BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006438.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP030642/SRP030642.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 = 2,140,433 number of mapped reads = 2,028,910 (94.79%) number of supplementary alignments = 7,972 (0.37%) number of secondary alignments = 0 number of mapped bases = 114,121,518 bp number of sequenced bases = 114,078,362 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 82,527 duplication rate = 3.43% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.977 >>>>>>> ACTG content number of A's = 32,259,485 bp (28.28%) number of C's = 23,804,747 bp (20.87%) number of T's = 33,258,809 bp (29.15%) number of G's = 24,752,728 bp (21.7%) number of N's = 2,593 bp (0%) GC percentage = 42.57% >>>>>>> Mismatches and indels general error rate = 0.0042 number of mismatches = 470,383 number of insertions = 7,566 mapped reads with insertion percentage = 0.37% number of deletions = 24,725 mapped reads with deletion percentage = 1.21% homopolymer indels = 41.57% >>>>>>> Coverage mean coverageData = 0.0369X std coverageData = 0.3633X There is a 3.11% of reference with a coverageData >= 1X There is a 0.43% of reference with a coverageData >= 2X There is a 0.07% of reference with a coverageData >= 3X There is a 0.02% 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% 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 9434505 0.03785148041817717 0.38825362694748666 chr2 243199373 9498220 0.039055281610450535 0.2618974626817721 chr3 198022430 7789973 0.03933884156456417 0.22682254632203197 chr4 191154276 7454873 0.038999247916379334 0.24126535145876896 chr5 180915260 7065142 0.03905221704349318 0.22949587827337886 chr6 171115067 6623764 0.03870941417449815 0.23405227919299154 chr7 159138663 6058427 0.038070113734711974 0.27015521232419404 chr8 146364022 6055455 0.041372564905328986 1.1923156619019057 chr9 141213431 4751204 0.0336455531627158 0.23146646771059654 chr10 135534747 5622842 0.04148635036002982 0.299625461642992 chr11 135006516 5369278 0.03977051003967838 0.24843485657133532 chr12 133851895 5197249 0.03882835577337176 0.22788682300570154 chr13 115169878 3729051 0.03237870061822936 0.20741175852514468 chr14 107349540 3539056 0.032967593526716556 0.21148331931140024 chr15 102531392 3392214 0.03308463811746553 0.20821062316064945 chr16 90354753 3298675 0.03650804070041561 0.24154042711086074 chr17 81195210 3207771 0.03950689948335622 0.2432458858047342 chr18 78077248 2965434 0.03798077001894329 0.31863129774579396 chr19 59128983 2225808 0.037643265401672815 0.32372574277317917 chr20 63025520 2471669 0.03921695529049185 0.22956309947750675 chr21 48129895 2140450 0.04447235964258804 0.2626596941850924 chr22 51304566 1432720 0.027925779549523917 0.21151272404072657 chrMT 16571 204115 12.31760304145797 7.027160608495902 chrX 155270560 3511382 0.02261460253637264 0.177215986802463 chrY 59373566 1082241 0.018227657068803985 0.2545875998178761