BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231747.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 4,731,516 number of mapped reads = 4,458,493 (94.23%) number of supplementary alignments = 42,271 (0.89%) number of secondary alignments = 0 number of mapped bases = 305,929,407 bp number of sequenced bases = 305,814,148 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 506,701 duplication rate = 4.91% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.0134 >>>>>>> ACTG content number of A's = 81,085,934 bp (26.51%) number of C's = 55,661,253 bp (18.2%) number of T's = 87,880,400 bp (28.74%) number of G's = 81,119,314 bp (26.53%) number of N's = 67,247 bp (0.02%) GC percentage = 44.73% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 1,978,292 number of insertions = 20,936 mapped reads with insertion percentage = 0.47% number of deletions = 70,305 mapped reads with deletion percentage = 1.56% homopolymer indels = 46.97% >>>>>>> Coverage mean coverageData = 0.0988X std coverageData = 35.5438X There is a 6.43% of reference with a coverageData >= 1X There is a 1.83% of reference with a coverageData >= 2X There is a 0.56% of reference with a coverageData >= 3X There is a 0.19% of reference with a coverageData >= 4X There is a 0.07% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% 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% 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 34284325 0.1375496071482205 1.8362333514178968 chr2 243199373 39023902 0.16046053704258523 126.77772740830572 chr3 198022430 20710049 0.10458435945867345 0.4365308452225951 chr4 191154276 9592146 0.050180127804203556 0.35199914617396366 chr5 180915260 15567288 0.08604740141876369 0.4062508697744798 chr6 171115067 27278193 0.15941432556608237 0.8136659639356714 chr7 159138663 18510927 0.11631948296561974 1.565233439288554 chr8 146364022 16836613 0.11503245654181327 0.837893436333823 chr9 141213431 8862868 0.06276221700186578 0.587355468186919 chr10 135534747 12547027 0.09257424592381465 0.7244876415916648 chr11 135006516 9598300 0.07109508699565287 0.7715883764892096 chr12 133851895 9045477 0.06757825132023719 0.3577376954621834 chr13 115169878 6431613 0.05584457595761281 0.31327734111701677 chr14 107349540 11100954 0.10340942308648923 0.5424268650145871 chr15 102531392 6018368 0.058697808374629304 0.3219622751860542 chr16 90354753 9520403 0.10536693072471794 0.4896854443750923 chr17 81195210 8234441 0.10141535442792746 0.5667313504451208 chr18 78077248 7045086 0.0902322530630178 1.2667850780549295 chr19 59128983 7204197 0.12183867596708031 1.170943292100403 chr20 63025520 7421344 0.11775141244372121 0.47888076738591207 chr21 48129895 7225892 0.15013313451026644 0.5745947325164812 chr22 51304566 2863063 0.055805227940140846 0.3144091381812365 chrMT 16571 15118 0.912316697845634 1.4981677568885097 chrX 155270560 10301201 0.06634355540419253 0.4346924536467588 chrY 59373566 690612 0.011631640922494028 0.2217046482494745