BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008761.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 = 1,298,194 number of mapped reads = 840,715 (64.76%) number of supplementary alignments = 3,070 (0.24%) number of secondary alignments = 0 number of mapped bases = 51,799,633 bp number of sequenced bases = 51,770,313 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 39,132 duplication rate = 3.24% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.0457 >>>>>>> ACTG content number of A's = 14,078,022 bp (27.19%) number of C's = 8,888,121 bp (17.17%) number of T's = 16,219,874 bp (31.33%) number of G's = 12,582,027 bp (24.3%) number of N's = 2,269 bp (0%) GC percentage = 41.47% >>>>>>> Mismatches and indels general error rate = 0.0097 number of mismatches = 497,350 number of insertions = 4,111 mapped reads with insertion percentage = 0.49% number of deletions = 19,149 mapped reads with deletion percentage = 2.25% homopolymer indels = 48.08% >>>>>>> Coverage mean coverageData = 0.0167X std coverageData = 0.1962X There is a 1.47% of reference with a coverageData >= 1X There is a 0.12% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 4404474 0.0176708646996711 0.2574060545363869 chr2 243199373 4473269 0.01839342324291272 0.26181727792942366 chr3 198022430 3947668 0.019935458826558183 0.1656198576317956 chr4 191154276 3116568 0.01630394080224499 0.1482785738310919 chr5 180915260 2878833 0.015912604608367475 0.14631687963833417 chr6 171115067 3071957 0.017952580411869867 0.17513655514123072 chr7 159138663 2950230 0.018538738131788877 0.31234309603071364 chr8 146364022 3217206 0.02198085264423794 0.21337861440377304 chr9 141213431 1900646 0.01345938546029662 0.19520199696131174 chr10 135534747 2600554 0.0191873601239688 0.18605126475817596 chr11 135006516 2250547 0.016669913917340108 0.18094585044517567 chr12 133851895 2519109 0.018820122046086834 0.16228161394092405 chr13 115169878 1596335 0.01386069888864517 0.14133255067253775 chr14 107349540 1612633 0.015022262787525685 0.14790041420338176 chr15 102531392 1414253 0.013793365840580805 0.14083766756036878 chr16 90354753 1287038 0.014244275561242473 0.14509402400922883 chr17 81195210 1369990 0.016872793358130363 0.1703171915142159 chr18 78077248 1144207 0.014654806993197302 0.27777154696565065 chr19 59128983 897773 0.015183298518765324 0.18479865963657705 chr20 63025520 1086285 0.017235637246626447 0.15390169145504054 chr21 48129895 614802 0.012773807214829786 0.13682171633466408 chr22 51304566 530016 0.010330776406918636 0.11948209742920113 chrMT 16571 25931 1.5648421941946775 2.100292998497388 chrX 155270560 2746333 0.01768740320122501 0.17031678517018603 chrY 59373566 142976 0.002408075000918759 0.06165586177332046