BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082471.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 = 1,444,876 number of mapped reads = 1,264,409 (87.51%) number of supplementary alignments = 10,552 (0.73%) number of secondary alignments = 0 number of mapped bases = 85,826,896 bp number of sequenced bases = 85,794,199 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 36,053 duplication rate = 2.19% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.7914 >>>>>>> ACTG content number of A's = 24,578,003 bp (28.65%) number of C's = 16,063,764 bp (18.72%) number of T's = 26,156,957 bp (30.49%) number of G's = 18,993,768 bp (22.14%) number of N's = 1,707 bp (0%) GC percentage = 40.86% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 749,050 number of insertions = 7,250 mapped reads with insertion percentage = 0.57% number of deletions = 20,019 mapped reads with deletion percentage = 1.57% homopolymer indels = 46.64% >>>>>>> Coverage mean coverageData = 0.0277X std coverageData = 0.2605X There is a 2.54% of reference with a coverageData >= 1X There is a 0.17% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% 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 6860295 0.027523682679209856 0.40412741535289803 chr2 243199373 7169030 0.029477995405851644 0.3003628874348422 chr3 198022430 5943654 0.030015054355206124 0.18413214709358247 chr4 191154276 5849723 0.030602103821104162 0.18981958419597483 chr5 180915260 5543099 0.03063920091649538 0.18652010232347638 chr6 171115067 4810248 0.028111189063205054 0.19776898073474564 chr7 159138663 4849322 0.030472305777760618 0.3309363223587174 chr8 146364022 4167150 0.028471136164869806 0.4528038145404316 chr9 141213431 3444001 0.02438862207094168 0.2310932454354271 chr10 135534747 4052834 0.02990254595008024 0.24263610799013774 chr11 135006516 3871366 0.028675401119157833 0.2363544982767482 chr12 133851895 3889074 0.029055053721876705 0.1819140081763903 chr13 115169878 2829554 0.024568524766519245 0.16605461438591676 chr14 107349540 2614774 0.02435757060533282 0.17159454222006174 chr15 102531392 2410553 0.023510389871620976 0.16659233264819637 chr16 90354753 2394258 0.026498417853015436 0.18978551210266437 chr17 81195210 2200081 0.02709619200442982 0.19194938766672948 chr18 78077248 2181015 0.02793406601626123 0.3955723225582341 chr19 59128983 1568679 0.02652978151171651 0.33216643846834215 chr20 63025520 1633148 0.025912487512994735 0.17323213574983592 chr21 48129895 1153848 0.023973623877633642 0.17070204599545227 chr22 51304566 923970 0.01800950815956615 0.14218340320952172 chrMT 16571 24647 1.4873574316577154 1.3998467723862116 chrX 155270560 5222089 0.03363219015890714 0.20871301205055628 chrY 59373566 220484 0.003713504423837369 0.08782686208727636