BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234117.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 = 802,854 number of mapped reads = 347,542 (43.29%) number of supplementary alignments = 1,388 (0.17%) number of secondary alignments = 0 number of mapped bases = 21,086,870 bp number of sequenced bases = 21,071,860 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 9,595 duplication rate = 2.23% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.2181 >>>>>>> ACTG content number of A's = 5,801,567 bp (27.53%) number of C's = 3,486,852 bp (16.55%) number of T's = 6,777,085 bp (32.16%) number of G's = 5,004,708 bp (23.75%) number of N's = 1,648 bp (0.01%) GC percentage = 40.3% >>>>>>> Mismatches and indels general error rate = 0.0118 number of mismatches = 244,407 number of insertions = 1,861 mapped reads with insertion percentage = 0.53% number of deletions = 8,425 mapped reads with deletion percentage = 2.39% homopolymer indels = 46.41% >>>>>>> Coverage mean coverageData = 0.0068X std coverageData = 0.0985X There is a 0.63% of reference with a coverageData >= 1X There is a 0.04% 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 1798001 0.0072136269622373374 0.11532273171997279 chr2 243199373 1528125 0.0062834249165601265 0.09725193831242578 chr3 198022430 1763471 0.008905410361846383 0.10096561755170776 chr4 191154276 1084695 0.005674448004500825 0.08115222154564729 chr5 180915260 1251592 0.006918111827603708 0.08976997665124543 chr6 171115067 1422892 0.008315410354834504 0.10375268854235141 chr7 159138663 1279207 0.008038316873379789 0.11547733540363585 chr8 146364022 1075951 0.007351198643612021 0.14427632476016097 chr9 141213431 851038 0.006026608049768297 0.09053269233277979 chr10 135534747 1004448 0.007410999926092753 0.0965278849948065 chr11 135006516 994692 0.007367733272962914 0.10446283689531705 chr12 133851895 826194 0.006172449034061117 0.0842465550693958 chr13 115169878 816523 0.007089727055194068 0.09145805740980041 chr14 107349540 850042 0.007918450325916628 0.09589536453503324 chr15 102531392 482311 0.004704032497676419 0.07290635657889002 chr16 90354753 554825 0.006140518141862443 0.0837129624059847 chr17 81195210 509177 0.006271022637911769 0.08594348411818586 chr18 78077248 500579 0.006411329969007104 0.1203388126228575 chr19 59128983 477173 0.008070035637176442 0.10096740547802426 chr20 63025520 489548 0.0077674567381594 0.09473490437595246 chr21 48129895 323504 0.006721477368691537 0.08800380798059791 chr22 51304566 197717 0.0038537895438000586 0.06508145053865474 chrMT 16571 15921 0.9607748476253696 1.4332522394178668 chrX 155270560 912033 0.005873830815062431 0.08300873885070949 chrY 59373566 77211 0.0013004271968437941 0.03985257486683742