BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094054.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 = 373,754 number of mapped reads = 358,104 (95.81%) number of supplementary alignments = 15,223 (4.07%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 179,878 number of mapped paired reads (second in pair) = 178,226 number of mapped paired reads (both in pair) = 355,642 number of mapped paired reads (singletons) = 2,462 number of mapped bases = 47,738,597 bp number of sequenced bases = 46,536,777 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 335,864 duplication rate = 50.88% >>>>>>> Insert size mean insert size = 632,399.6342 std insert size = 6,975,041.0464 median insert size = 169 >>>>>>> Mapping quality mean mapping quality = 43.0898 >>>>>>> ACTG content number of A's = 12,852,241 bp (27.62%) number of C's = 10,459,269 bp (22.48%) number of T's = 12,383,606 bp (26.61%) number of G's = 10,841,151 bp (23.3%) number of N's = 510 bp (0%) GC percentage = 45.77% >>>>>>> Mismatches and indels general error rate = 0.0452 number of mismatches = 2,030,406 number of insertions = 34,735 mapped reads with insertion percentage = 9.49% number of deletions = 162,535 mapped reads with deletion percentage = 42.13% homopolymer indels = 28.35% >>>>>>> Coverage mean coverageData = 0.0154X std coverageData = 3.4979X 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% 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 977997 0.003923749501911974 1.553262601714903 chr2 243199373 2149212 0.008837243178254411 2.696885827997245 chr3 198022430 1206088 0.0060906635677584605 1.6725200413630867 chr4 191154276 1337651 0.006997756095186696 2.4495442383769306 chr5 180915260 445520 0.0024625893912984453 1.0659815361332707 chr6 171115067 1274451 0.00744791807257978 3.2897551055455914 chr7 159138663 1260923 0.007923423360670059 2.1354544596896483 chr8 146364022 663422 0.004532684951770456 1.254623292808623 chr9 141213431 441482 0.0031263456802490693 1.003769283874812 chr10 135534747 1256242 0.009268781827585513 3.1769878107146936 chr11 135006516 1788501 0.013247516142109762 3.2511031364466394 chr12 133851895 1531745 0.011443580981800818 3.064425523064301 chr13 115169878 1305363 0.011334239669855342 2.7433157589433796 chr14 107349540 288109 0.0026838400984298583 1.1293937913111447 chr15 102531392 628538 0.006130200592614601 1.737827387863389 chr16 90354753 501644 0.005551938147625726 2.078854784880228 chr17 81195210 1282798 0.01579893690773138 3.942146921923017 chr18 78077248 144077 0.0018453135028529695 0.5401280423768974 chr19 59128983 196182 0.0033178652844409653 0.9505113173356794 chr20 63025520 158883 0.002520931203740961 0.5969599699932912 chr21 48129895 243813 0.005065728898847588 1.4696109257808274 chr22 51304566 88127 0.001717722356329844 0.34724183844830825 chrMT 16571 2670511 161.15569368173314 654.8942083332716 chrX 155270560 25534770 0.16445339026277744 10.070028599685324 chrY 59373566 362548 0.006106219053778916 1.5229895608572324