BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094103.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP024468/ERP024468.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 = 361,876 number of mapped reads = 351,116 (97.03%) number of supplementary alignments = 27,558 (7.62%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 176,550 number of mapped paired reads (second in pair) = 174,566 number of mapped paired reads (both in pair) = 348,236 number of mapped paired reads (singletons) = 2,880 number of mapped bases = 45,019,155 bp number of sequenced bases = 44,232,552 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 334,371 duplication rate = 51.68% >>>>>>> Insert size mean insert size = 1,829,975.2076 std insert size = 11,768,228.4862 median insert size = 163 >>>>>>> Mapping quality mean mapping quality = 40.1206 >>>>>>> ACTG content number of A's = 12,926,423 bp (29.22%) number of C's = 9,321,678 bp (21.07%) number of T's = 12,099,473 bp (27.35%) number of G's = 9,884,524 bp (22.35%) number of N's = 454 bp (0%) GC percentage = 43.42% >>>>>>> Mismatches and indels general error rate = 0.0345 number of mismatches = 1,456,342 number of insertions = 29,757 mapped reads with insertion percentage = 8.34% number of deletions = 108,897 mapped reads with deletion percentage = 29.76% homopolymer indels = 28.61% >>>>>>> Coverage mean coverageData = 0.0145X std coverageData = 2.8156X There is a 0.02% of reference with a coverageData >= 1X There is a 0.01% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% 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 914274 0.003668091161947396 1.4200093432835779 chr2 243199373 1865713 0.0076715370479182934 2.189400242291202 chr3 198022430 1225417 0.006188273722325294 2.120780703393486 chr4 191154276 1968379 0.010297331774048308 2.877394283443161 chr5 180915260 771150 0.004262492837807048 1.4119129922211362 chr6 171115067 980880 0.005732283060731291 1.730783725528446 chr7 159138663 855965 0.005378736906945109 1.605943764765823 chr8 146364022 748416 0.005113387769570858 1.3425614235513634 chr9 141213431 617717 0.00437435019902604 1.4838226460328734 chr10 135534747 1216558 0.008975986062083401 2.8761980312657753 chr11 135006516 1282697 0.009501000677626553 2.3611360970785533 chr12 133851895 1495273 0.01117110071545868 2.7538248845325266 chr13 115169878 816112 0.0070861584137477335 2.130935819207957 chr14 107349540 191133 0.0017804733956009499 0.564683237066185 chr15 102531392 335713 0.0032742459987278824 0.7775890343568234 chr16 90354753 157531 0.0017434722000734151 0.5945003435667069 chr17 81195210 278584 0.0034310398359706194 0.9536464414535495 chr18 78077248 284028 0.0036377819054278144 0.8586687445666551 chr19 59128983 110904 0.0018756284037559042 0.602936711562382 chr20 63025520 156113 0.0024769807531933095 0.837247457862025 chr21 48129895 157224 0.003266659941809555 0.8024217006809304 chr22 51304566 51824 0.0010101245179620075 0.28978278718152395 chrMT 16571 392787 23.70327680888299 110.46039830361353 chrX 155270560 27610737 0.1778233877690658 9.608688003707234 chrY 59373566 534026 0.008994339332759633 1.9154378653107471