BamQC report ----------------------------------- >>>>>>> Input bam file = SRR089663.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 22,449,905 number of mapped reads = 17,267,531 (76.92%) number of supplementary alignments = 685 (0%) number of secondary alignments = 0 number of mapped bases = 792,312,196 bp number of sequenced bases = 792,142,900 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,693,530 duplication rate = 7.5% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.277 >>>>>>> ACTG content number of A's = 258,173,958 bp (32.59%) number of C's = 161,429,852 bp (20.38%) number of T's = 203,059,968 bp (25.63%) number of G's = 169,432,763 bp (21.39%) number of N's = 46,359 bp (0.01%) GC percentage = 41.77% >>>>>>> Mismatches and indels general error rate = 0.0047 number of mismatches = 3,683,547 number of insertions = 38,739 mapped reads with insertion percentage = 0.22% number of deletions = 112,777 mapped reads with deletion percentage = 0.65% homopolymer indels = 41.97% >>>>>>> Coverage mean coverageData = 0.2559X std coverageData = 1.2968X There is a 14.01% of reference with a coverageData >= 1X There is a 5.3% of reference with a coverageData >= 2X There is a 2.46% of reference with a coverageData >= 3X There is a 1.3% of reference with a coverageData >= 4X There is a 0.74% of reference with a coverageData >= 5X There is a 0.45% of reference with a coverageData >= 6X There is a 0.29% of reference with a coverageData >= 7X There is a 0.2% of reference with a coverageData >= 8X There is a 0.14% of reference with a coverageData >= 9X There is a 0.1% of reference with a coverageData >= 10X There is a 0.08% of reference with a coverageData >= 11X There is a 0.06% of reference with a coverageData >= 12X There is a 0.05% of reference with a coverageData >= 13X There is a 0.04% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% 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% 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 66961988 0.26865324439853655 1.4841979384933075 chr2 243199373 76886794 0.3161471719748225 1.8537241200794146 chr3 198022430 76175371 0.3846805182625019 1.1764995155093751 chr4 191154276 36162695 0.18918067519452195 0.7767031177233309 chr5 180915260 33071614 0.18280168295366572 0.72142591070991 chr6 171115067 50828733 0.29704416969897807 1.1456419018191697 chr7 159138663 51303112 0.3223799360435748 1.7017788802455054 chr8 146364022 61896128 0.422891685772341 2.5625010270304736 chr9 141213431 27768038 0.1966387885582923 1.1281749374879142 chr10 135534747 33186358 0.24485498172656786 1.3025593248746945 chr11 135006516 37975505 0.281286460277221 1.1927103709505928 chr12 133851895 26945616 0.2013091857982287 0.7924633124113727 chr13 115169878 22613508 0.1963491530311424 0.7546064176632193 chr14 107349540 24864183 0.2316189058658286 0.9160529312358208 chr15 102531392 19484094 0.19003052255449726 0.7394298245715644 chr16 90354753 15149898 0.16767129007590778 0.7916651150564097 chr17 81195210 17624821 0.21706725064200216 0.8921327822922179 chr18 78077248 38499088 0.49308971545718416 1.779791921476244 chr19 59128983 12919177 0.21849144606461438 1.3552192956180362 chr20 63025520 17315712 0.2747412794055487 0.9471341593271513 chr21 48129895 12599499 0.2617811445464404 1.043748676695776 chr22 51304566 6200467 0.12085604622403394 0.5799102470345593 chrMT 16571 238078 14.36714742622654 13.853097136803733 chrX 155270560 23802050 0.15329403075508968 0.9546827817752427 chrY 59373566 1839669 0.03098464727552325 0.556985039618263