BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818908.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 1,970,723 number of mapped reads = 1,942,362 (98.56%) number of supplementary alignments = 27,674 (1.4%) number of secondary alignments = 0 number of mapped bases = 179,909,870 bp number of sequenced bases = 179,798,384 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 442,473 duplication rate = 19.12% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.2509 >>>>>>> ACTG content number of A's = 52,271,026 bp (29.07%) number of C's = 38,733,196 bp (21.54%) number of T's = 50,919,143 bp (28.32%) number of G's = 37,872,410 bp (21.06%) number of N's = 2,609 bp (0%) GC percentage = 42.61% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 1,092,069 number of insertions = 25,499 mapped reads with insertion percentage = 1.27% number of deletions = 58,006 mapped reads with deletion percentage = 2.92% homopolymer indels = 41.73% >>>>>>> Coverage mean coverageData = 0.0581X std coverageData = 0.714X There is a 3.98% of reference with a coverageData >= 1X There is a 1.08% of reference with a coverageData >= 2X There is a 0.35% of reference with a coverageData >= 3X There is a 0.13% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 16820123 0.06748277269086524 1.069683425538928 chr2 243199373 13539279 0.055671520995245326 0.972367766620886 chr3 198022430 11072844 0.055917120095940645 0.3207805121513006 chr4 191154276 8971232 0.04693189285496287 0.39859922539557524 chr5 180915260 7835746 0.04331169189376286 0.29705133955592017 chr6 171115067 8672605 0.0506828834657792 0.3370450464740563 chr7 159138663 16209188 0.10185575079262793 1.662763973331076 chr8 146364022 15491893 0.10584495279857778 0.586983282090944 chr9 141213431 6632479 0.04696776328591577 0.6419546913650669 chr10 135534747 8333106 0.06148317080637632 0.9361588141430699 chr11 135006516 7876214 0.058339510072239774 0.4220297051728656 chr12 133851895 6964562 0.05203185207052915 0.3131111573920806 chr13 115169878 5447633 0.04730084892509828 0.2929499535239128 chr14 107349540 6380418 0.05943591374494944 0.3570222817919257 chr15 102531392 4877974 0.04757541963343285 0.29146703668989904 chr16 90354753 4525483 0.05008572155578799 0.6506360608206798 chr17 81195210 4410207 0.05431609820332998 0.43079222364191333 chr18 78077248 3472298 0.04447259718990096 0.7220768677492971 chr19 59128983 3133626 0.05299644676790737 0.9712925298800257 chr20 63025520 7249783 0.11502932462913436 0.4982247630902068 chr21 48129895 2162457 0.044929601446252895 0.3341482513632455 chr22 51304566 1595439 0.03109740758746502 0.27095988541964966 chrMT 16571 259657 15.669362138676 10.719184671999047 chrX 155270560 7331382 0.04721681946661363 0.36636271487179034 chrY 59373566 644242 0.01085065363936537 0.7956620745731959