BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975240.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP029757/SRP029757.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 = 47,450,380 number of mapped reads = 47,295,238 (99.67%) number of supplementary alignments = 105,122 (0.22%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 23,647,590 number of mapped paired reads (second in pair) = 23,647,648 number of mapped paired reads (both in pair) = 47,229,156 number of mapped paired reads (singletons) = 66,082 number of mapped bases = 4,310,619,757 bp number of sequenced bases = 4,309,136,598 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 25,354,010 duplication rate = 39.24% >>>>>>> Insert size mean insert size = 33,901.7872 std insert size = 1,806,873.9089 median insert size = 183 >>>>>>> Mapping quality mean mapping quality = 55.7479 >>>>>>> ACTG content number of A's = 1,139,355,180 bp (26.44%) number of C's = 922,072,863 bp (21.4%) number of T's = 1,217,194,423 bp (28.25%) number of G's = 1,030,331,825 bp (23.91%) number of N's = 182,307 bp (0%) GC percentage = 45.31% >>>>>>> Mismatches and indels general error rate = 0.0063 number of mismatches = 26,229,877 number of insertions = 443,790 mapped reads with insertion percentage = 0.93% number of deletions = 991,368 mapped reads with deletion percentage = 2.07% homopolymer indels = 46.28% >>>>>>> Coverage mean coverageData = 1.3925X std coverageData = 19.4044X There is a 14.11% of reference with a coverageData >= 1X There is a 7.23% of reference with a coverageData >= 2X There is a 4.08% of reference with a coverageData >= 3X There is a 2.98% of reference with a coverageData >= 4X There is a 2.3% of reference with a coverageData >= 5X There is a 1.98% of reference with a coverageData >= 6X There is a 1.75% of reference with a coverageData >= 7X There is a 1.61% of reference with a coverageData >= 8X There is a 1.51% of reference with a coverageData >= 9X There is a 1.43% of reference with a coverageData >= 10X There is a 1.36% of reference with a coverageData >= 11X There is a 1.3% of reference with a coverageData >= 12X There is a 1.25% of reference with a coverageData >= 13X There is a 1.21% of reference with a coverageData >= 14X There is a 1.17% of reference with a coverageData >= 15X There is a 1.13% of reference with a coverageData >= 16X There is a 1.1% of reference with a coverageData >= 17X There is a 1.06% of reference with a coverageData >= 18X There is a 1.04% of reference with a coverageData >= 19X There is a 1.01% of reference with a coverageData >= 20X There is a 0.98% of reference with a coverageData >= 21X There is a 0.96% of reference with a coverageData >= 22X There is a 0.93% of reference with a coverageData >= 23X There is a 0.91% of reference with a coverageData >= 24X There is a 0.89% of reference with a coverageData >= 25X There is a 0.87% of reference with a coverageData >= 26X There is a 0.85% of reference with a coverageData >= 27X There is a 0.83% of reference with a coverageData >= 28X There is a 0.82% of reference with a coverageData >= 29X There is a 0.8% of reference with a coverageData >= 30X There is a 0.78% of reference with a coverageData >= 31X There is a 0.77% of reference with a coverageData >= 32X There is a 0.75% of reference with a coverageData >= 33X There is a 0.74% of reference with a coverageData >= 34X There is a 0.72% of reference with a coverageData >= 35X There is a 0.71% of reference with a coverageData >= 36X There is a 0.7% of reference with a coverageData >= 37X There is a 0.69% of reference with a coverageData >= 38X There is a 0.67% of reference with a coverageData >= 39X There is a 0.66% of reference with a coverageData >= 40X There is a 0.65% of reference with a coverageData >= 41X There is a 0.64% of reference with a coverageData >= 42X There is a 0.63% of reference with a coverageData >= 43X There is a 0.62% of reference with a coverageData >= 44X There is a 0.61% of reference with a coverageData >= 45X There is a 0.6% of reference with a coverageData >= 46X There is a 0.59% of reference with a coverageData >= 47X There is a 0.58% of reference with a coverageData >= 48X There is a 0.57% of reference with a coverageData >= 49X There is a 0.56% of reference with a coverageData >= 50X There is a 0.55% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 375656210 1.5071425238294591 18.293520254721177 chr2 243199373 393887866 1.6196088877252164 19.981742338387484 chr3 198022430 257647007 1.3011001177997865 17.735481599931767 chr4 191154276 151929419 0.7948000022766951 12.16319930249196 chr5 180915260 203004005 1.1220944269709476 16.069281705345563 chr6 171115067 225489264 1.31776393483807 17.809687167003318 chr7 159138663 166296280 1.044977234727679 15.053801090246228 chr8 146364022 196005640 1.3391654405342865 18.876368387066037 chr9 141213431 199681697 1.4140418201438643 18.375923991276 chr10 135534747 189038014 1.394756829405525 18.239890946317722 chr11 135006516 320598095 2.374686085521976 26.984106424373113 chr12 133851895 289760567 2.1647849438366187 26.59970486866401 chr13 115169878 103431067 0.8980739477730453 15.564075649926513 chr14 107349540 154232772 1.4367343539618334 17.930881895355583 chr15 102531392 79847028 0.7787568903775344 11.652646520333265 chr16 90354753 104860317 1.1605401322938707 14.793608354990026 chr17 81195210 168030099 2.069458272230591 22.674128436600217 chr18 78077248 80570997 1.0319395094458248 15.339147662784157 chr19 59128983 184669123 3.123157437022044 39.118377305800415 chr20 63025520 261300539 4.1459481651242225 46.17789853403395 chr21 48129895 33028028 0.6862268866366735 10.826647835082001 chr22 51304566 59577911 1.1612594286442264 15.253743496836497 chrMT 16571 353888 21.3558626516203 25.73763285513178 chrX 155270560 102464512 0.6599094638416967 11.03858443641883 chrY 59373566 9259412 0.15595175806014414 3.265268736029716