BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3083626.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 = 1,220,211 number of mapped reads = 1,125,310 (92.22%) number of supplementary alignments = 8,394 (0.69%) number of secondary alignments = 0 number of mapped bases = 76,387,420 bp number of sequenced bases = 76,355,583 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 39,912 duplication rate = 2.52% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4584 >>>>>>> ACTG content number of A's = 21,267,905 bp (27.85%) number of C's = 14,108,353 bp (18.48%) number of T's = 23,989,814 bp (31.42%) number of G's = 16,985,242 bp (22.24%) number of N's = 4,269 bp (0.01%) GC percentage = 40.72% >>>>>>> Mismatches and indels general error rate = 0.0076 number of mismatches = 570,673 number of insertions = 6,190 mapped reads with insertion percentage = 0.55% number of deletions = 19,858 mapped reads with deletion percentage = 1.75% homopolymer indels = 47.39% >>>>>>> Coverage mean coverageData = 0.0247X std coverageData = 0.3283X There is a 2.24% of reference with a coverageData >= 1X There is a 0.15% of reference with a coverageData >= 2X There is a 0.02% 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 7667195 0.030760986549357484 0.7705261581002768 chr2 243199373 6440513 0.026482440807937446 0.3509947942183121 chr3 198022430 6361199 0.03212362862126275 0.19263350636481477 chr4 191154276 3558386 0.018615257133981142 0.14905716252129822 chr5 180915260 3657723 0.020217879906869105 0.15258460706211913 chr6 171115067 5410431 0.031618670961336214 0.2328849160235415 chr7 159138663 5044458 0.031698506854993494 0.5047166684376364 chr8 146364022 5203531 0.035551981483536985 0.32877783751078 chr9 141213431 3027516 0.021439292130788892 0.22478417864164915 chr10 135534747 3407277 0.025139509058883625 0.23952857524889598 chr11 135006516 2804115 0.020770219712950743 0.2173277358077868 chr12 133851895 2669686 0.01994507436745666 0.1532231049340282 chr13 115169878 2297760 0.01995105004799953 0.15147706161230926 chr14 107349540 1553996 0.014476037810688337 0.13510106146518439 chr15 102531392 1867343 0.018212402695166763 0.14921888819299345 chr16 90354753 2064151 0.02284496311998108 0.17391064785060614 chr17 81195210 1558363 0.019192794747374876 0.15711158955683113 chr18 78077248 2656925 0.034029439664676704 0.4482991421813014 chr19 59128983 2297392 0.038853906890297774 0.48045039369429837 chr20 63025520 1588014 0.025196364901074995 0.1737468797539853 chr21 48129895 1196601 0.02486190755246817 0.1702266315185095 chr22 51304566 553146 0.010781613472765758 0.10976173898223035 chrMT 16571 1480 0.08931265463761993 0.3097413926491217 chrX 155270560 3344061 0.021536993232973464 0.1705812973932487 chrY 59373566 156158 0.002630092994582808 0.06944677439899692