BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818867.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 = 2,300,381 number of mapped reads = 2,271,676 (98.75%) number of supplementary alignments = 30,584 (1.33%) number of secondary alignments = 0 number of mapped bases = 210,882,254 bp number of sequenced bases = 210,753,145 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 602,565 duplication rate = 22.57% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.3686 >>>>>>> ACTG content number of A's = 59,841,131 bp (28.39%) number of C's = 44,137,562 bp (20.94%) number of T's = 58,101,891 bp (27.57%) number of G's = 48,669,192 bp (23.09%) number of N's = 3,369 bp (0%) GC percentage = 44.04% >>>>>>> Mismatches and indels general error rate = 0.0062 number of mismatches = 1,248,324 number of insertions = 24,726 mapped reads with insertion percentage = 1.05% number of deletions = 66,740 mapped reads with deletion percentage = 2.87% homopolymer indels = 42.97% >>>>>>> Coverage mean coverageData = 0.0681X std coverageData = 0.7954X There is a 4.33% of reference with a coverageData >= 1X There is a 1.37% of reference with a coverageData >= 2X There is a 0.51% of reference with a coverageData >= 3X There is a 0.21% of reference with a coverageData >= 4X There is a 0.1% of reference with a coverageData >= 5X There is a 0.05% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% 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 0.01% of reference with a coverageData >= 11X There is a 0.01% 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 19032209 0.07635771948588245 1.3134813559431457 chr2 243199373 15112813 0.062141661031338266 1.0829151707563096 chr3 198022430 12255667 0.061890296972923725 0.3576868817675462 chr4 191154276 12031627 0.06294197154135334 0.48509590169874534 chr5 180915260 10900424 0.06025154539202497 0.3691054200573123 chr6 171115067 9942988 0.05810702806199994 0.3874634049361928 chr7 159138663 17822802 0.11199542376449399 1.7093352759704303 chr8 146364022 21110936 0.14423582866559925 0.7128349947991078 chr9 141213431 7287382 0.051605445377217694 0.6250627952710748 chr10 135534747 9219155 0.06802060138866087 0.9435894775356832 chr11 135006516 8843455 0.06550391241856801 0.46649665179803146 chr12 133851895 7840375 0.05857500187053758 0.35435879208308424 chr13 115169878 5073113 0.0440489569677238 0.2951671132268311 chr14 107349540 6766841 0.06303558450273751 0.39025352654013923 chr15 102531392 4674968 0.04559547967514183 0.30337654353786475 chr16 90354753 4987543 0.05519956432175737 0.7061608964952208 chr17 81195210 5723187 0.07048675654635292 0.5131892980712502 chr18 78077248 3564809 0.04565746220973362 0.7616541503041081 chr19 59128983 4111836 0.06954011030428174 1.184379728508466 chr20 63025520 8383812 0.13302249628404494 0.5781465014398754 chr21 48129895 1933388 0.04017021021965662 0.3572392735653917 chr22 51304566 2495035 0.04863183132666983 0.35505872211228345 chrMT 16571 322129 19.43932170659586 12.511033639654244 chrX 155270560 10652503 0.06860607059058717 0.46094275953756325 chrY 59373566 793257 0.013360440570472051 0.9473136447032476