BamQC report ----------------------------------- >>>>>>> Input bam file = SRR089598.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 = 8,998,489 number of mapped reads = 6,584,472 (73.17%) number of supplementary alignments = 216 (0%) number of secondary alignments = 0 number of mapped bases = 306,258,108 bp number of sequenced bases = 306,198,646 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,873,424 duplication rate = 21.97% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.6574 >>>>>>> ACTG content number of A's = 98,405,013 bp (32.14%) number of C's = 60,288,515 bp (19.69%) number of T's = 77,131,629 bp (25.19%) number of G's = 70,333,279 bp (22.97%) number of N's = 40,210 bp (0.01%) GC percentage = 42.66% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 2,704,252 number of insertions = 17,040 mapped reads with insertion percentage = 0.26% number of deletions = 40,346 mapped reads with deletion percentage = 0.61% homopolymer indels = 41.03% >>>>>>> Coverage mean coverageData = 0.0989X std coverageData = 0.8504X There is a 3.88% of reference with a coverageData >= 1X There is a 1.73% of reference with a coverageData >= 2X There is a 1.06% of reference with a coverageData >= 3X There is a 0.73% of reference with a coverageData >= 4X There is a 0.53% of reference with a coverageData >= 5X There is a 0.39% of reference with a coverageData >= 6X There is a 0.3% of reference with a coverageData >= 7X There is a 0.23% of reference with a coverageData >= 8X There is a 0.18% of reference with a coverageData >= 9X There is a 0.14% of reference with a coverageData >= 10X There is a 0.11% of reference with a coverageData >= 11X There is a 0.09% of reference with a coverageData >= 12X There is a 0.07% of reference with a coverageData >= 13X There is a 0.06% of reference with a coverageData >= 14X There is a 0.05% of reference with a coverageData >= 15X There is a 0.04% of reference with a coverageData >= 16X There is a 0.04% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% 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 0.01% 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% 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 24478740 0.09820934408023 0.9005599344319837 chr2 243199373 24863942 0.10223686719784429 0.927551303281892 chr3 198022430 20983767 0.1059666170140423 0.8353131932252431 chr4 191154276 19803019 0.10359704953709746 0.8611706701623304 chr5 180915260 18568240 0.10263501265730707 0.8196355320763873 chr6 171115067 17281260 0.10099204180541273 0.8614676189422152 chr7 159138663 16458768 0.10342406860613125 0.8745872375869868 chr8 146364022 15692215 0.10721360881979589 1.0115989485406267 chr9 141213431 12772367 0.09044725356187967 0.7877629566153013 chr10 135534747 14309251 0.1055762549215516 0.8700109124555455 chr11 135006516 13864286 0.10269345814390174 0.8928044472033525 chr12 133851895 13921300 0.1040052514758943 0.8299839185226513 chr13 115169878 9734873 0.08452620745156993 0.7457546850822847 chr14 107349540 9431464 0.08785751666937744 0.7914500847449559 chr15 102531392 8910234 0.08690249713960774 0.7384378604962485 chr16 90354753 9045463 0.10011053873391697 0.8209340719090069 chr17 81195210 8701471 0.10716729472095707 0.828970785963395 chr18 78077248 7656817 0.0980671987824161 0.8358887681481103 chr19 59128983 6473150 0.1094750775605256 0.8768475194425196 chr20 63025520 6438416 0.10215569819971339 0.8251978562569305 chr21 48129895 4048866 0.08412372393498885 0.7892814747334608 chr22 51304566 3754216 0.07317508543001806 0.7121988223890283 chrMT 16571 65321 3.9418864280972783 7.042043393945933 chrX 155270560 18109495 0.11663186504898289 0.9075430912804731 chrY 59373566 891167 0.015009490923957642 0.29163431243576543