BamQC report ----------------------------------- >>>>>>> Input bam file = SRR926989.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 26,427,250 number of mapped reads = 26,067,779 (98.64%) number of supplementary alignments = 279,467 (1.06%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 13,081,239 number of mapped paired reads (second in pair) = 12,986,540 number of mapped paired reads (both in pair) = 25,870,368 number of mapped paired reads (singletons) = 197,411 number of mapped bases = 2,510,733,042 bp number of sequenced bases = 2,508,863,891 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,709,723 duplication rate = 5.07% >>>>>>> Insert size mean insert size = 105,225.7595 std insert size = 3,169,403.4919 median insert size = 178 >>>>>>> Mapping quality mean mapping quality = 53.4589 >>>>>>> ACTG content number of A's = 712,409,975 bp (28.4%) number of C's = 518,511,633 bp (20.67%) number of T's = 719,668,394 bp (28.69%) number of G's = 558,073,307 bp (22.24%) number of N's = 200,582 bp (0.01%) GC percentage = 42.91% >>>>>>> Mismatches and indels general error rate = 0.0095 number of mismatches = 23,275,700 number of insertions = 390,601 mapped reads with insertion percentage = 1.48% number of deletions = 1,331,856 mapped reads with deletion percentage = 4.98% homopolymer indels = 52.96% >>>>>>> Coverage mean coverageData = 0.811X std coverageData = 3.7253X There is a 28.83% of reference with a coverageData >= 1X There is a 17.05% of reference with a coverageData >= 2X There is a 10.4% of reference with a coverageData >= 3X There is a 6.8% of reference with a coverageData >= 4X There is a 4.6% of reference with a coverageData >= 5X There is a 3.2% of reference with a coverageData >= 6X There is a 2.27% of reference with a coverageData >= 7X There is a 1.64% of reference with a coverageData >= 8X There is a 1.2% of reference with a coverageData >= 9X There is a 0.89% of reference with a coverageData >= 10X There is a 0.67% of reference with a coverageData >= 11X There is a 0.5% of reference with a coverageData >= 12X There is a 0.39% of reference with a coverageData >= 13X There is a 0.3% of reference with a coverageData >= 14X There is a 0.23% of reference with a coverageData >= 15X There is a 0.18% of reference with a coverageData >= 16X There is a 0.14% of reference with a coverageData >= 17X There is a 0.11% of reference with a coverageData >= 18X There is a 0.09% of reference with a coverageData >= 19X There is a 0.07% of reference with a coverageData >= 20X There is a 0.06% of reference with a coverageData >= 21X There is a 0.05% of reference with a coverageData >= 22X There is a 0.04% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% 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 240997941 0.9668900323421862 5.890647746256722 chr2 243199373 218047189 0.8965779241544344 4.749741510645076 chr3 198022430 166744842 0.8420502768297511 1.9594981088322585 chr4 191154276 181489124 0.9494379503182027 2.5636027881481165 chr5 180915260 112287616 0.6206641496134709 1.6297777425564415 chr6 171115067 147141644 0.8598988188456835 3.879195146639573 chr7 159138663 163431351 1.0269745134153854 3.3501757339335687 chr8 146364022 156434328 1.0688031516379073 2.5944985686830093 chr9 141213431 72663163 0.5145626905701343 5.133257470145466 chr10 135534747 127659167 0.9418925391877553 6.612218720954271 chr11 135006516 152539890 1.1298705760246417 4.323902606890056 chr12 133851895 82270597 0.6146390157569305 1.8893925228043196 chr13 115169878 71126253 0.6175768719664703 1.7130803446999379 chr14 107349540 90246073 0.8406749856589977 2.0279298413097866 chr15 102531392 76353605 0.7446851496954221 1.9317278778560576 chr16 90354753 61567862 0.6814014753601285 4.388144666501489 chr17 81195210 48439128 0.5965761773385401 2.1441701986688972 chr18 78077248 75941858 0.9726502911578031 5.58535737750898 chr19 59128983 27840801 0.47084863610794725 3.2189739050367 chr20 63025520 66199673 1.05036297994844 2.374798670742866 chr21 48129895 33844787 0.7031967761408996 3.005054630078349 chr22 51304566 21074178 0.41076612947081553 1.4352613378151764 chrMT 16571 248599 15.002051777201135 11.073400657402354 chrX 155270560 111890991 0.7206194851103777 2.252367886510673 chrY 59373566 4252382 0.07162079501844305 1.7722258627442786