BamQC report ----------------------------------- >>>>>>> Input bam file = SRR090213.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 29,073,567 number of mapped reads = 25,315,407 (87.07%) number of supplementary alignments = 1,364 (0%) number of secondary alignments = 0 number of mapped bases = 1,193,565,244 bp number of sequenced bases = 1,193,338,628 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 4,637,146 duplication rate = 12.07% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8524 >>>>>>> ACTG content number of A's = 355,529,697 bp (29.79%) number of C's = 239,273,262 bp (20.05%) number of T's = 349,761,264 bp (29.31%) number of G's = 248,770,297 bp (20.85%) number of N's = 4,108 bp (0%) GC percentage = 40.9% >>>>>>> Mismatches and indels general error rate = 0.0037 number of mismatches = 4,319,040 number of insertions = 43,468 mapped reads with insertion percentage = 0.17% number of deletions = 149,476 mapped reads with deletion percentage = 0.59% homopolymer indels = 48.28% >>>>>>> Coverage mean coverageData = 0.3856X std coverageData = 1.8799X There is a 16% of reference with a coverageData >= 1X There is a 8.38% of reference with a coverageData >= 2X There is a 4.85% of reference with a coverageData >= 3X There is a 2.97% of reference with a coverageData >= 4X There is a 1.89% of reference with a coverageData >= 5X There is a 1.23% of reference with a coverageData >= 6X There is a 0.82% of reference with a coverageData >= 7X There is a 0.56% of reference with a coverageData >= 8X There is a 0.39% of reference with a coverageData >= 9X There is a 0.28% of reference with a coverageData >= 10X There is a 0.2% of reference with a coverageData >= 11X There is a 0.15% of reference with a coverageData >= 12X There is a 0.11% of reference with a coverageData >= 13X There is a 0.08% of reference with a coverageData >= 14X There is a 0.07% of reference with a coverageData >= 15X There is a 0.05% of reference with a coverageData >= 16X There is a 0.04% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% 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% 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 96402139 0.3867678989654353 2.791654085324113 chr2 243199373 124865050 0.5134266937439843 2.062249877467832 chr3 198022430 114367111 0.5775462456450009 1.6099502552104636 chr4 191154276 63635193 0.3328996574473699 1.145973993984339 chr5 180915260 56722533 0.3135309481356078 1.115001573785592 chr6 171115067 66392018 0.3879963299783531 1.3957253678809494 chr7 159138663 86451891 0.543248820684135 3.1643426457930595 chr8 146364022 106928667 0.730566607413945 3.6784780737231966 chr9 141213431 39099238 0.27688044772455106 1.5654354746552726 chr10 135534747 36581764 0.2699069043896175 1.3911437643913351 chr11 135006516 37910973 0.28080846853347435 1.383891366846449 chr12 133851895 43343906 0.3238198906335992 1.1712419478537985 chr13 115169878 37401137 0.3247475611635188 1.1308717648952533 chr14 107349540 43429296 0.40455968418681626 1.3309906999914014 chr15 102531392 31811706 0.31026308508520006 1.1199039497786194 chr16 90354753 23861003 0.2640813261921041 1.0508737946892122 chr17 81195210 23249401 0.28633956362696766 1.1560641558034424 chr18 78077248 45483279 0.5825420358053603 2.655359201074967 chr19 59128983 18875635 0.31922813554902507 2.0570904293068972 chr20 63025520 28659876 0.4547344631190667 1.4154434582469955 chr21 48129895 17881805 0.37153218389526926 1.3136560709436256 chr22 51304566 9223533 0.17977996344418937 0.822056134296048 chrMT 16571 138606 8.364371492366182 6.815347109948221 chrX 155270560 38239040 0.24627360138328863 1.1050758914607957 chrY 59373566 2610444 0.04396643449039258 0.8896721298268873