BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818863.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 = 326,367 number of mapped reads = 317,788 (97.37%) number of supplementary alignments = 5,059 (1.55%) number of secondary alignments = 0 number of mapped bases = 29,388,721 bp number of sequenced bases = 29,369,601 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 29,510 duplication rate = 7.74% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.2764 >>>>>>> ACTG content number of A's = 8,514,365 bp (28.99%) number of C's = 6,467,727 bp (22.02%) number of T's = 8,263,784 bp (28.14%) number of G's = 6,123,160 bp (20.85%) number of N's = 565 bp (0%) GC percentage = 42.87% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 179,643 number of insertions = 4,409 mapped reads with insertion percentage = 1.33% number of deletions = 9,746 mapped reads with deletion percentage = 3% homopolymer indels = 39.77% >>>>>>> Coverage mean coverageData = 0.0095X std coverageData = 0.1486X There is a 0.83% of reference with a coverageData >= 1X There is a 0.09% of reference with a coverageData >= 2X There is a 0.01% 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 2669164 0.010708755666450276 0.2024102875244556 chr2 243199373 2146696 0.008826897756845779 0.21134185543200562 chr3 198022430 1709492 0.008632820029528978 0.10314243690400146 chr4 191154276 1702936 0.008908699484179992 0.11475856155078237 chr5 180915260 1525209 0.008430516032754782 0.10329974937974586 chr6 171115067 1380717 0.008068938780241952 0.1013154758175366 chr7 159138663 2515950 0.0158097972709498 0.2573337443464529 chr8 146364022 2814353 0.019228448094983343 0.16262831642045725 chr9 141213431 1019921 0.007222549532133385 0.11708796306267172 chr10 135534747 1295898 0.009561371003997964 0.17553097692750086 chr11 135006516 1265620 0.009374510486590144 0.11368715422684873 chr12 133851895 1073618 0.008020939860433056 0.09935392148251043 chr13 115169878 695601 0.006039782381292442 0.08517264502825868 chr14 107349540 936754 0.008726204136505848 0.10590163133664668 chr15 102531392 844865 0.00824006173640947 0.09992467779005983 chr16 90354753 716212 0.007926666569494136 0.15465404423330986 chr17 81195210 766826 0.009444227067089302 0.1150319703162286 chr18 78077248 494951 0.0063392475103630705 0.12509968665276985 chr19 59128983 555789 0.009399603575119837 0.17758915735117067 chr20 63025520 1160099 0.018406813620895156 0.15608000478973236 chr21 48129895 294214 0.006112915891464131 0.09513430460629342 chr22 51304566 345878 0.006741661161308723 0.09309728136061493 chrMT 16571 31646 1.9097218031500816 1.7263298432662937 chrX 155270560 1303146 0.00839274360831828 0.10736324048088991 chrY 59373566 123166 0.002074424837477338 0.16455384962359204