BamQC report ----------------------------------- >>>>>>> Input bam file = SRR089542.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 = 12,232,694 number of mapped reads = 10,160,992 (83.06%) number of supplementary alignments = 357 (0%) number of secondary alignments = 0 number of mapped bases = 477,823,218 bp number of sequenced bases = 477,732,680 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,116,866 duplication rate = 20.55% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.9577 >>>>>>> ACTG content number of A's = 154,649,714 bp (32.37%) number of C's = 89,419,248 bp (18.72%) number of T's = 130,854,431 bp (27.39%) number of G's = 102,786,206 bp (21.52%) number of N's = 23,081 bp (0%) GC percentage = 40.23% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 2,355,471 number of insertions = 19,152 mapped reads with insertion percentage = 0.19% number of deletions = 60,936 mapped reads with deletion percentage = 0.6% homopolymer indels = 45.84% >>>>>>> Coverage mean coverageData = 0.1544X std coverageData = 1.297X There is a 5.46% of reference with a coverageData >= 1X There is a 2.52% of reference with a coverageData >= 2X There is a 1.55% of reference with a coverageData >= 3X There is a 1.06% of reference with a coverageData >= 4X There is a 0.78% of reference with a coverageData >= 5X There is a 0.59% of reference with a coverageData >= 6X There is a 0.47% of reference with a coverageData >= 7X There is a 0.37% of reference with a coverageData >= 8X There is a 0.31% of reference with a coverageData >= 9X There is a 0.26% of reference with a coverageData >= 10X There is a 0.22% of reference with a coverageData >= 11X There is a 0.18% of reference with a coverageData >= 12X There is a 0.16% of reference with a coverageData >= 13X There is a 0.14% of reference with a coverageData >= 14X There is a 0.12% of reference with a coverageData >= 15X There is a 0.11% of reference with a coverageData >= 16X There is a 0.09% of reference with a coverageData >= 17X There is a 0.08% of reference with a coverageData >= 18X There is a 0.07% of reference with a coverageData >= 19X There is a 0.07% of reference with a coverageData >= 20X There is a 0.06% of reference with a coverageData >= 21X There is a 0.05% of reference with a coverageData >= 22X There is a 0.05% of reference with a coverageData >= 23X There is a 0.04% of reference with a coverageData >= 24X There is a 0.04% of reference with a coverageData >= 25X There is a 0.04% of reference with a coverageData >= 26X There is a 0.03% of reference with a coverageData >= 27X There is a 0.03% of reference with a coverageData >= 28X There is a 0.03% of reference with a coverageData >= 29X There is a 0.03% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% 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 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 37390403 0.15001127319157212 1.2568281420990566 chr2 243199373 44622814 0.1834824385011881 1.5226343962193611 chr3 198022430 45747099 0.23101978397093703 1.6663659004819986 chr4 191154276 20835314 0.10899737340952813 0.9786059284250268 chr5 180915260 18910345 0.10452598083765847 0.9464013081432606 chr6 171115067 33376345 0.19505205231284514 1.4608974430168105 chr7 159138663 34477152 0.2166484960351841 1.6338638997731456 chr8 146364022 35869464 0.24507022634291917 1.828332958454064 chr9 141213431 16607100 0.11760283623446555 1.0954516492534514 chr10 135534747 21043912 0.1552658079628835 1.2441916980222039 chr11 135006516 23332833 0.17282745819468448 1.3563746047075576 chr12 133851895 18972181 0.14174010013081997 1.1389995928940868 chr13 115169878 12476368 0.1083301312518539 0.9906397545038258 chr14 107349540 14484040 0.13492409934872568 1.1745284557483004 chr15 102531392 12390735 0.12084820812732162 1.0394554177432767 chr16 90354753 8229254 0.0910771567268852 0.8595381246500505 chr17 81195210 10471010 0.12896093254762195 1.0509641027498202 chr18 78077248 22258260 0.28507997617948827 1.898256738036539 chr19 59128983 6539920 0.11060430381493286 1.0960959434696487 chr20 63025520 9866143 0.1565420324973122 1.2741904834023736 chr21 48129895 7698130 0.15994487417851214 1.336828118371085 chr22 51304566 3993244 0.07783408595640395 0.790476756698902 chrMT 16571 122462 7.390139400156901 14.929753222679485 chrX 155270560 17168831 0.11057363997399121 0.990570469688482 chrY 59373566 939859 0.01582958652003486 0.36132006173955517