BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094088.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 = 166 number of mapped reads = 141 (84.94%) number of supplementary alignments = 4 (2.41%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 72 number of mapped paired reads (second in pair) = 69 number of mapped paired reads (both in pair) = 134 number of mapped paired reads (singletons) = 7 number of mapped bases = 18,577 bp number of sequenced bases = 18,263 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 30 duplication rate = 19.13% >>>>>>> Insert size mean insert size = 3,514,229.7812 std insert size = 19,828,445.3831 median insert size = 170 >>>>>>> Mapping quality mean mapping quality = 4.4668 >>>>>>> ACTG content number of A's = 4,998 bp (27.37%) number of C's = 4,112 bp (22.52%) number of T's = 4,660 bp (25.52%) number of G's = 4,493 bp (24.6%) number of N's = 0 bp (0%) GC percentage = 47.12% >>>>>>> Mismatches and indels general error rate = 0.0342 number of mismatches = 621 number of insertions = 4 mapped reads with insertion percentage = 2.84% number of deletions = 41 mapped reads with deletion percentage = 29.08% homopolymer indels = 24.44% >>>>>>> Coverage mean coverageData = 0X std coverageData = 0.0037X There is a 0% 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 0 0.0 0.0 chr2 243199373 1190 4.893104720298765E-6 0.0028798581852227645 chr3 198022430 503 2.5401162888466724E-6 0.0021068660700353375 chr4 191154276 320 1.6740405011918227E-6 0.0016301954465134905 chr5 180915260 0 0.0 0.0 chr6 171115067 0 0.0 0.0 chr7 159138663 214 1.3447392102320226E-6 0.0015774645428084076 chr8 146364022 555 3.791915474965562E-6 0.0027526322477172795 chr9 141213431 36 2.5493325772957105E-7 5.049090935392282E-4 chr10 135534747 30 2.2134545320691821E-7 4.704735956598506E-4 chr11 135006516 363 2.6887591114491096E-6 0.002063746314206697 chr12 133851895 635 4.744049383835769E-6 0.0027510077565136046 chr13 115169878 868 7.53669288422794E-6 0.0036921511164546305 chr14 107349540 0 0.0 0.0 chr15 102531392 0 0.0 0.0 chr16 90354753 0 0.0 0.0 chr17 81195210 98 1.2069677509301349E-6 0.0010986201773856984 chr18 78077248 288 3.688654600121152E-6 0.002668546379682237 chr19 59128983 0 0.0 0.0 chr20 63025520 106 1.681858396408312E-6 0.0012968637429432001 chr21 48129895 112 2.3270360344646505E-6 0.0014414251594650634 chr22 51304566 0 0.0 0.0 chrMT 16571 2106 0.12708949369380243 0.684706151781439 chrX 155270560 10939 7.045121753924247E-5 0.012508299765895674 chrY 59373566 214 3.604297575793241E-6 0.0026848802879505572