BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818942.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 = 1,951,596 number of mapped reads = 1,921,098 (98.44%) number of supplementary alignments = 24,547 (1.26%) number of secondary alignments = 0 number of mapped bases = 177,907,257 bp number of sequenced bases = 177,812,211 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 722,516 duplication rate = 32.26% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.2175 >>>>>>> ACTG content number of A's = 51,849,478 bp (29.16%) number of C's = 38,153,981 bp (21.46%) number of T's = 50,149,243 bp (28.2%) number of G's = 37,651,400 bp (21.17%) number of N's = 8,109 bp (0%) GC percentage = 42.63% >>>>>>> Mismatches and indels general error rate = 0.0068 number of mismatches = 1,161,981 number of insertions = 23,127 mapped reads with insertion percentage = 1.17% number of deletions = 52,116 mapped reads with deletion percentage = 2.66% homopolymer indels = 42.8% >>>>>>> Coverage mean coverageData = 0.0575X std coverageData = 0.6471X There is a 3.04% of reference with a coverageData >= 1X There is a 1.29% of reference with a coverageData >= 2X There is a 0.62% of reference with a coverageData >= 3X There is a 0.31% of reference with a coverageData >= 4X There is a 0.16% of reference with a coverageData >= 5X There is a 0.08% of reference with a coverageData >= 6X There is a 0.05% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% 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% 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 21265237 0.0853166861317469 1.2268796094229923 chr2 243199373 14859742 0.06110107035514438 0.8553345213343047 chr3 198022430 10982412 0.055460444556710065 0.3957243709937005 chr4 191154276 11380095 0.05953356230440798 0.4593509110096903 chr5 180915260 9125189 0.05043902322004236 0.3875333040434958 chr6 171115067 9300431 0.05435191162914953 0.4207350307978405 chr7 159138663 9010802 0.056622330677743596 0.5277837240594663 chr8 146364022 11448714 0.07822082123433312 0.5652629037878025 chr9 141213431 6848704 0.048498956165154004 0.6819031086044248 chr10 135534747 9046834 0.06674918572725856 0.8249955416641095 chr11 135006516 6585868 0.04878185286997555 0.46496548357122197 chr12 133851895 8411389 0.06284101543724877 0.43133907186005377 chr13 115169878 2849549 0.024742137870459497 0.2561916079105124 chr14 107349540 5629722 0.05244290753365129 0.4207653137185909 chr15 102531392 5013250 0.04889478141484707 0.3725941654131722 chr16 90354753 5298910 0.05864561435965632 0.6604726038091675 chr17 81195210 3845644 0.04736294173018334 0.4119021157941607 chr18 78077248 4396385 0.0563081449797001 0.9281755391027843 chr19 59128983 2929496 0.049544163477325494 1.0480031060325061 chr20 63025520 3931620 0.062381397249875924 0.44830194168022414 chr21 48129895 2356370 0.048958552683316676 0.4166308412827405 chr22 51304566 2308413 0.04499429933780163 0.38844353866647086 chrMT 16571 61928 3.7371311327017076 3.6110742970189165 chrX 155270560 10457168 0.06734804073611894 0.5169388489512159 chrY 59373566 563385 0.0094888186436368 0.4829968602667868