BamQC report ----------------------------------- >>>>>>> Input bam file = SRR926948.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 = 15,140,640 number of mapped reads = 14,885,767 (98.32%) number of supplementary alignments = 363,503 (2.4%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,449,083 number of mapped paired reads (second in pair) = 7,436,684 number of mapped paired reads (both in pair) = 14,737,092 number of mapped paired reads (singletons) = 148,675 number of mapped bases = 1,373,371,177 bp number of sequenced bases = 1,372,390,921 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 933,030 duplication rate = 4.77% >>>>>>> Insert size mean insert size = 260,253.2764 std insert size = 5,014,282.5601 median insert size = 177 >>>>>>> Mapping quality mean mapping quality = 53.2379 >>>>>>> ACTG content number of A's = 388,690,761 bp (28.32%) number of C's = 276,154,699 bp (20.12%) number of T's = 394,492,897 bp (28.74%) number of G's = 313,001,517 bp (22.81%) number of N's = 51,047 bp (0%) GC percentage = 42.93% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 12,107,847 number of insertions = 229,022 mapped reads with insertion percentage = 1.51% number of deletions = 661,319 mapped reads with deletion percentage = 4.33% homopolymer indels = 51.41% >>>>>>> Coverage mean coverageData = 0.4436X std coverageData = 2.2053X There is a 23.28% of reference with a coverageData >= 1X There is a 9.77% of reference with a coverageData >= 2X There is a 4.2% of reference with a coverageData >= 3X There is a 2.09% of reference with a coverageData >= 4X There is a 1.14% of reference with a coverageData >= 5X There is a 0.69% of reference with a coverageData >= 6X There is a 0.45% 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 0.19% of reference with a coverageData >= 10X There is a 0.16% of reference with a coverageData >= 11X There is a 0.13% of reference with a coverageData >= 12X There is a 0.11% of reference with a coverageData >= 13X There is a 0.1% of reference with a coverageData >= 14X There is a 0.08% of reference with a coverageData >= 15X There is a 0.07% of reference with a coverageData >= 16X There is a 0.06% of reference with a coverageData >= 17X There is a 0.06% of reference with a coverageData >= 18X There is a 0.05% of reference with a coverageData >= 19X There is a 0.05% of reference with a coverageData >= 20X There is a 0.04% of reference with a coverageData >= 21X There is a 0.04% 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 0.03% of reference with a coverageData >= 25X There is a 0.03% 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 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% 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 120730344 0.48437329269482543 2.589466656918514 chr2 243199373 121252142 0.49857094820717324 3.523918143394167 chr3 198022430 93771948 0.47354205278664646 1.2435775985810642 chr4 191154276 80377991 0.4204875385575994 1.915605983674996 chr5 180915260 77994351 0.4311098522037334 1.151988820895985 chr6 171115067 78049075 0.4561204128213911 1.486777778299721 chr7 159138663 74212188 0.46633663121827285 1.7299158415909663 chr8 146364022 63733058 0.43544210612086076 1.2823292236674497 chr9 141213431 57190683 0.40499464247136663 2.2565568435487844 chr10 135534747 65777035 0.4853149207560774 4.96159134802111 chr11 135006516 69023360 0.5112594713576639 1.8380477054454467 chr12 133851895 60552799 0.45238656501650576 1.3489747742418503 chr13 115169878 38815209 0.3370257021545165 0.9704657262646132 chr14 107349540 37384893 0.3482538723500818 1.0512008566735103 chr15 102531392 42411017 0.4136393369164441 1.2004921899597065 chr16 90354753 46498939 0.5146263749954582 3.465631016357073 chr17 81195210 39974247 0.49232272445628256 1.743208285041729 chr18 78077248 31412662 0.4023279867651073 2.1960014230658413 chr19 59128983 29769858 0.5034731952010743 2.2291331318706398 chr20 63025520 34093888 0.5409536962170245 1.7094764966364506 chr21 48129895 15665916 0.3254924200437171 1.4386138680173843 chr22 51304566 16204945 0.3158577542591433 1.08969232589401 chrMT 16571 130557 7.87864341319172 5.271284976262424 chrX 155270560 74377260 0.47901714272171103 1.352177720509307 chrY 59373566 3966812 0.06681107885620345 2.0166972880596563