BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234054.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 5,128,458 number of mapped reads = 132,171 (2.58%) number of supplementary alignments = 659 (0.01%) number of secondary alignments = 0 number of mapped bases = 7,377,117 bp number of sequenced bases = 7,355,625 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 49,962 duplication rate = 9.28% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.0247 >>>>>>> ACTG content number of A's = 1,920,039 bp (26.1%) number of C's = 1,478,214 bp (20.1%) number of T's = 2,240,024 bp (30.45%) number of G's = 1,716,831 bp (23.34%) number of N's = 517 bp (0.01%) GC percentage = 43.44% >>>>>>> Mismatches and indels general error rate = 0.0156 number of mismatches = 86,553 number of insertions = 8,704 mapped reads with insertion percentage = 5.3% number of deletions = 10,068 mapped reads with deletion percentage = 6.11% homopolymer indels = 39.87% >>>>>>> Coverage mean coverageData = 0.0024X std coverageData = 1.2149X There is a 0.15% of reference with a coverageData >= 1X There is a 0.02% of reference with a coverageData >= 2X There is a 0.01% 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 797773 0.003200686107819166 2.2142445389852212 chr2 243199373 864602 0.0035551160734283637 1.9406622767292758 chr3 198022430 588844 0.002973622735565865 0.14881025089168307 chr4 191154276 259568 0.001357897952541747 0.09170153209595269 chr5 180915260 675314 0.0037327641681525374 2.5345351110686103 chr6 171115067 535166 0.0031275212018588637 2.2882639681942845 chr7 159138663 445444 0.0027990935175822105 0.11115252017448278 chr8 146364022 321672 0.0021977532156092295 0.16008289893823413 chr9 141213431 252119 0.0017853755001533812 0.1019107423987561 chr10 135534747 310453 0.002290578666148246 0.3594580913222168 chr11 135006516 429894 0.0031842463070449133 1.5529043451559428 chr12 133851895 167215 0.0012492538861702332 0.05313130589716825 chr13 115169878 280970 0.002439613594103139 0.08476866111453465 chr14 107349540 199107 0.0018547541051410188 0.0714480229120315 chr15 102531392 125965 0.0012285505691759261 0.06116733584068001 chr16 90354753 155815 0.0017244803934110694 0.06384083853098825 chr17 81195210 150233 0.0018502692461784384 0.17556106728270676 chr18 78077248 160062 0.002050046640988166 0.286924851724586 chr19 59128983 171923 0.0029075927113442826 0.15690880919115355 chr20 63025520 125205 0.0019865762313424785 0.08050683900003465 chr21 48129895 100991 0.0020983008585412455 0.21581836981971889 chr22 51304566 58052 0.0011315172220733726 0.0682063586879457 chrMT 16571 5783 0.34898316335767304 1.0131246129083558 chrX 155270560 175676 0.0011314186024704233 0.07739736917852508 chrY 59373566 19271 3.2457204945379227E-4 0.023812451470829988