BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818988.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 2,596,453 number of mapped reads = 2,552,469 (98.31%) number of supplementary alignments = 40,701 (1.57%) number of secondary alignments = 0 number of mapped bases = 235,959,508 bp number of sequenced bases = 235,821,942 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,658,672 duplication rate = 50.57% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.3323 >>>>>>> ACTG content number of A's = 68,009,090 bp (28.84%) number of C's = 52,956,143 bp (22.46%) number of T's = 67,940,858 bp (28.81%) number of G's = 46,904,563 bp (19.89%) number of N's = 11,288 bp (0%) GC percentage = 42.35% >>>>>>> Mismatches and indels general error rate = 0.0067 number of mismatches = 1,504,135 number of insertions = 37,638 mapped reads with insertion percentage = 1.44% number of deletions = 78,350 mapped reads with deletion percentage = 3.01% homopolymer indels = 43.48% >>>>>>> Coverage mean coverageData = 0.0762X std coverageData = 0.9402X There is a 2.05% of reference with a coverageData >= 1X There is a 1.31% of reference with a coverageData >= 2X There is a 0.97% of reference with a coverageData >= 3X There is a 0.74% of reference with a coverageData >= 4X There is a 0.57% of reference with a coverageData >= 5X There is a 0.44% of reference with a coverageData >= 6X There is a 0.34% of reference with a coverageData >= 7X There is a 0.26% of reference with a coverageData >= 8X There is a 0.2% of reference with a coverageData >= 9X There is a 0.15% of reference with a coverageData >= 10X There is a 0.11% of reference with a coverageData >= 11X There is a 0.09% of reference with a coverageData >= 12X There is a 0.07% of reference with a coverageData >= 13X There is a 0.05% of reference with a coverageData >= 14X There is a 0.04% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% 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 24001139 0.09629319639689082 1.4071843317580552 chr2 243199373 20737726 0.0852704747721533 1.425474187120536 chr3 198022430 12663959 0.06395214420911813 0.659450498657085 chr4 191154276 13464471 0.07043771806600863 0.7641016593099998 chr5 180915260 12297777 0.06797534381566264 0.6988280614048605 chr6 171115067 9802457 0.05728576198377668 0.6953430352005835 chr7 159138663 11203251 0.07039930327930428 0.9285290607836204 chr8 146364022 24088052 0.1645763191722075 1.1492124700458308 chr9 141213431 9883790 0.06999185509485992 0.8844971665397773 chr10 135534747 11864476 0.08753826057608681 0.9982700010568216 chr11 135006516 7757007 0.05745653787554965 0.6898487112777776 chr12 133851895 10403192 0.07772166393311054 0.7394716765729386 chr13 115169878 4861891 0.04221495311473717 0.5403650788185199 chr14 107349540 5391250 0.05022145413944019 0.5956140865513819 chr15 102531392 5911111 0.057651718997436416 0.6432263316502123 chr16 90354753 7089963 0.07846806907877885 0.9754865240833511 chr17 81195210 8229276 0.10135174230105445 0.9241757118448746 chr18 78077248 5237269 0.06707804301708994 0.91522499260896 chr19 59128983 4742657 0.08020866856445003 1.2555197758712573 chr20 63025520 6729287 0.10677082870557832 0.9249524281742495 chr21 48129895 3208139 0.0666558487193874 0.70606583695913 chr22 51304566 1864447 0.03634076156106651 0.6116849813212045 chrMT 16571 32845 1.9820771226842073 3.979615078147243 chrX 155270560 13787399 0.08879596363921145 0.8483046031455533 chrY 59373566 706677 0.011902215878359067 0.6784069222667454