BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238064.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 = 1,601,886 number of mapped reads = 1,332,413 (83.18%) number of supplementary alignments = 12,287 (0.77%) number of secondary alignments = 0 number of mapped bases = 85,982,049 bp number of sequenced bases = 85,939,254 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 62,281 duplication rate = 3.67% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0896 >>>>>>> ACTG content number of A's = 22,875,480 bp (26.62%) number of C's = 16,223,878 bp (18.88%) number of T's = 26,908,339 bp (31.31%) number of G's = 19,919,666 bp (23.18%) number of N's = 11,891 bp (0.01%) GC percentage = 42.06% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 702,991 number of insertions = 6,462 mapped reads with insertion percentage = 0.48% number of deletions = 23,853 mapped reads with deletion percentage = 1.77% homopolymer indels = 45.5% >>>>>>> Coverage mean coverageData = 0.0278X std coverageData = 0.2947X There is a 2.26% of reference with a coverageData >= 1X There is a 0.35% of reference with a coverageData >= 2X There is a 0.07% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% 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 6686111 0.026824851922836332 0.5368127086791739 chr2 243199373 7312242 0.03006686205560242 0.34880525945077395 chr3 198022430 5723251 0.02890203397665608 0.20074964844898274 chr4 191154276 6657328 0.034826989692869854 0.2451356415091671 chr5 180915260 5464692 0.030205810167699507 0.20603418845222343 chr6 171115067 5064723 0.029598346240310915 0.24949293605970663 chr7 159138663 4192891 0.02634740622396708 0.32783087214823475 chr8 146364022 4157832 0.028407472978571196 0.25570113292674895 chr9 141213431 3493801 0.024741279744134252 0.2396527646730408 chr10 135534747 3836246 0.028304520316107574 0.31768063874433816 chr11 135006516 3946101 0.029228966992970916 0.2831796955646749 chr12 133851895 4780403 0.035714122687616784 0.22461957552661646 chr13 115169878 2613133 0.02268937890166038 0.17759219278553687 chr14 107349540 2515260 0.023430561509625473 0.19018262155018248 chr15 102531392 2257111 0.022013853084136416 0.17439150692597397 chr16 90354753 2231967 0.02470226441767817 0.20594918762595588 chr17 81195210 2688372 0.03310998271942397 0.23362698283752928 chr18 78077248 2119985 0.027152404244575833 0.3709200943533547 chr19 59128983 1772025 0.029968805653227622 0.3678683967981191 chr20 63025520 1793817 0.028461756444056314 0.20736730918811502 chr21 48129895 1122088 0.023313742945003307 0.20498119605019963 chr22 51304566 1093564 0.021315139864939117 0.18022862006971987 chrMT 16571 372458 22.476495081769357 12.748467150959263 chrX 155270560 3336534 0.021488516561027408 0.189620740074713 chrY 59373566 750114 0.012633804073684913 0.2178042576709951