BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004165.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 = 1,597,543 number of mapped reads = 1,331,441 (83.34%) number of supplementary alignments = 8,222 (0.51%) number of secondary alignments = 0 number of mapped bases = 85,292,761 bp number of sequenced bases = 85,239,065 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 42,040 duplication rate = 2.41% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.5019 >>>>>>> ACTG content number of A's = 23,898,236 bp (28.04%) number of C's = 15,737,644 bp (18.46%) number of T's = 26,216,596 bp (30.76%) number of G's = 19,370,155 bp (22.72%) number of N's = 16,434 bp (0.02%) GC percentage = 41.19% >>>>>>> Mismatches and indels general error rate = 0.0103 number of mismatches = 865,204 number of insertions = 7,508 mapped reads with insertion percentage = 0.56% number of deletions = 33,326 mapped reads with deletion percentage = 2.46% homopolymer indels = 47% >>>>>>> Coverage mean coverageData = 0.0276X std coverageData = 0.264X There is a 2.4% of reference with a coverageData >= 1X There is a 0.26% 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% 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 7221257 0.028971871648817277 0.3734573358282621 chr2 243199373 6897627 0.028362026245848916 0.32920052107568515 chr3 198022430 5470648 0.027626405756156006 0.18579796622856715 chr4 191154276 5782261 0.03024918469519353 0.19743879207814152 chr5 180915260 4612408 0.025494853225758844 0.17959023694436568 chr6 171115067 5092159 0.029758682793257475 0.20926957194551846 chr7 159138663 5460062 0.03431009094251345 0.467594445560486 chr8 146364022 5626029 0.038438606176045095 0.2948466164209887 chr9 141213431 2840133 0.020112343279868328 0.2335727556074749 chr10 135534747 4117473 0.03037946424174164 0.22391786390027385 chr11 135006516 3706004 0.027450556534619412 0.2665000211273463 chr12 133851895 3768191 0.028151943609016516 0.18859208355228163 chr13 115169878 2481193 0.02154376685195412 0.16423673149347515 chr14 107349540 2048883 0.019086090168621124 0.17916649134621654 chr15 102531392 2204311 0.021498888847622393 0.17218051283285843 chr16 90354753 2382696 0.026370455575259 0.1961676032956618 chr17 81195210 2069458 0.02548743946841199 0.19236928644531057 chr18 78077248 2581825 0.033067571746381225 0.4513744496862743 chr19 59128983 1497034 0.025318108380115383 0.269388000798517 chr20 63025520 1934817 0.030698945443052274 0.205963353048641 chr21 48129895 1288863 0.026778845040073326 0.1907773598636439 chr22 51304566 951710 0.018550200775502127 0.15158956792533831 chrMT 16571 72974 4.4037173375173495 3.656359878763014 chrX 155270560 4975570 0.032044516359057376 0.22278906046395008 chrY 59373566 209175 0.0035230324552175288 0.07779529913990829