BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094050.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 = 289,566 number of mapped reads = 269,858 (93.19%) number of supplementary alignments = 9,074 (3.13%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 135,594 number of mapped paired reads (second in pair) = 134,264 number of mapped paired reads (both in pair) = 267,788 number of mapped paired reads (singletons) = 2,070 number of mapped bases = 35,515,114 bp number of sequenced bases = 34,603,537 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 251,873 duplication rate = 47.6% >>>>>>> Insert size mean insert size = 409,419.2009 std insert size = 5,919,861.1928 median insert size = 170 >>>>>>> Mapping quality mean mapping quality = 41.2879 >>>>>>> ACTG content number of A's = 9,647,087 bp (27.88%) number of C's = 7,682,487 bp (22.2%) number of T's = 9,264,503 bp (26.77%) number of G's = 8,008,977 bp (23.14%) number of N's = 483 bp (0%) GC percentage = 45.35% >>>>>>> Mismatches and indels general error rate = 0.0455 number of mismatches = 1,513,487 number of insertions = 25,696 mapped reads with insertion percentage = 9.35% number of deletions = 119,716 mapped reads with deletion percentage = 41.47% homopolymer indels = 31% >>>>>>> Coverage mean coverageData = 0.0115X std coverageData = 3.0484X There is a 0.02% of reference with a coverageData >= 1X There is a 0.01% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 0.01% 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 621637 0.002494023876474113 1.1096870147224112 chr2 243199373 1921125 0.007899383030070558 2.315570621211612 chr3 198022430 1037897 0.005241310289950487 2.4911465511834856 chr4 191154276 480819 0.002515345249195472 0.8892278018974885 chr5 180915260 380184 0.002101447937559275 1.063645765621092 chr6 171115067 656470 0.003836424293367457 1.9516525190367031 chr7 159138663 1171737 0.007362993869063736 2.233133823641946 chr8 146364022 1060738 0.007247259165917154 3.441431445654786 chr9 141213431 507849 0.003596322222352915 1.598341719590414 chr10 135534747 1090548 0.008046261376796609 3.0761910191834247 chr11 135006516 749076 0.005548443306247529 1.5493005500360444 chr12 133851895 784204 0.005858744099215032 1.4664512931471034 chr13 115169878 802016 0.006963765299812161 2.1512229458773557 chr14 107349540 207335 0.0019314009170416566 0.7802801168009011 chr15 102531392 653251 0.006371229213390568 1.9207093308870964 chr16 90354753 348699 0.0038592214401825657 1.5561879471428397 chr17 81195210 1469139 0.01809391219014028 4.2290543481841425 chr18 78077248 142195 0.0018212091696674555 0.5558619144420957 chr19 59128983 354135 0.0059891948420624785 2.038774256448209 chr20 63025520 247144 0.003921332184169206 0.95116841515532 chr21 48129895 132638 0.0027558339780296634 0.8911380350191477 chr22 51304566 116825 0.002277087774214872 0.6958827075664844 chrMT 16571 1816912 109.64407700199143 446.365461191549 chrX 155270560 18405898 0.11854081031201279 9.309067886584575 chrY 59373566 356643 0.006006764020203873 1.546522786600437