BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068117.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 = 2,320,545 number of mapped reads = 2,039,655 (87.9%) number of supplementary alignments = 22,212 (0.96%) number of secondary alignments = 0 number of mapped bases = 136,557,934 bp number of sequenced bases = 136,484,629 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 149,352 duplication rate = 5.94% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 37.0799 >>>>>>> ACTG content number of A's = 38,704,873 bp (28.36%) number of C's = 24,373,679 bp (17.86%) number of T's = 44,179,885 bp (32.37%) number of G's = 29,080,199 bp (21.31%) number of N's = 145,993 bp (0.11%) GC percentage = 39.16% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 1,227,462 number of insertions = 10,083 mapped reads with insertion percentage = 0.49% number of deletions = 44,833 mapped reads with deletion percentage = 2.17% homopolymer indels = 45.61% >>>>>>> Coverage mean coverageData = 0.0441X std coverageData = 0.3966X There is a 3.03% of reference with a coverageData >= 1X There is a 0.89% of reference with a coverageData >= 2X There is a 0.29% of reference with a coverageData >= 3X There is a 0.1% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 22008439 0.08829843196258275 0.45861742023779023 chr2 243199373 10156115 0.041760448946552176 0.49557483901370203 chr3 198022430 2004961 0.010124918677141777 0.1297594283165764 chr4 191154276 1185897 0.006203873775755871 0.12317424344782159 chr5 180915260 7507125 0.04149525584519515 0.27557187479994233 chr6 171115067 954511 0.005578182077911351 0.1136355652247648 chr7 159138663 20001445 0.12568564183551045 0.5414073187942934 chr8 146364022 2852136 0.01948659213532681 0.5194506809228613 chr9 141213431 740609 0.005244607363162219 0.2325148723542072 chr10 135534747 17824167 0.13150994408835986 0.6075741981303351 chr11 135006516 5475577 0.04055787203633934 0.7360311419633669 chr12 133851895 15537725 0.11608147198812538 0.46767190127717156 chr13 115169878 876766 0.007612806536097919 0.11446741793589922 chr14 107349540 1361917 0.01268675208109881 0.16496030192415106 chr15 102531392 3001373 0.02927272264088641 0.22710467862813702 chr16 90354753 3919720 0.043381447791683965 0.28336211393927807 chr17 81195210 342211 0.004214669806260739 0.24437812158481229 chr18 78077248 4667080 0.059775160108102174 0.6773125964613506 chr19 59128983 1702387 0.028791075266760464 0.3534977802820775 chr20 63025520 268178 0.004255070009735739 0.13903784048407583 chr21 48129895 5233629 0.10873967208945708 0.46816333483364514 chr22 51304566 164666 0.0032095778765578098 0.06903855090409242 chrMT 16571 5415 0.32677569247480537 0.746408285884572 chrX 155270560 8541124 0.0550080066691329 0.3903930362648946 chrY 59373566 224761 0.0037855398478171248 0.07943382520986021