BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124817.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 28,143,050 number of mapped reads = 27,884,201 (99.08%) number of supplementary alignments = 81,487 (0.29%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 13,967,605 number of mapped paired reads (second in pair) = 13,916,596 number of mapped paired reads (both in pair) = 27,789,924 number of mapped paired reads (singletons) = 94,277 number of mapped bases = 2,430,214,975 bp number of sequenced bases = 2,428,986,321 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 4,790,923 duplication rate = 11.7% >>>>>>> Insert size mean insert size = 27,517.3636 std insert size = 1,568,897.7415 median insert size = 206 >>>>>>> Mapping quality mean mapping quality = 53.1033 >>>>>>> ACTG content number of A's = 678,099,186 bp (27.92%) number of C's = 457,148,792 bp (18.82%) number of T's = 716,201,394 bp (29.49%) number of G's = 577,514,499 bp (23.78%) number of N's = 22,450 bp (0%) GC percentage = 42.6% >>>>>>> Mismatches and indels general error rate = 0.0075 number of mismatches = 17,489,592 number of insertions = 306,490 mapped reads with insertion percentage = 1.08% number of deletions = 754,624 mapped reads with deletion percentage = 2.66% homopolymer indels = 48.81% >>>>>>> Coverage mean coverageData = 0.785X std coverageData = 5.7207X There is a 31.13% of reference with a coverageData >= 1X There is a 16.61% of reference with a coverageData >= 2X There is a 9.51% of reference with a coverageData >= 3X There is a 5.84% of reference with a coverageData >= 4X There is a 3.73% of reference with a coverageData >= 5X There is a 2.48% of reference with a coverageData >= 6X There is a 1.69% of reference with a coverageData >= 7X There is a 1.19% of reference with a coverageData >= 8X There is a 0.86% of reference with a coverageData >= 9X There is a 0.63% of reference with a coverageData >= 10X There is a 0.47% of reference with a coverageData >= 11X There is a 0.36% of reference with a coverageData >= 12X There is a 0.28% of reference with a coverageData >= 13X There is a 0.22% of reference with a coverageData >= 14X There is a 0.18% of reference with a coverageData >= 15X There is a 0.15% of reference with a coverageData >= 16X There is a 0.12% of reference with a coverageData >= 17X There is a 0.1% of reference with a coverageData >= 18X There is a 0.09% of reference with a coverageData >= 19X There is a 0.07% of reference with a coverageData >= 20X There is a 0.06% of reference with a coverageData >= 21X There is a 0.06% of reference with a coverageData >= 22X There is a 0.05% of reference with a coverageData >= 23X There is a 0.04% of reference with a coverageData >= 24X There is a 0.04% of reference with a coverageData >= 25X There is a 0.04% of reference with a coverageData >= 26X There is a 0.03% of reference with a coverageData >= 27X There is a 0.03% of reference with a coverageData >= 28X There is a 0.03% of reference with a coverageData >= 29X There is a 0.03% 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 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% 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 214000791 0.8585767615800645 8.082228491573078 chr2 243199373 183755030 0.755573617371127 5.738883074679381 chr3 198022430 160283962 0.8094232658391274 1.7660509733624608 chr4 191154276 127764360 0.6683834789026639 3.462706369176481 chr5 180915260 141612350 0.7827551418271737 1.7596958552119362 chr6 171115067 111672817 0.652618258332564 3.552506951277107 chr7 159138663 211102913 1.3265344135761654 10.603812271311002 chr8 146364022 187311624 1.279765487723479 4.022360224586917 chr9 141213431 110659866 0.7836355594249388 6.841665776192635 chr10 135534747 107943758 0.7964286678455968 12.407097330872531 chr11 135006516 115419199 0.8549157656953388 4.114934708883382 chr12 133851895 120414411 0.8996093107236173 1.9064361236902096 chr13 115169878 74406836 0.646061603017414 1.5342839552703866 chr14 107349540 63332721 0.5899673254305514 1.7692411251574198 chr15 102531392 49270022 0.4805359708761196 1.3637041684141298 chr16 90354753 80672728 0.8928443199883463 6.150902062400569 chr17 81195210 68622036 0.8451488209710893 10.20995172442936 chr18 78077248 45111851 0.5777848496914235 6.937577775405791 chr19 59128983 31585463 0.5341790336559653 4.680133950497608 chr20 63025520 48293395 0.7662514327529547 1.9332426227894004 chr21 48129895 20253277 0.42080451245530454 1.92350894622619 chr22 51304566 21388719 0.41689698729738794 1.331900868821736 chrMT 16571 813958 49.119425502383685 30.64285556041848 chrX 155270560 118043878 0.7602463596447389 2.8560161075821506 chrY 59373566 16479010 0.2775479242732363 4.456778603520001