BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008815.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 = 2,477,247 number of mapped reads = 883,639 (35.67%) number of supplementary alignments = 4,721 (0.19%) number of secondary alignments = 0 number of mapped bases = 56,448,913 bp number of sequenced bases = 56,417,124 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 35,137 duplication rate = 3.14% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.2775 >>>>>>> ACTG content number of A's = 16,948,997 bp (30.04%) number of C's = 10,175,319 bp (18.04%) number of T's = 16,049,808 bp (28.45%) number of G's = 13,233,854 bp (23.46%) number of N's = 9,146 bp (0.02%) GC percentage = 41.49% >>>>>>> Mismatches and indels general error rate = 0.0105 number of mismatches = 584,468 number of insertions = 3,996 mapped reads with insertion percentage = 0.45% number of deletions = 21,217 mapped reads with deletion percentage = 2.37% homopolymer indels = 48.42% >>>>>>> Coverage mean coverageData = 0.0182X std coverageData = 0.1845X There is a 1.55% of reference with a coverageData >= 1X There is a 0.19% of reference with a coverageData >= 2X There is a 0.04% 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 4556283 0.018279926371778228 0.20945942079622643 chr2 243199373 4991543 0.02052448959233131 0.23040305575698006 chr3 198022430 4423978 0.02234079240417361 0.17896330642040895 chr4 191154276 3017267 0.015784459877842334 0.14848788714891506 chr5 180915260 2973735 0.016437170640000186 0.1507966611201531 chr6 171115067 3061054 0.01788886305377188 0.17185403671209704 chr7 159138663 3180373 0.019984917178800226 0.22667543735632154 chr8 146364022 4253583 0.029061670633784578 0.24507517499857917 chr9 141213431 1949525 0.013805521090978946 0.162406595903802 chr10 135534747 2990319 0.02206311714294195 0.19501790968221897 chr11 135006516 2576546 0.019084604775668753 0.17903115461689328 chr12 133851895 2564424 0.01915866786943883 0.1648523311528753 chr13 115169878 1675942 0.014551912610344173 0.14556443294096658 chr14 107349540 1973073 0.018379892452263884 0.1636301706245114 chr15 102531392 1555848 0.01517435752749753 0.14467265722399567 chr16 90354753 1473791 0.016311161848895764 0.15718628107263957 chr17 81195210 1502907 0.01850979879231792 0.1778115868177522 chr18 78077248 1094879 0.014023022430298774 0.26905919820334456 chr19 59128983 1007563 0.01704008675407118 0.17042410871104635 chr20 63025520 1318861 0.020925824967410026 0.17254465509723863 chr21 48129895 658022 0.013671793798843734 0.14424367177351075 chr22 51304566 688505 0.013419955642934392 0.14329110927989847 chrMT 16571 22230 1.3415002112123589 1.607490956263572 chrX 155270560 2806884 0.018077374101053027 0.16335959039540554 chrY 59373566 131778 0.002219472551134961 0.06033005006577727