BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975310.sorted.bam outfile = /mainsd/zhouyj/SRP029757/SRP029757.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 = 4,278,512 number of mapped reads = 4,194,880 (98.05%) number of supplementary alignments = 16,973 (0.4%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,096,739 number of mapped paired reads (second in pair) = 2,098,141 number of mapped paired reads (both in pair) = 4,180,656 number of mapped paired reads (singletons) = 14,224 number of mapped bases = 381,582,337 bp number of sequenced bases = 381,370,703 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 207,134 duplication rate = 2.94% >>>>>>> Insert size mean insert size = 46,046.0812 std insert size = 2,055,482.5844 median insert size = 166 >>>>>>> Mapping quality mean mapping quality = 52.8203 >>>>>>> ACTG content number of A's = 110,184,937 bp (28.89%) number of C's = 73,938,069 bp (19.39%) number of T's = 113,851,046 bp (29.85%) number of G's = 83,389,059 bp (21.87%) number of N's = 7,592 bp (0%) GC percentage = 41.25% >>>>>>> Mismatches and indels general error rate = 0.0078 number of mismatches = 2,822,697 number of insertions = 64,144 mapped reads with insertion percentage = 1.49% number of deletions = 121,213 mapped reads with deletion percentage = 2.83% homopolymer indels = 44.92% >>>>>>> Coverage mean coverageData = 0.1233X std coverageData = 1.1359X There is a 8.29% of reference with a coverageData >= 1X There is a 2.57% of reference with a coverageData >= 2X There is a 0.64% of reference with a coverageData >= 3X There is a 0.21% of reference with a coverageData >= 4X There is a 0.08% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.02% 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% 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 35650145 0.1430293126531468 1.135115431444979 chr2 243199373 33714008 0.13862703502940363 1.4533165681791018 chr3 198022430 20491606 0.10348123694876384 0.436204137102198 chr4 191154276 24994630 0.13075632166345053 0.8597880482058704 chr5 180915260 23951992 0.13239343104611517 0.484218577051691 chr6 171115067 27640613 0.16153231556166822 0.984937653820639 chr7 159138663 22054029 0.13858372682193515 1.2998341510479035 chr8 146364022 19828277 0.13547234305982656 0.6208947249571131 chr9 141213431 16318399 0.11555840605558262 1.7010167052074252 chr10 135534747 20426593 0.15071111616860877 2.726816811202909 chr11 135006516 13946695 0.10330386571859984 0.9822737023987843 chr12 133851895 17188250 0.1284124516877404 0.47571262709276113 chr13 115169878 13131236 0.11401623608561955 0.4485195941687546 chr14 107349540 11389877 0.10610084589090926 0.478162015827593 chr15 102531392 11222395 0.10945325895897327 0.43680571915921035 chr16 90354753 12247260 0.13554638348687645 1.6723643388827112 chr17 81195210 7946336 0.09786705398015474 0.9676142636494317 chr18 78077248 11034919 0.141333349761508 1.7981455897272165 chr19 59128983 4916145 0.08314272883739604 0.7380020105767213 chr20 63025520 8000505 0.1269407217901574 0.5082565791736059 chr21 48129895 4923971 0.10230587455052624 0.5843662577959748 chr22 51304566 3819255 0.07444278936108728 0.3836020770395663 chrMT 16571 116851 7.051535815581437 6.485114010794487 chrX 155270560 12675027 0.08163187535357637 0.5307467761070724 chrY 59373566 3953323 0.06658389021134423 1.3103481435734823