BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082896.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 3,813,574 number of mapped reads = 3,296,138 (86.43%) number of supplementary alignments = 23,186 (0.61%) number of secondary alignments = 0 number of mapped bases = 227,533,038 bp number of sequenced bases = 227,447,754 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 165,383 duplication rate = 4% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.8467 >>>>>>> ACTG content number of A's = 65,595,872 bp (28.84%) number of C's = 41,377,244 bp (18.19%) number of T's = 73,918,400 bp (32.5%) number of G's = 46,543,752 bp (20.46%) number of N's = 12,486 bp (0.01%) GC percentage = 38.66% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 1,987,784 number of insertions = 18,491 mapped reads with insertion percentage = 0.56% number of deletions = 49,601 mapped reads with deletion percentage = 1.49% homopolymer indels = 47.63% >>>>>>> Coverage mean coverageData = 0.0735X std coverageData = 0.5603X There is a 5.56% of reference with a coverageData >= 1X There is a 1.24% of reference with a coverageData >= 2X There is a 0.31% of reference with a coverageData >= 3X There is a 0.09% of reference with a coverageData >= 4X There is a 0.03% 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% 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 21510371 0.08630017014079977 1.076895917548423 chr2 243199373 23686192 0.09739413267319566 0.6460061444123391 chr3 198022430 16752687 0.08459994658180894 0.3629278211475363 chr4 191154276 13021094 0.06811824601820574 0.33829299458091505 chr5 180915260 12880862 0.07119831682523631 0.3373297225244475 chr6 171115067 16781962 0.09807413393935673 0.5680783015608241 chr7 159138663 10904875 0.06852435979055574 0.45004870361124283 chr8 146364022 17936551 0.12254754108902528 0.8385759601118798 chr9 141213431 6990243 0.049501261675314726 0.5150588035154383 chr10 135534747 9353036 0.06900839974268738 0.45091868567734295 chr11 135006516 9175827 0.06796580840586983 0.43712177652139733 chr12 133851895 7034193 0.05255206136603445 0.30164073385401524 chr13 115169878 5658780 0.04913420156614215 0.27443412261055594 chr14 107349540 4908383 0.04572337245227134 0.3068987851421664 chr15 102531392 4515972 0.0440447741117179 0.2588333144958347 chr16 90354753 8019109 0.08875137979736385 0.42128723090979125 chr17 81195210 6642691 0.08181136547340662 0.4511742894415279 chr18 78077248 6872221 0.08801822779409438 1.0603258782806981 chr19 59128983 2897978 0.04901112539006463 0.6914323433087085 chr20 63025520 4256037 0.06752878833843814 0.34555596375102904 chr21 48129895 5390478 0.11199854061597267 0.43551001063359424 chr22 51304566 2706644 0.05275639599017366 0.28147677140221267 chrMT 16571 177797 10.72940679500332 6.941246851195375 chrX 155270560 9094865 0.05857430410504091 0.35135458195294045 chrY 59373566 364190 0.006133874458542713 0.12946568847081294