BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082742.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 = 3,383,224 number of mapped reads = 2,927,443 (86.53%) number of supplementary alignments = 17,099 (0.51%) number of secondary alignments = 0 number of mapped bases = 196,732,284 bp number of sequenced bases = 196,658,655 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 158,870 duplication rate = 4.42% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.9147 >>>>>>> ACTG content number of A's = 54,925,673 bp (27.93%) number of C's = 35,383,985 bp (17.99%) number of T's = 64,129,935 bp (32.61%) number of G's = 42,208,288 bp (21.46%) number of N's = 10,774 bp (0.01%) GC percentage = 39.46% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 1,678,840 number of insertions = 15,431 mapped reads with insertion percentage = 0.52% number of deletions = 43,054 mapped reads with deletion percentage = 1.46% homopolymer indels = 48.59% >>>>>>> Coverage mean coverageData = 0.0636X std coverageData = 0.4916X There is a 5.08% of reference with a coverageData >= 1X There is a 0.91% of reference with a coverageData >= 2X There is a 0.19% 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 19124714 0.07672885196141598 0.9412147889286079 chr2 243199373 20424071 0.08398077161161102 0.653136323233543 chr3 198022430 14718462 0.07432724666594587 0.32525635233236666 chr4 191154276 11486200 0.06008863751496723 0.30128045360104855 chr5 180915260 9345148 0.051654835529075876 0.2720222768236112 chr6 171115067 14620736 0.08544388437752241 0.5173138339753784 chr7 159138663 9842406 0.06184798724870524 0.4433069653059492 chr8 146364022 14925790 0.1019771785172725 0.6040570602252293 chr9 141213431 6011435 0.04256985300498789 0.44989120185489695 chr10 135534747 7272284 0.05365623326098067 0.37642927572104135 chr11 135006516 8088611 0.05991274524853304 0.36349196869552153 chr12 133851895 6292500 0.047010914563443425 0.27091507764496453 chr13 115169878 4631814 0.04021723457934027 0.23796732238848434 chr14 107349540 4217465 0.03928722004770584 0.2687540929912709 chr15 102531392 3877637 0.03781902229514254 0.2315847591688317 chr16 90354753 7839815 0.08676704589076792 0.39704026608095383 chr17 81195210 4734000 0.0583039319684006 0.33742142166175854 chr18 78077248 7671986 0.09826148073251763 0.8865498087298199 chr19 59128983 2710929 0.04584771904499017 0.6585864000974637 chr20 63025520 3903744 0.06193910022479783 0.3092841085709108 chr21 48129895 3950175 0.08207321042358393 0.3488642599482734 chr22 51304566 2517783 0.049075222661468375 0.26209986578329986 chrMT 16571 156626 9.451813408967473 5.925067603428925 chrX 155270560 8033898 0.05174128308676158 0.321832705381476 chrY 59373566 334055 0.005626325358325286 0.1163107518671697