BamQC report ----------------------------------- >>>>>>> Input bam file = SRR631030.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP017516/SRP017516.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 = 107,984,286 number of mapped reads = 107,638,398 (99.68%) number of supplementary alignments = 619,261 (0.57%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 53,943,457 number of mapped paired reads (second in pair) = 53,694,941 number of mapped paired reads (both in pair) = 107,357,960 number of mapped paired reads (singletons) = 280,438 number of mapped bases = 10,703,593,379 bp number of sequenced bases = 10,701,379,182 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 26,413,464 duplication rate = 19.63% >>>>>>> Insert size mean insert size = 47,042.2316 std insert size = 2,036,775.8543 median insert size = 316 >>>>>>> Mapping quality mean mapping quality = 53.5597 >>>>>>> ACTG content number of A's = 3,349,549,488 bp (31.3%) number of C's = 1,984,166,451 bp (18.54%) number of T's = 3,334,936,028 bp (31.16%) number of G's = 1,998,533,210 bp (18.68%) number of N's = 34,194,005 bp (0.32%) GC percentage = 37.22% >>>>>>> Mismatches and indels general error rate = 0.0122 number of mismatches = 128,913,593 number of insertions = 929,232 mapped reads with insertion percentage = 0.85% number of deletions = 1,008,593 mapped reads with deletion percentage = 0.91% homopolymer indels = 43.86% >>>>>>> Coverage mean coverageData = 3.4576X std coverageData = 16.5201X There is a 32.55% of reference with a coverageData >= 1X There is a 22.56% of reference with a coverageData >= 2X There is a 17.85% of reference with a coverageData >= 3X There is a 14.91% of reference with a coverageData >= 4X There is a 12.85% of reference with a coverageData >= 5X There is a 11.31% of reference with a coverageData >= 6X There is a 10.1% of reference with a coverageData >= 7X There is a 9.12% of reference with a coverageData >= 8X There is a 8.31% of reference with a coverageData >= 9X There is a 7.62% of reference with a coverageData >= 10X There is a 7.04% of reference with a coverageData >= 11X There is a 6.53% of reference with a coverageData >= 12X There is a 6.09% of reference with a coverageData >= 13X There is a 5.69% of reference with a coverageData >= 14X There is a 5.34% of reference with a coverageData >= 15X There is a 5.03% of reference with a coverageData >= 16X There is a 4.74% of reference with a coverageData >= 17X There is a 4.48% of reference with a coverageData >= 18X There is a 4.25% of reference with a coverageData >= 19X There is a 4.04% of reference with a coverageData >= 20X There is a 3.84% of reference with a coverageData >= 21X There is a 3.66% of reference with a coverageData >= 22X There is a 3.49% of reference with a coverageData >= 23X There is a 3.34% of reference with a coverageData >= 24X There is a 3.19% of reference with a coverageData >= 25X There is a 3.06% of reference with a coverageData >= 26X There is a 2.93% of reference with a coverageData >= 27X There is a 2.82% of reference with a coverageData >= 28X There is a 2.71% of reference with a coverageData >= 29X There is a 2.61% of reference with a coverageData >= 30X There is a 2.51% of reference with a coverageData >= 31X There is a 2.42% of reference with a coverageData >= 32X There is a 2.33% of reference with a coverageData >= 33X There is a 2.25% of reference with a coverageData >= 34X There is a 2.17% of reference with a coverageData >= 35X There is a 2.1% of reference with a coverageData >= 36X There is a 2.03% of reference with a coverageData >= 37X There is a 1.96% of reference with a coverageData >= 38X There is a 1.9% of reference with a coverageData >= 39X There is a 1.84% of reference with a coverageData >= 40X There is a 1.78% of reference with a coverageData >= 41X There is a 1.73% of reference with a coverageData >= 42X There is a 1.67% of reference with a coverageData >= 43X There is a 1.62% of reference with a coverageData >= 44X There is a 1.58% of reference with a coverageData >= 45X There is a 1.53% of reference with a coverageData >= 46X There is a 1.49% of reference with a coverageData >= 47X There is a 1.44% of reference with a coverageData >= 48X There is a 1.4% of reference with a coverageData >= 49X There is a 1.37% of reference with a coverageData >= 50X There is a 1.33% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 883319283 3.5439000290394462 20.066140155026208 chr2 243199373 929566596 3.822240923293828 16.288762692066978 chr3 198022430 815934610 4.120415096411048 17.393447284527262 chr4 191154276 830169210 4.342927751195061 15.669205978883062 chr5 180915260 744753562 4.116587854446331 17.687606213021343 chr6 171115067 689087581 4.0270421131296406 17.090201843067454 chr7 159138663 537082024 3.3749311064653096 16.46329120491325 chr8 146364022 594201795 4.059753120203269 16.32162379440604 chr9 141213431 439187797 3.110099329007876 14.687245248027718 chr10 135534747 364258320 2.6875640974930213 11.941415019996981 chr11 135006516 453362937 3.3580818943583433 14.408133687925583 chr12 133851895 528187067 3.946055952364365 19.415541876213382 chr13 115169878 425820358 3.697324034675108 20.68427231978725 chr14 107349540 306762527 2.8576044853103237 16.287858135489287 chr15 102531392 261334183 2.5488211746896012 14.354807742142247 chr16 90354753 181191268 2.0053318943830214 12.732126172783822 chr17 81195210 161955840 1.9946477138244978 9.998110332087395 chr18 78077248 253071734 3.241299360346307 14.03315488592771 chr19 59128983 55606863 0.9404332727995677 6.446859041744951 chr20 63025520 147042522 2.333063209950509 14.556369776344262 chr21 48129895 97409550 2.023888687062376 7.401108604292052 chr22 51304566 48018018 0.9359404385176945 10.143829909943953 chrMT 16571 3838 0.23160943817512522 0.8496639630919087 chrX 155270560 948963187 6.111674917640537 24.28127867914681 chrY 59373566 7302709 0.12299596423095085 1.5464490194714706