BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238601.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 = 3,147,366 number of mapped reads = 2,745,609 (87.24%) number of supplementary alignments = 22,444 (0.71%) number of secondary alignments = 0 number of mapped bases = 167,356,424 bp number of sequenced bases = 167,268,422 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 908,977 duplication rate = 20.51% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 39.8757 >>>>>>> ACTG content number of A's = 40,914,052 bp (24.46%) number of C's = 29,544,010 bp (17.66%) number of T's = 56,171,748 bp (33.58%) number of G's = 40,630,956 bp (24.29%) number of N's = 7,656 bp (0%) GC percentage = 41.95% >>>>>>> Mismatches and indels general error rate = 0.0067 number of mismatches = 1,104,950 number of insertions = 11,680 mapped reads with insertion percentage = 0.42% number of deletions = 52,299 mapped reads with deletion percentage = 1.89% homopolymer indels = 40.61% >>>>>>> Coverage mean coverageData = 0.0541X std coverageData = 0.966X There is a 2.16% of reference with a coverageData >= 1X There is a 1.06% of reference with a coverageData >= 2X There is a 0.68% of reference with a coverageData >= 3X There is a 0.45% of reference with a coverageData >= 4X There is a 0.3% of reference with a coverageData >= 5X There is a 0.2% of reference with a coverageData >= 6X There is a 0.13% of reference with a coverageData >= 7X There is a 0.09% of reference with a coverageData >= 8X There is a 0.06% of reference with a coverageData >= 9X There is a 0.05% of reference with a coverageData >= 10X There is a 0.03% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% 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 13841648 0.05553305321554244 1.0330103084077653 chr2 243199373 10316269 0.04241897860485027 2.3068324385374117 chr3 198022430 25721949 0.12989411856020552 0.8073902754572508 chr4 191154276 3074085 0.016081696231582076 0.26113342482521384 chr5 180915260 11757946 0.06499145511550546 0.5599982123268032 chr6 171115067 3543842 0.020710286137456266 0.73989327324012 chr7 159138663 8994155 0.05651772379160933 1.0810189514935684 chr8 146364022 13964587 0.09540997035459985 0.7744748211268552 chr9 141213431 15089214 0.10685395782218478 0.8922565891403775 chr10 135534747 7888859 0.05820543568801586 0.5927961858628176 chr11 135006516 2687418 0.01990583921149406 0.38172656878520483 chr12 133851895 6323683 0.047243881007437365 0.5041871504777661 chr13 115169878 6765188 0.05874094960836895 0.672547453813683 chr14 107349540 2123624 0.019782329761263998 0.3677664492467973 chr15 102531392 4631216 0.04516876158279408 0.5965266015336249 chr16 90354753 1411004 0.01561626758030095 0.40737496670081236 chr17 81195210 3796829 0.04676173631424809 0.494912496919729 chr18 78077248 3679715 0.04712915854821113 1.8687027413593202 chr19 59128983 5654665 0.09563271196462148 0.8386014557730325 chr20 63025520 3950335 0.06267834045637387 0.585766644873612 chr21 48129895 4026977 0.08366893383000316 0.6631612991617135 chr22 51304566 3495768 0.0681375610895919 0.589163535528532 chrMT 16571 29877 1.8029690423028182 4.325635390299852 chrX 155270560 4249477 0.027368208113630815 0.4017561156653266 chrY 59373566 338094 0.005694352264440374 0.34606869601207685