BamQC report ----------------------------------- >>>>>>> Input bam file = SRR090142.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 = 25,129,587 number of mapped reads = 22,441,111 (89.3%) number of supplementary alignments = 146,464 (0.58%) number of secondary alignments = 0 number of mapped bases = 1,459,679,399 bp number of sequenced bases = 1,459,146,557 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,269,146 duplication rate = 9.99% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.9035 >>>>>>> ACTG content number of A's = 396,044,840 bp (27.14%) number of C's = 268,041,143 bp (18.37%) number of T's = 457,888,327 bp (31.38%) number of G's = 336,693,207 bp (23.07%) number of N's = 479,040 bp (0.03%) GC percentage = 41.44% >>>>>>> Mismatches and indels general error rate = 0.0078 number of mismatches = 11,181,878 number of insertions = 103,295 mapped reads with insertion percentage = 0.46% number of deletions = 315,501 mapped reads with deletion percentage = 1.39% homopolymer indels = 46.51% >>>>>>> Coverage mean coverageData = 0.4715X std coverageData = 4.0385X There is a 22.41% of reference with a coverageData >= 1X There is a 10.5% of reference with a coverageData >= 2X There is a 5.37% of reference with a coverageData >= 3X There is a 2.92% of reference with a coverageData >= 4X There is a 1.67% of reference with a coverageData >= 5X There is a 1.01% of reference with a coverageData >= 6X There is a 0.64% of reference with a coverageData >= 7X There is a 0.42% of reference with a coverageData >= 8X There is a 0.29% of reference with a coverageData >= 9X There is a 0.2% of reference with a coverageData >= 10X There is a 0.15% of reference with a coverageData >= 11X There is a 0.11% of reference with a coverageData >= 12X There is a 0.08% of reference with a coverageData >= 13X There is a 0.07% of reference with a coverageData >= 14X There is a 0.05% of reference with a coverageData >= 15X There is a 0.04% 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 0.02% 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 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% 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 119256344 0.4784595662050527 7.01025756778565 chr2 243199373 151311682 0.6221713491012989 5.535646403687843 chr3 198022430 137214698 0.692925028745481 1.6116531391684734 chr4 191154276 78382292 0.41004728557576187 1.5239619497120374 chr5 180915260 65674817 0.36301424766490126 1.1533707833937668 chr6 171115067 82841120 0.4841252231751164 1.8516641023811335 chr7 159138663 108190428 0.6798500500158154 8.248381636220687 chr8 146364022 125898261 0.8601721876705465 7.836065980955397 chr9 141213431 46621424 0.3301486527864336 3.4378326560112415 chr10 135534747 44415938 0.327708864207346 2.6915665761869088 chr11 135006516 61188734 0.4532280056764075 2.9668726028040844 chr12 133851895 51934531 0.38799996817377896 1.2452374324617619 chr13 115169878 44476269 0.3861797005637186 1.0916337238582166 chr14 107349540 52342055 0.48758527516745764 1.5192033672793328 chr15 102531392 38336638 0.3739014681474333 1.185798639150833 chr16 90354753 26388808 0.29205777365137614 1.1686191484361628 chr17 81195210 27639973 0.3404138372202006 1.5687609702141332 chr18 78077248 55790178 0.7145510302822149 5.15553149977213 chr19 59128983 24131887 0.4081228151683245 3.8783244633685845 chr20 63025520 34536707 0.5479797231343748 1.5394835184254954 chr21 48129895 21506167 0.44683594260905823 1.4650049542595949 chr22 51304566 11208372 0.21846733875499502 0.8003101102239644 chrMT 16571 2007112 121.12196005069097 63.705176657329 chrX 155270560 45098469 0.2904508684711384 1.623342158733053 chrY 59373566 3286495 0.05535283159512434 2.0010798900297595