BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5038439.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP093555/SRP093555.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 = 11,266,762 number of mapped reads = 11,030,304 (97.9%) number of supplementary alignments = 212,955 (1.89%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 5,569,757 number of mapped paired reads (second in pair) = 5,460,547 number of mapped paired reads (both in pair) = 10,907,538 number of mapped paired reads (singletons) = 122,766 number of mapped bases = 1,568,953,028 bp number of sequenced bases = 1,567,847,247 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,579,809 duplication rate = 7.74% >>>>>>> Insert size mean insert size = 89,067.5847 std insert size = 2,844,128.3351 median insert size = 264 >>>>>>> Mapping quality mean mapping quality = 53.6231 >>>>>>> ACTG content number of A's = 456,282,080 bp (29.1%) number of C's = 319,877,099 bp (20.4%) number of T's = 456,955,610 bp (29.15%) number of G's = 334,698,495 bp (21.35%) number of N's = 33,963 bp (0%) GC percentage = 41.75% >>>>>>> Mismatches and indels general error rate = 0.0146 number of mismatches = 22,025,828 number of insertions = 279,853 mapped reads with insertion percentage = 2.39% number of deletions = 521,403 mapped reads with deletion percentage = 4.54% homopolymer indels = 46.72% >>>>>>> Coverage mean coverageData = 0.5068X std coverageData = 9.3655X There is a 25.24% of reference with a coverageData >= 1X There is a 11.3% of reference with a coverageData >= 2X There is a 4.86% of reference with a coverageData >= 3X There is a 2.37% of reference with a coverageData >= 4X There is a 1.14% of reference with a coverageData >= 5X There is a 0.58% of reference with a coverageData >= 6X There is a 0.31% of reference with a coverageData >= 7X There is a 0.17% of reference with a coverageData >= 8X There is a 0.11% of reference with a coverageData >= 9X There is a 0.07% of reference with a coverageData >= 10X There is a 0.05% of reference with a coverageData >= 11X There is a 0.04% of reference with a coverageData >= 12X There is a 0.03% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.03% 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 0.02% 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 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 97741672 0.3921421403399432 15.547698591696308 chr2 243199373 172297222 0.7084607985399699 9.137346190693801 chr3 198022430 95334271 0.4814316792294691 1.0893799419961288 chr4 191154276 91478766 0.4785598727595296 8.648382105173628 chr5 180915260 94510688 0.5224030742348655 1.214020648670554 chr6 171115067 110508047 0.645811318298464 15.38962144631203 chr7 159138663 108864814 0.6840877757028787 8.273564398272589 chr8 146364022 75564854 0.516280250893898 2.225278563473798 chr9 141213431 62499145 0.4425864066711898 13.260018803472017 chr10 135534747 68815074 0.5077301247332539 18.75684036997335 chr11 135006516 68809086 0.5096723331487201 7.2382997235811395 chr12 133851895 52556678 0.39264799351551954 0.979027786075436 chr13 115169878 85115233 0.7390407498738516 1.4030342472232353 chr14 107349540 28193685 0.26263442768362116 0.8944006643494383 chr15 102531392 26592069 0.2593553884453261 0.7232361453306857 chr16 90354753 63873534 0.7069194688629163 12.317135657089862 chr17 81195210 36358269 0.4477883485983964 7.474716465627336 chr18 78077248 25609928 0.32800756502073436 11.266499338853679 chr19 59128983 20616935 0.34867731447368205 8.364231776264113 chr20 63025520 44098474 0.6996923468461664 2.8230492942218555 chr21 48129895 13655762 0.2837272343935095 3.4081466308231714 chr22 51304566 9331087 0.1818763460546572 0.6491638930942488 chrMT 16571 3691365 222.76054553134995 150.14713587545694 chrX 155270560 88390026 0.5692645534349847 1.9909878824246732 chrY 59373566 24446344 0.4117378430663909 12.108341071911692