BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818812.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 2,635,849 number of mapped reads = 2,401,477 (91.11%) number of supplementary alignments = 18,395 (0.7%) number of secondary alignments = 0 number of mapped bases = 163,156,936 bp number of sequenced bases = 163,087,442 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,104,246 duplication rate = 39.77% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.609 >>>>>>> ACTG content number of A's = 47,255,855 bp (28.98%) number of C's = 34,448,128 bp (21.12%) number of T's = 47,549,119 bp (29.16%) number of G's = 33,823,974 bp (20.74%) number of N's = 10,366 bp (0.01%) GC percentage = 41.86% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 836,963 number of insertions = 20,730 mapped reads with insertion percentage = 0.85% number of deletions = 42,375 mapped reads with deletion percentage = 1.75% homopolymer indels = 39.23% >>>>>>> Coverage mean coverageData = 0.0527X std coverageData = 0.6306X There is a 2.42% of reference with a coverageData >= 1X There is a 1.2% of reference with a coverageData >= 2X There is a 0.67% of reference with a coverageData >= 3X There is a 0.38% of reference with a coverageData >= 4X There is a 0.21% of reference with a coverageData >= 5X There is a 0.12% of reference with a coverageData >= 6X There is a 0.07% of reference with a coverageData >= 7X There is a 0.04% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.02% 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% 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 13172069 0.05284668478318455 0.8955693230876303 chr2 243199373 14335731 0.058946414306750704 1.0598305129977055 chr3 198022430 11045422 0.05577864083376818 0.43346042738990587 chr4 191154276 10712142 0.05603924863286867 0.5218599205277404 chr5 180915260 10171390 0.05622184662587335 0.4529283635861613 chr6 171115067 9728022 0.05685076230020118 0.508655574969358 chr7 159138663 8952834 0.05625806973130094 0.5453081902859483 chr8 146364022 8504615 0.05810591212094458 0.5264574427421999 chr9 141213431 7105131 0.05031483867848236 0.518777127611649 chr10 135534747 7570370 0.05585556595313525 0.6564578514212029 chr11 135006516 7679238 0.05688049901235878 0.516981472807548 chr12 133851895 7579137 0.05662330742497146 0.470358214119742 chr13 115169878 5196781 0.04512274468155641 0.3877401388410052 chr14 107349540 5017838 0.04674298557776773 0.4686226048867076 chr15 102531392 4759136 0.04641637948307578 0.3990637133867528 chr16 90354753 4840830 0.053575820189558816 0.7502124766162778 chr17 81195210 4406480 0.05427019648080225 0.4567269182003964 chr18 78077248 4450846 0.05700567212614871 0.7114099581863432 chr19 59128983 3300377 0.05581656968461642 0.7995370603435413 chr20 63025520 3510043 0.05569240840853039 0.47087641667291646 chr21 48129895 2193571 0.04557606036747015 0.4145716730138824 chr22 51304566 1983269 0.038656773746024865 0.402193680255365 chrMT 16571 260276 15.706716553014303 12.486651276592301 chrX 155270560 5176238 0.03333689271166408 0.39118266489055714 chrY 59373566 1505150 0.025350506991613068 1.1159858567425152