BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238630.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 = 2,670,290 number of mapped reads = 2,091,951 (78.34%) number of supplementary alignments = 18,201 (0.68%) number of secondary alignments = 0 number of mapped bases = 126,257,640 bp number of sequenced bases = 126,196,139 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 707,921 duplication rate = 23.21% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.3895 >>>>>>> ACTG content number of A's = 31,517,217 bp (24.97%) number of C's = 21,596,204 bp (17.11%) number of T's = 42,911,003 bp (34%) number of G's = 30,165,583 bp (23.9%) number of N's = 6,132 bp (0%) GC percentage = 41.02% >>>>>>> Mismatches and indels general error rate = 0.0063 number of mismatches = 782,235 number of insertions = 7,586 mapped reads with insertion percentage = 0.36% number of deletions = 36,422 mapped reads with deletion percentage = 1.72% homopolymer indels = 41.74% >>>>>>> Coverage mean coverageData = 0.0408X std coverageData = 0.7327X There is a 1.68% of reference with a coverageData >= 1X There is a 0.84% of reference with a coverageData >= 2X There is a 0.52% of reference with a coverageData >= 3X There is a 0.33% of reference with a coverageData >= 4X There is a 0.21% of reference with a coverageData >= 5X There is a 0.13% of reference with a coverageData >= 6X There is a 0.09% of reference with a coverageData >= 7X There is a 0.06% of reference with a coverageData >= 8X There is a 0.04% of reference with a coverageData >= 9X There is a 0.03% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% 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% 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 21511422 0.08630438678024396 0.8820018477398465 chr2 243199373 4741022 0.01949438414053806 1.1739136563719514 chr3 198022430 5466157 0.02760372650714366 0.35125021605637025 chr4 191154276 6468253 0.03383786716861097 0.38357347816012693 chr5 180915260 3032240 0.016760554084824023 0.26886076082993393 chr6 171115067 16510286 0.09648645376154982 0.9763876804939706 chr7 159138663 8610114 0.054104476169942434 1.5358772777492893 chr8 146364022 3874513 0.026471758202982424 0.5120066720389913 chr9 141213431 2417603 0.017120205796855116 0.35176721798737837 chr10 135534747 2672067 0.019714996037141677 0.6585058961994502 chr11 135006516 3137659 0.023240796762728104 0.3193719473851768 chr12 133851895 6034958 0.0450868327265744 0.4603102302077679 chr13 115169878 1851940 0.016080072603706325 0.3714396206327037 chr14 107349540 1451313 0.01351950832765562 0.2663687097757905 chr15 102531392 2877249 0.0280621275482147 0.4233454338815408 chr16 90354753 2286763 0.025308718402450837 0.35113785510829437 chr17 81195210 1394897 0.017179547906828494 0.2664899210468861 chr18 78077248 1778746 0.022781873664399648 1.4196330299902478 chr19 59128983 2286241 0.03866531917181799 0.5854706256893665 chr20 63025520 1522100 0.02415053457710464 0.3313259735437434 chr21 48129895 1771160 0.036799581632164374 0.39384119592304956 chr22 51304566 546034 0.010642990333452972 0.20140280687046036 chrMT 16571 28648 1.7288033311206323 2.766584619312562 chrX 155270560 23314880 0.15015647525197306 0.839533715259734 chrY 59373566 671375 0.011307641518449473 0.3148898065730718