BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975198.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP029757/SRP029757.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 = 34,199,330 number of mapped reads = 34,105,366 (99.73%) number of supplementary alignments = 60,887 (0.18%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 17,047,267 number of mapped paired reads (second in pair) = 17,058,099 number of mapped paired reads (both in pair) = 34,047,374 number of mapped paired reads (singletons) = 57,992 number of mapped bases = 3,170,573,066 bp number of sequenced bases = 3,169,411,574 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 18,538,242 duplication rate = 41% >>>>>>> Insert size mean insert size = 144,819.4014 std insert size = 3,745,999.8683 median insert size = 233 >>>>>>> Mapping quality mean mapping quality = 55.6138 >>>>>>> ACTG content number of A's = 840,085,814 bp (26.51%) number of C's = 704,459,741 bp (22.23%) number of T's = 874,710,176 bp (27.6%) number of G's = 749,995,900 bp (23.66%) number of N's = 159,943 bp (0.01%) GC percentage = 45.89% >>>>>>> Mismatches and indels general error rate = 0.0073 number of mismatches = 22,555,466 number of insertions = 284,937 mapped reads with insertion percentage = 0.83% number of deletions = 826,186 mapped reads with deletion percentage = 2.39% homopolymer indels = 50% >>>>>>> Coverage mean coverageData = 1.0242X std coverageData = 15.6069X There is a 9.77% of reference with a coverageData >= 1X There is a 4.61% of reference with a coverageData >= 2X There is a 2.77% of reference with a coverageData >= 3X There is a 2.11% of reference with a coverageData >= 4X There is a 1.77% of reference with a coverageData >= 5X There is a 1.59% of reference with a coverageData >= 6X There is a 1.46% of reference with a coverageData >= 7X There is a 1.37% of reference with a coverageData >= 8X There is a 1.29% of reference with a coverageData >= 9X There is a 1.23% of reference with a coverageData >= 10X There is a 1.17% of reference with a coverageData >= 11X There is a 1.12% of reference with a coverageData >= 12X There is a 1.08% of reference with a coverageData >= 13X There is a 1.04% of reference with a coverageData >= 14X There is a 1% of reference with a coverageData >= 15X There is a 0.97% of reference with a coverageData >= 16X There is a 0.94% of reference with a coverageData >= 17X There is a 0.91% of reference with a coverageData >= 18X There is a 0.88% of reference with a coverageData >= 19X There is a 0.86% of reference with a coverageData >= 20X There is a 0.83% of reference with a coverageData >= 21X There is a 0.81% of reference with a coverageData >= 22X There is a 0.79% of reference with a coverageData >= 23X There is a 0.77% of reference with a coverageData >= 24X There is a 0.75% of reference with a coverageData >= 25X There is a 0.73% of reference with a coverageData >= 26X There is a 0.71% of reference with a coverageData >= 27X There is a 0.69% of reference with a coverageData >= 28X There is a 0.68% of reference with a coverageData >= 29X There is a 0.66% of reference with a coverageData >= 30X There is a 0.65% of reference with a coverageData >= 31X There is a 0.63% of reference with a coverageData >= 32X There is a 0.62% of reference with a coverageData >= 33X There is a 0.61% of reference with a coverageData >= 34X There is a 0.59% of reference with a coverageData >= 35X There is a 0.58% of reference with a coverageData >= 36X There is a 0.57% of reference with a coverageData >= 37X There is a 0.56% of reference with a coverageData >= 38X There is a 0.55% of reference with a coverageData >= 39X There is a 0.54% of reference with a coverageData >= 40X There is a 0.53% of reference with a coverageData >= 41X There is a 0.52% of reference with a coverageData >= 42X There is a 0.51% of reference with a coverageData >= 43X There is a 0.5% of reference with a coverageData >= 44X There is a 0.49% of reference with a coverageData >= 45X There is a 0.48% of reference with a coverageData >= 46X There is a 0.47% of reference with a coverageData >= 47X There is a 0.46% of reference with a coverageData >= 48X There is a 0.45% of reference with a coverageData >= 49X There is a 0.45% of reference with a coverageData >= 50X There is a 0.44% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 386742712 1.5516218593493494 20.57850603212134 chr2 243199373 206021021 0.8471280927192193 12.180542045948465 chr3 198022430 238972957 1.2067974168380824 15.671663719949336 chr4 191154276 128996330 0.6748283778909555 10.573304924003587 chr5 180915260 228757636 1.2644463269709807 17.707150733388104 chr6 171115067 191182301 1.1172733316347883 18.36487224781078 chr7 159138663 134643528 0.8460767827363235 14.105567508789917 chr8 146364022 110059743 0.751958995770149 11.550630144845131 chr9 141213431 112953340 0.799876748267663 11.822679799735184 chr10 135534747 129243894 0.95358494305523 14.523275776879629 chr11 135006516 159632267 1.1824041663292755 16.967374119141788 chr12 133851895 154707874 1.1558138493295145 16.62610879748688 chr13 115169878 38861958 0.33743161558267865 6.462164396119116 chr14 107349540 113355444 1.055947179652563 16.121525467816088 chr15 102531392 97516621 0.9510903841040216 13.93830894419119 chr16 90354753 76362155 0.8451371119347756 12.115134437099677 chr17 81195210 96488979 1.188358020134439 16.580278512164348 chr18 78077248 51680483 0.6619147616473368 10.483950525542527 chr19 59128983 102816351 1.7388486285989393 21.936878960381677 chr20 63025520 65360225 1.0370438038432686 15.153901688385659 chr21 48129895 24768877 0.5146256188591312 8.174208836518286 chr22 51304566 39868346 0.7770915750461664 12.316494907834876 chrMT 16571 126250 7.618731518918593 11.548533549408269 chrX 155270560 280342626 1.8055104972893767 25.55403240659728 chrY 59373566 1111148 0.018714523564240693 0.8323850086733905