BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549058.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 = 9,694,440 number of mapped reads = 8,335,228 (85.98%) number of secondary alignments = 0 number of mapped bases = 331,419,261 bp number of sequenced bases = 331,388,717 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 458,461 duplication rate = 4.05% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7186 >>>>>>> ACTG content number of A's = 96,169,071 bp (29.02%) number of C's = 69,310,898 bp (20.92%) number of T's = 96,418,904 bp (29.1%) number of G's = 69,483,723 bp (20.97%) number of N's = 6,121 bp (0%) GC percentage = 41.88% >>>>>>> Mismatches and indels general error rate = 0.003 number of mismatches = 997,307 number of insertions = 7,740 mapped reads with insertion percentage = 0.09% number of deletions = 24,346 mapped reads with deletion percentage = 0.29% homopolymer indels = 45.25% >>>>>>> Coverage mean coverageData = 0.1071X std coverageData = 1.1649X There is a 7.68% of reference with a coverageData >= 1X There is a 2% of reference with a coverageData >= 2X There is a 0.56% of reference with a coverageData >= 3X There is a 0.17% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.02% 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% 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 27401026 0.10993363182031951 2.24277396821846 chr2 243199373 28303591 0.11638019724664339 0.6626319012485109 chr3 198022430 22654776 0.11440510047270908 0.44705869951538596 chr4 191154276 21701495 0.11352869239503698 0.5778179927030327 chr5 180915260 20628388 0.11402237710627616 0.4513660357253447 chr6 171115067 19354650 0.11310897596177197 0.4890166522168931 chr7 159138663 18469985 0.11606221047615563 0.8878989985510346 chr8 146364022 17692019 0.12087682996303559 3.5597350167595527 chr9 141213431 14014921 0.09924637409312716 0.5905629178272527 chr10 135534747 16273410 0.12006817705573317 0.8240016819777145 chr11 135006516 15611542 0.11563547051314176 0.6553077468296441 chr12 133851895 15009945 0.11213845721048626 0.45725097066845954 chr13 115169878 10572440 0.091798655895077 0.3899419800419681 chr14 107349540 10214237 0.09514933179965186 0.44807213609983515 chr15 102531392 9760919 0.09519932197936024 0.39653266532458453 chr16 90354753 9569364 0.10590880592634679 0.4912507042376757 chr17 81195210 9085037 0.11189129260211286 0.4852047738740501 chr18 78077248 8745565 0.1120116964163491 1.1758030470427212 chr19 59128983 6607811 0.11175248862304972 1.546414737866137 chr20 63025520 7279036 0.11549346994677712 0.48704410288878963 chr21 48129895 4436310 0.09217368955407029 0.5437176838914098 chr22 51304566 4089886 0.07971777794592395 0.39457342681645347 chrMT 16571 8842 0.5335827650715105 1.0364214412353572 chrX 155270560 10430556 0.06717664958508554 0.4230659375382903 chrY 59373566 3503510 0.05900790934470737 0.8252368852953553