BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081732.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 = 2,730,705 number of mapped reads = 2,490,233 (91.19%) number of supplementary alignments = 15,184 (0.56%) number of secondary alignments = 0 number of mapped bases = 167,181,317 bp number of sequenced bases = 167,123,814 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 99,090 duplication rate = 3.09% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6163 >>>>>>> ACTG content number of A's = 45,562,124 bp (27.26%) number of C's = 32,619,938 bp (19.52%) number of T's = 50,670,317 bp (30.32%) number of G's = 38,269,680 bp (22.9%) number of N's = 1,755 bp (0%) GC percentage = 42.42% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 1,354,845 number of insertions = 12,209 mapped reads with insertion percentage = 0.49% number of deletions = 32,116 mapped reads with deletion percentage = 1.28% homopolymer indels = 46.37% >>>>>>> Coverage mean coverageData = 0.054X std coverageData = 0.4022X There is a 4.5% of reference with a coverageData >= 1X There is a 0.65% of reference with a coverageData >= 2X There is a 0.12% of reference with a coverageData >= 3X There is a 0.03% 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 13266752 0.05322655545159103 0.5881821543467731 chr2 243199373 14013870 0.05762296928290189 0.5476378529486934 chr3 198022430 11256946 0.05684682285739045 0.27843431715334893 chr4 191154276 10979085 0.05743572798758632 0.31113520874268824 chr5 180915260 10322776 0.05705862512648187 0.27793851861694785 chr6 171115067 9547226 0.05579418672699348 0.3130510250285017 chr7 159138663 9222865 0.05795489811297459 0.5240384039860976 chr8 146364022 8312646 0.05679432613569474 0.46041253867098336 chr9 141213431 7076527 0.05011228004225746 0.40278883164792667 chr10 135534747 7931431 0.05851953964248002 0.4559753136887865 chr11 135006516 7672635 0.05683159026191002 0.3663481279341952 chr12 133851895 7433586 0.0555359040677011 0.2759534308502497 chr13 115169878 5213324 0.04526638467047781 0.24768537462109333 chr14 107349540 5159162 0.04805947002660654 0.27291493290080066 chr15 102531392 4808274 0.04689562782879218 0.2566529533548397 chr16 90354753 4793879 0.0530561906355939 0.3193079648891513 chr17 81195210 4601126 0.056667456122103756 0.29503728700983456 chr18 78077248 4459014 0.05711028646911326 0.705210145937581 chr19 59128983 3312626 0.056023726976667264 0.5054104007166104 chr20 63025520 3339670 0.05298917010125422 0.2760131170273761 chr21 48129895 2210100 0.045919485176520745 0.28163045960698774 chr22 51304566 1873868 0.03652439044119387 0.2206521073913423 chrMT 16571 988 0.05962223160943818 0.24257649302376175 chrX 155270560 9903383 0.06378145992389027 0.33354110482303545 chrY 59373566 469558 0.0079085362667959 0.20014490580686478