BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013304.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 = 2,097,614 number of mapped reads = 349,509 (16.66%) number of supplementary alignments = 4,433 (0.21%) number of secondary alignments = 0 number of mapped bases = 21,744,260 bp number of sequenced bases = 21,731,633 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 66,262 duplication rate = 12.79% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.5896 >>>>>>> ACTG content number of A's = 5,819,495 bp (26.78%) number of C's = 3,947,103 bp (18.16%) number of T's = 6,965,706 bp (32.05%) number of G's = 4,997,039 bp (22.99%) number of N's = 2,290 bp (0.01%) GC percentage = 41.16% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 194,193 number of insertions = 1,462 mapped reads with insertion percentage = 0.42% number of deletions = 7,397 mapped reads with deletion percentage = 2.09% homopolymer indels = 42.93% >>>>>>> Coverage mean coverageData = 0.007X std coverageData = 0.1707X There is a 0.36% of reference with a coverageData >= 1X There is a 0.13% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.02% 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% 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 1912799 0.007674199535896041 0.1994329980948077 chr2 243199373 1738893 0.007150071887726454 0.2089813395363308 chr3 198022430 1655552 0.008360426644597786 0.173662437494689 chr4 191154276 1893049 0.00990325217731462 0.19197071569576463 chr5 180915260 1059408 0.005855824434047189 0.13948730609573032 chr6 171115067 1114078 0.006510694934888463 0.16576833283945433 chr7 159138663 958693 0.006024261998481161 0.14951761566147462 chr8 146364022 1599025 0.01092498674298524 0.2047909248009964 chr9 141213431 675540 0.004783822581295401 0.12893309756404295 chr10 135534747 1097750 0.008099399041929816 0.18269515112138668 chr11 135006516 840085 0.006222551510032301 0.1583746810109006 chr12 133851895 1167580 0.008722924692250342 0.18627036571447225 chr13 115169878 398659 0.003461486691858786 0.11364629745774085 chr14 107349540 847942 0.007898888062305624 0.1896509556450606 chr15 102531392 527621 0.005145945936245555 0.14509499627131806 chr16 90354753 630296 0.006975792407954455 0.1678195985320117 chr17 81195210 706965 0.008706979143227784 0.17106341135036357 chr18 78077248 540393 0.006921260851816908 0.18646923158855772 chr19 59128983 502859 0.008504441891043518 0.1763298751385318 chr20 63025520 474840 0.007534090952363424 0.1596217073143187 chr21 48129895 320361 0.0066561749199743735 0.18439078705797435 chr22 51304566 293902 0.005728573944081312 0.1422231119741555 chrMT 16571 8511 0.5136081105545833 1.1972713699210178 chrX 155270560 720268 0.004638793084793408 0.12421565090171643 chrY 59373566 59191 9.969251299475595E-4 0.047172042646057046