BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082419.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 = 2,958,556 number of mapped reads = 2,670,320 (90.26%) number of supplementary alignments = 21,060 (0.71%) number of secondary alignments = 0 number of mapped bases = 179,109,992 bp number of sequenced bases = 179,043,695 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 111,603 duplication rate = 2.97% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.9881 >>>>>>> ACTG content number of A's = 50,170,152 bp (28.02%) number of C's = 33,657,801 bp (18.8%) number of T's = 55,283,412 bp (30.88%) number of G's = 39,928,772 bp (22.3%) number of N's = 3,558 bp (0%) GC percentage = 41.1% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 1,514,486 number of insertions = 14,925 mapped reads with insertion percentage = 0.55% number of deletions = 40,870 mapped reads with deletion percentage = 1.51% homopolymer indels = 46.78% >>>>>>> Coverage mean coverageData = 0.0579X std coverageData = 0.5283X There is a 4.95% of reference with a coverageData >= 1X There is a 0.59% of reference with a coverageData >= 2X There is a 0.09% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% 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% 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 14136028 0.05671411346252975 0.9490367193985765 chr2 243199373 15303464 0.06292558986161531 0.6885670888013878 chr3 198022430 12045165 0.06082727598080682 0.2793435922339388 chr4 191154276 12006273 0.06280933521989328 0.3007748120386325 chr5 180915260 11056140 0.06111225774984377 0.2838484729465553 chr6 171115067 10564117 0.06173691881849305 0.37188233091887307 chr7 159138663 10008780 0.0628934528625517 0.7133741194914459 chr8 146364022 9234077 0.06308980085283526 0.823796244278511 chr9 141213431 7560656 0.053540629573684106 0.47846592266815624 chr10 135534747 8319068 0.06137959589063902 0.48149682780092173 chr11 135006516 8096250 0.05996932770267177 0.4271722300982626 chr12 133851895 8092430 0.06045809063816392 0.28581104506572724 chr13 115169878 5768505 0.05008692463840241 0.2523824453396983 chr14 107349540 5414003 0.0504334066079836 0.2970538491738443 chr15 102531392 5034881 0.049105750948938647 0.25652406804568284 chr16 90354753 4921202 0.05446533620649707 0.3177922347412308 chr17 81195210 4542079 0.05594023342017343 0.3138264957647778 chr18 78077248 4796649 0.06143465763547404 0.9370877035091172 chr19 59128983 3480535 0.0588634341977436 0.7397924910844087 chr20 63025520 3543910 0.05622976216618284 0.2798034807309623 chr21 48129895 2351865 0.04886495181425183 0.2756589016805175 chr22 51304566 1870437 0.03645751530185442 0.21346810915909514 chrMT 16571 1726 0.10415786615171083 0.3390957527910765 chrX 155270560 10490493 0.06756266609716613 0.3511002188407718 chrY 59373566 471259 0.007937185379769845 0.16955171090323187