BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237788.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 = 621,625 number of mapped reads = 458,382 (73.74%) number of supplementary alignments = 3,214 (0.52%) number of secondary alignments = 0 number of mapped bases = 29,277,015 bp number of sequenced bases = 29,260,419 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 9,350 duplication rate = 1.73% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.8973 >>>>>>> ACTG content number of A's = 8,594,948 bp (29.37%) number of C's = 5,075,946 bp (17.35%) number of T's = 9,097,926 bp (31.09%) number of G's = 6,465,756 bp (22.1%) number of N's = 25,843 bp (0.09%) GC percentage = 39.44% >>>>>>> Mismatches and indels general error rate = 0.0097 number of mismatches = 280,982 number of insertions = 2,351 mapped reads with insertion percentage = 0.51% number of deletions = 10,725 mapped reads with deletion percentage = 2.3% homopolymer indels = 47.91% >>>>>>> Coverage mean coverageData = 0.0095X std coverageData = 0.1208X There is a 0.88% of reference with a coverageData >= 1X There is a 0.05% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% 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 2954568 0.011853803967052103 0.1992190383594304 chr2 243199373 1879982 0.007730209074182112 0.10505165769587178 chr3 198022430 2230505 0.011263900761141048 0.11169217526535621 chr4 191154276 2530087 0.01323583784230911 0.12187310991623408 chr5 180915260 1404748 0.0077646739141850165 0.09271831889612044 chr6 171115067 1940293 0.01133911252829653 0.11501698713819056 chr7 159138663 1173815 0.007376051663824774 0.11226854508151365 chr8 146364022 1783653 0.012186416959763514 0.1679998273860927 chr9 141213431 1084493 0.007679814818747658 0.10017760924298509 chr10 135534747 1164522 0.008592054995314227 0.11313850428078567 chr11 135006516 1339665 0.009922965495976505 0.11588512326049316 chr12 133851895 1336392 0.009984109675847324 0.10536948489013118 chr13 115169878 1431422 0.012428788020423187 0.11760782284840704 chr14 107349540 1133253 0.010556663773314726 0.1097281981249255 chr15 102531392 543098 0.0052968948280737276 0.07680546222077232 chr16 90354753 850810 0.009416328103957077 0.10328475570741975 chr17 81195210 593264 0.0073066379162021996 0.09602058684056014 chr18 78077248 426736 0.0054655614911017355 0.1291887257755747 chr19 59128983 491732 0.008316260064882225 0.12454688103527085 chr20 63025520 437731 0.0069452977143227065 0.0886115092553651 chr21 48129895 336386 0.006989128066869874 0.0893380694302458 chr22 51304566 308440 0.006011940535663044 0.08106278488151372 chrMT 16571 15934 0.9615593506728622 1.2265631616356134 chrX 155270560 1797581 0.01157708840619883 0.11535089069766431 chrY 59373566 87905 0.0014805410205612375 0.0437950767310854