BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008755.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 = 1,484,064 number of mapped reads = 1,278,416 (86.14%) number of supplementary alignments = 10,920 (0.74%) number of secondary alignments = 0 number of mapped bases = 84,048,000 bp number of sequenced bases = 84,008,921 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 127,919 duplication rate = 7.73% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.9642 >>>>>>> ACTG content number of A's = 22,487,307 bp (26.77%) number of C's = 16,252,491 bp (19.35%) number of T's = 25,913,301 bp (30.85%) number of G's = 19,234,508 bp (22.9%) number of N's = 121,314 bp (0.14%) GC percentage = 42.24% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 707,877 number of insertions = 6,029 mapped reads with insertion percentage = 0.47% number of deletions = 22,004 mapped reads with deletion percentage = 1.7% homopolymer indels = 45.37% >>>>>>> Coverage mean coverageData = 0.0271X std coverageData = 0.3561X There is a 1.67% of reference with a coverageData >= 1X There is a 0.58% of reference with a coverageData >= 2X There is a 0.23% of reference with a coverageData >= 3X There is a 0.1% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 7611072 0.030535819607847636 0.41993342286716884 chr2 243199373 8207462 0.03374787483518718 0.413491266809295 chr3 198022430 6094699 0.030777821482142198 0.26340881956059375 chr4 191154276 3271408 0.01711396714975918 0.1944253790640704 chr5 180915260 2824568 0.015612657550280722 0.18998017939552564 chr6 171115067 5016793 0.02931824232637562 0.2666573455844298 chr7 159138663 5135323 0.03226948689395487 0.4066516710375352 chr8 146364022 6851888 0.04681401827014565 0.3450422465956704 chr9 141213431 2402251 0.01701149092539222 0.2736514971868304 chr10 135534747 6228271 0.04595331557301686 0.3840672091183248 chr11 135006516 4308932 0.031916474312987976 0.34167146430779544 chr12 133851895 3375457 0.025217849922856903 0.23908830220437652 chr13 115169878 1648023 0.01430949679394468 0.18750412745292722 chr14 107349540 2068429 0.019268168266021447 0.20768954512452825 chr15 102531392 2092703 0.0204103636864698 0.21260621807345653 chr16 90354753 1826899 0.02021917983661579 0.27291039242703163 chr17 81195210 2868559 0.03532916535347344 0.30305119356603805 chr18 78077248 1574742 0.020169025424666608 0.5883435652987851 chr19 59128983 1683732 0.028475578550031886 0.3257480669145993 chr20 63025520 1858913 0.02949460789851476 0.25850488651581727 chr21 48129895 783852 0.016286177229349868 0.19715812949054434 chr22 51304566 1093148 0.02130703142484433 0.2192693741665017 chrMT 16571 1087314 65.61547281395208 33.44841231837869 chrX 155270560 3923839 0.02527097860663348 0.24802984833765934 chrY 59373566 209723 0.0035322621518134854 0.11576905085925246