BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081242.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 3,192,467 number of mapped reads = 2,795,693 (87.57%) number of supplementary alignments = 30,121 (0.94%) number of secondary alignments = 0 number of mapped bases = 178,864,578 bp number of sequenced bases = 178,798,526 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 145,908 duplication rate = 4.2% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3221 >>>>>>> ACTG content number of A's = 52,004,992 bp (29.09%) number of C's = 34,117,093 bp (19.08%) number of T's = 55,007,757 bp (30.77%) number of G's = 37,646,649 bp (21.06%) number of N's = 22,035 bp (0.01%) GC percentage = 40.14% >>>>>>> Mismatches and indels general error rate = 0.0094 number of mismatches = 1,652,030 number of insertions = 13,600 mapped reads with insertion percentage = 0.48% number of deletions = 40,721 mapped reads with deletion percentage = 1.44% homopolymer indels = 47.02% >>>>>>> Coverage mean coverageData = 0.0578X std coverageData = 0.4555X There is a 4.55% of reference with a coverageData >= 1X There is a 0.87% of reference with a coverageData >= 2X There is a 0.2% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% 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% 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 20839006 0.08360663622980502 0.9361978581462808 chr2 243199373 9632890 0.039609024814385524 0.46018005496480585 chr3 198022430 11584024 0.0584985448365622 0.2991750747167619 chr4 191154276 8572999 0.04484858607086561 0.2632774248589036 chr5 180915260 10242433 0.056614533235062645 0.2911136834991751 chr6 171115067 10604735 0.06197429125279774 0.35180374281046267 chr7 159138663 11651470 0.07321583441982292 0.5672357634105949 chr8 146364022 10036593 0.06857281497771359 0.5264497379182589 chr9 141213431 5205640 0.03686363232687123 0.32299327130890343 chr10 135534747 5784894 0.0426819994727994 0.4739802095481971 chr11 135006516 10184033 0.07543364055109755 0.4806479856522588 chr12 133851895 5651000 0.042218304044182565 0.25544154713629064 chr13 115169878 5325786 0.04624287263723593 0.2655182347418686 chr14 107349540 5999701 0.05588939645200156 0.3013146368119492 chr15 102531392 4120041 0.04018321530248999 0.26328729158999387 chr16 90354753 6018923 0.06661434844495674 0.3312304590294597 chr17 81195210 3685777 0.04539402016449 0.2945054685542286 chr18 78077248 5396676 0.06911970053042853 0.5122247946557701 chr19 59128983 5707241 0.09652188673700003 0.6597714815570092 chr20 63025520 4750968 0.07538165492327552 0.34086430776063337 chr21 48129895 2424866 0.05038170143525142 0.2876564331549255 chr22 51304566 1340132 0.02612110586804301 0.1919228583868687 chrMT 16571 30704 1.8528755054010018 1.927342144548278 chrX 155270560 13621136 0.08772516824825002 0.39675531202686903 chrY 59373566 452910 0.00762814212641363 0.13481601657456854