 135006516 1459855 0.010813218822712231 5.493985378537066 chr12 133851895 144720 0.001081195002879862 0.7188461549589398 chr13 115169878 32069 2.784495438989698E-4 0.0938448295272106 chr14 107349540 53249 4.960337976296871E-4 0.1503162654906838 chr15 102531392 78405 7.64692631891704E-4 0.4566897756507414 chr16 90354753 251115 0.002779211847328054 1.5804430268546303 chr17 81195210 1558456 0.019193940135138515 9.570701233134791 chr18 78077248 45098 5.77607448459249E-4 0.16810325969709836 chr19 59128983 40140 6.788549026794525E-4 0.22039412510486397 chr20 63025520 40522 6.42945905087336E-4 0.1794344126169904 chr21 48129895 62878 0.0013064229622773954 0.4619073173830466 chr22 51304566 11623 2.2654903659062237E-4 0.04879313399020527 chrMT 16571 45210446 2728.287128115382 11124.939166069098 chrX 155270560 6580537 0.042381099160072586 14.684251634493123 chrY 59373566 13266 2.2343276467510812E-4 0.08734348195435479