BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549047.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 4,304,547 number of mapped reads = 3,729,580 (86.64%) number of secondary alignments = 0 number of mapped bases = 147,557,938 bp number of sequenced bases = 147,542,621 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 118,050 duplication rate = 2.17% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 39.6176 >>>>>>> ACTG content number of A's = 41,654,856 bp (28.23%) number of C's = 31,714,080 bp (21.49%) number of T's = 42,433,621 bp (28.76%) number of G's = 31,738,868 bp (21.51%) number of N's = 1,196 bp (0%) GC percentage = 43.01% >>>>>>> Mismatches and indels general error rate = 0.0028 number of mismatches = 402,754 number of insertions = 4,601 mapped reads with insertion percentage = 0.12% number of deletions = 11,583 mapped reads with deletion percentage = 0.31% homopolymer indels = 40.92% >>>>>>> Coverage mean coverageData = 0.0477X std coverageData = 0.4647X There is a 4.23% of reference with a coverageData >= 1X There is a 0.4% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% 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 12023204 0.04823740840348799 0.7634037174706102 chr2 243199373 12550161 0.051604413470260055 0.36229623655983295 chr3 198022430 10014209 0.05057108429585477 0.24591820178797827 chr4 191154276 9664764 0.05056001990768964 0.25937607084739356 chr5 180915260 9182151 0.050753877809975784 0.2490547110904502 chr6 171115067 8662254 0.05062239200712816 0.2579269459899062 chr7 159138663 8390491 0.052724402994387354 0.5693583159909423 chr8 146364022 7689693 0.052538136728710556 1.2438297543188446 chr9 141213431 6304766 0.04464707043340658 0.34588247774415815 chr10 135534747 7027724 0.05185182512643787 0.3468896621334098 chr11 135006516 6851114 0.050746543226106215 0.30113540031763697 chr12 133851895 6864370 0.05128332325814289 0.25598036995304496 chr13 115169878 4787524 0.04156923740077245 0.2206320994602226 chr14 107349540 4585137 0.04271221842217489 0.2561147306209598 chr15 102531392 4257183 0.04152077638817193 0.22257708608014906 chr16 90354753 4227890 0.04679211507556221 0.2554021244229629 chr17 81195210 4049096 0.04986865604510414 0.2527157963130112 chr18 78077248 3965778 0.050793004384580766 0.611812964243346 chr19 59128983 3204678 0.05419809097680574 0.7016526749749963 chr20 63025520 3074808 0.0487867136994665 0.24913434049588934 chr21 48129895 1917557 0.03984128783160653 0.25618190684954345 chr22 51304566 1748767 0.03408599148855484 0.2641745668745247 chrMT 16571 5441 0.3283446985697906 0.6424936190460272 chrX 155270560 5118656 0.032966043273109855 0.2502430232795281 chrY 59373566 1390522 0.02341988352190266 0.26134245216038354