BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094089.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP024468/ERP024468.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 = 2,119,866 number of mapped reads = 1,963,310 (92.61%) number of supplementary alignments = 137,380 (6.48%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 985,907 number of mapped paired reads (second in pair) = 977,403 number of mapped paired reads (both in pair) = 1,947,876 number of mapped paired reads (singletons) = 15,434 number of mapped bases = 242,368,111 bp number of sequenced bases = 237,774,423 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,989,285 duplication rate = 55.11% >>>>>>> Insert size mean insert size = 1,715,742.1986 std insert size = 11,591,019.3969 median insert size = 147 >>>>>>> Mapping quality mean mapping quality = 41.2146 >>>>>>> ACTG content number of A's = 69,077,853 bp (29.05%) number of C's = 50,424,773 bp (21.21%) number of T's = 64,758,869 bp (27.24%) number of G's = 53,510,212 bp (22.5%) number of N's = 2,716 bp (0%) GC percentage = 43.71% >>>>>>> Mismatches and indels general error rate = 0.036 number of mismatches = 8,236,718 number of insertions = 168,888 mapped reads with insertion percentage = 8.43% number of deletions = 676,112 mapped reads with deletion percentage = 33.34% homopolymer indels = 28.29% >>>>>>> Coverage mean coverageData = 0.0783X std coverageData = 14.7369X There is a 0.04% of reference with a coverageData >= 1X There is a 0.02% of reference with a coverageData >= 2X There is a 0.02% 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 0.01% 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 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% 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 4497947 0.018045880816481497 7.021359768631068 chr2 243199373 10348054 0.04254967384311472 12.033532258998259 chr3 198022430 4270274 0.021564597505444205 6.387495565064927 chr4 191154276 8968921 0.046919803143718325 11.49604438889218 chr5 180915260 4826791 0.02667984447525322 10.859190859731774 chr6 171115067 5392684 0.03151495712531264 9.960612118878515 chr7 159138663 5873643 0.036908962845817045 11.065715072475118 chr8 146364022 5576202 0.038098174153754806 11.919611297410208 chr9 141213431 4871346 0.034496336258553195 13.468646435572026 chr10 135534747 4859353 0.035853189735913255 10.609749135025211 chr11 135006516 5467219 0.040495963913326966 9.761200195054213 chr12 133851895 5451575 0.04072841105462123 9.511166106376287 chr13 115169878 4341349 0.037695177553283506 10.568650029792318 chr14 107349540 1181255 0.011003819858007776 3.730718632633146 chr15 102531392 1397539 0.013630352351014605 3.29223096558564 chr16 90354753 842233 0.009321402273104549 2.962970929833934 chr17 81195210 2248309 0.027690167929856947 8.082705394612573 chr18 78077248 1837657 0.02353639564755151 7.42801281249939 chr19 59128983 516279 0.008731403345800822 2.6810388867209367 chr20 63025520 913820 0.014499206035904186 4.246561423790031 chr21 48129895 817067 0.016976288853320788 6.361225187485399 chr22 51304566 362771 0.007070930100061659 2.463275746438136 chrMT 16571 605283 36.526642930420614 215.3579072352539 chrX 155270560 153936740 0.9914097044539545 51.45005921607434 chrY 59373566 2963800 0.04991783717353275 9.531321454864619