BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068102.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 = 4,123,846 number of mapped reads = 3,828,111 (92.83%) number of supplementary alignments = 16,479 (0.4%) number of secondary alignments = 0 number of mapped bases = 244,129,034 bp number of sequenced bases = 244,033,550 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 382,420 duplication rate = 8.44% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.3332 >>>>>>> ACTG content number of A's = 64,131,338 bp (26.28%) number of C's = 43,380,017 bp (17.78%) number of T's = 79,500,648 bp (32.58%) number of G's = 56,993,713 bp (23.35%) number of N's = 27,834 bp (0.01%) GC percentage = 41.13% >>>>>>> Mismatches and indels general error rate = 0.0056 number of mismatches = 1,330,389 number of insertions = 15,142 mapped reads with insertion percentage = 0.39% number of deletions = 55,312 mapped reads with deletion percentage = 1.43% homopolymer indels = 45.14% >>>>>>> Coverage mean coverageData = 0.0789X std coverageData = 0.7261X There is a 6.14% of reference with a coverageData >= 1X There is a 1.2% of reference with a coverageData >= 2X There is a 0.27% of reference with a coverageData >= 3X There is a 0.08% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.01% 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 0.01% 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 21004160 0.08426923839038299 1.2320971958191256 chr2 243199373 20388791 0.08383570544813863 1.1029629615849688 chr3 198022430 18978181 0.09583854212878813 0.382534362633827 chr4 191154276 13566196 0.07096987984720782 0.34563840163673 chr5 180915260 14024583 0.07752017712602022 0.3519719199526781 chr6 171115067 16911461 0.09883092878080689 0.5168207492765114 chr7 159138663 20612547 0.12952570174603012 1.3931524903321417 chr8 146364022 9938413 0.0679020217140521 0.7751712070356657 chr9 141213431 9100826 0.06444731167249948 0.686702316737284 chr10 135534747 13331625 0.09836315258698937 0.5083099367414028 chr11 135006516 12548873 0.09295012842194965 0.6002406074370489 chr12 133851895 10225685 0.07639551909220262 0.3821326233239888 chr13 115169878 5693371 0.04943454919696971 0.30228481031507104 chr14 107349540 5432477 0.05060549863557869 0.3771973303804542 chr15 102531392 4590569 0.04477232689867314 0.3162253097090065 chr16 90354753 4728584 0.05233353911110797 0.3359752564137184 chr17 81195210 7724271 0.09513210200453943 0.4331970284198187 chr18 78077248 5656843 0.07245187484067062 1.1501088543438307 chr19 59128983 4515532 0.0763674896962121 0.8768248063493331 chr20 63025520 3307185 0.05247374396910966 0.3225515364221949 chr21 48129895 4680128 0.09723952233845513 0.409342399342135 chr22 51304566 2162851 0.04215708597944284 0.24726706695835926 chrMT 16571 132681 8.00681914187436 5.176579747084973 chrX 155270560 14315154 0.09219490159628457 0.4980928048181068 chrY 59373566 558047 0.009398913314386406 0.17863388013233664